Microbial compositions and methods for improving ruminant digestion

Abstract

Disclosed herein are compositions and using said compositions in methods for enhancing plant fiber digestion and plant protein digestion in a ruminant, in methods of increasing milk production in a dairy cow, in methods of increasing meat production in beef cattle, and in methods of modulating microbiome of ruminants.

Description

[0001] MICROBIAL COMPOSITIONS AND METHODS FOR

[0002] IMPROVING RUMINANT DIGESTION

[0003] CROSS REFERENCE TO RELATED APPLICATIONS

[0004] This application claims the benefit of U.S. Provisional Application No. 63 / 559,001, filed February 28, 2024. The content of this earlier filed application is hereby incorporated by reference herein in its entirety.

[0005] FIELD

[0006] The present disclosure relates to compositions and methods for increasing fiber and protein digestion in the rumen of a ruminant. The disclosure provides a microbial consortia, and further relates to methods of using the microbial consortia.

[0007] SUMMARY

[0008] The present disclosure relates to compositions comprising a purified population of bacteria, and methods for using said compositions for enhancing plant fiber digestion in a ruminant, enhancing digestibility of fiber in a ruminant, enhancing digestibility of protein in a ruminant, increasing milk production in a dairy cow, increasing meat production in beef cattle, modulating the microbiome of a ruminant, increasing the digestibility of a plant, modulating a rumen microbiome, and reducing methane emissions in the rumen of a ruminant.

[0009] In some aspects, the present disclosure relates to compositions comprising a Pseudomonas spp. and a Clostridium spp., and methods for using said compositions to modulate the rumen microbiome, reducing methane emissions in the rumen of a ruminant, and enhancing the digestibility of fiber and plant in a ruminant.

[0010] In some aspects, the present disclosure relates to compositions comprising a Pseudomonas spp. and a Clostridium spp., and methods for using said compositions to enhance plant fiber digestion in a ruminant, enhance digestibility of fiber in a ruminant, enhance digestibility’ of protein in a ruminant, increase milk production in a dairy cow, increase meat production in beef cattle, modulate the microbiome of a ruminant, increase the digestibility of a plant, modulate a rumen microbiome, and reduce methane emissions in the rumen of a ruminant.

[0011] Disclosed herein are methods of enhancing plant fiber digestion in a ruminant, the methods comprising: administering to a ruminant an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to enhance the plant fiber digestion in the ruminant administered the composition, as compared to a ruminant that was not administered the composition.

[0012] Disclosed herein are methods of enhancing plant protein digestion in a ruminant, the methods comprising: administering to a ruminant an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1. Table 2 or Table 3; and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to enhance the digestibility of plant protein in the ruminant administered the composition, as compared to a ruminant that was not administered the composition.

[0013] Disclosed herein are methods of enhancing digestibility of fiber in a ruminant, the methods comprising: administering to a ruminant an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the feedstock or foodstuff in an amount effective to enhance the digestibility of fiber in the ruminant administered the feedstock or foodstuff, as compared to a ruminant that was not administered the feedstock or foodstuff. Disclosed herein are methods of enhancing digestibility of protein in a ruminant, the methods comprising: administering to a ruminant an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2. (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the feedstock or foodstuff in an amount effective to enhance the digestibility of protein in the ruminant administered the feedstock or foodstuff, as compared to a ruminant that was not administered the feedstock or foodstuff.

[0014] Disclosed herein are methods of increasing milk production in a dairy cow, the methods comprising: administering to the dairy’ cow an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the milk production from the dairy cow administered the composition, as compared to a dairy cow not administered the composition.

[0015] Disclosed herein are methods of increasing milk production in a dairy cow, the methods comprising: administering to the daily' cow an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the milk production from the dairy cow administered the composition, as compared to a dairy cow not administered the composition.

[0016] Disclosed herein are methods of increasing meat production in beef cattle, the methods comprising: administering to the beef cattle an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the meat production from the beef cattle administered the composition, as compared to a beef cattle not administered the composition.

[0017] Disclosed herein are methods of increasing meat production in a beef cattle, the methods comprising: administering to the beef cattle an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the meat production from the beef cattle administered the composition, as compared to a beef cattle not administered the composition.

[0018] Disclosed herein are methods of enhancing plant fiber digestion in a ruminant, the methods comprising: administering to the rumen of the ruminant an effective amount of a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; wherein the purified population of bacteria is present in the composition in an amount effective to enhance the fiber digestion in the ruminant administered the composition, as compared to a ruminant not administered the composition.

[0019] Disclosed herein are method of enhancing plant protein digestion in a ruminant, the methods comprising: administering to the rumen of the ruminant an effective amount of a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; wherein the purified population of bacteria is present in the composition in an amount effective to enhance the digestibility of protein in the ruminant administered the composition, as compared to a ruminant not administered the composition.

[0020] Disclosed herein are methods of modulating the microbiome of a ruminant, the methods comprising: administering to the rumen of the ruminant an effective amount of a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; wherein the purified population of bacteria is present in the composition in an amount effective to impart at least one improved trait upon the ruminant.

[0021] Disclosed herein are methods of increasing the digestibility of a plant, the methods comprising: applying a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 to a plant, plant seed, or to a growth medium in which the plant is located; culturing the plant under conditions suitable for plant growth; and harvesting the plant, wherein the digestibility of the plant is increased.

[0022] BRIEF DESCRIPTION OF FIGURES

[0023] FIG. 1 shows a microbial analysis results.

[0024] FIG. 2 shows a principal component analysis.

[0025] DETAILED DESCRIPTION

[0026] The present disclosure can be understood more readily by reference to the following detailed description of the invention, the figures and the examples included herein.

[0027] Before the present methods and compositions are disclosed and described, it is to be understood that they are not limited to specific synthetic methods unless otherwise specified, or to particular reagents unless otherwise specified, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only and is not intended to be limiting. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, example methods and materials are now described.

[0028] Moreover, it is to be understood that unless otherw ise expressly stated, it is in no way intended that any method set forth herein be construed as requiring that its steps be performed in a specific order. Accordingly, where a method claim does not actually recite an order to be followed by its steps or it is not otherwise specifically stated in the claims or descriptions that the steps are to be limited to a specific order, it is in no way intended that an order be inferred, in any respect. This holds for any possible non-express basis for interpretation, including matters of logic with respect to arrangement of steps or operational flow, plain meaning derived from grammatical organization or punctuation, and the number or type of aspects described in the specification.

[0029] All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and / or materials in connection with which the publications are cited. The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided herein can be different from the actual publication dates, which can require independent confirmation.

[0030] DEFINITIONS As used in the specification and the appended claims, the singular forms “a,” “an’" and ■'the" include plural referents unless the context clearly dictates otherwise.

[0031] The word “or” as used herein means any one member of a particular list and also includes any combination of members of that list.

[0032] Ranges can be expressed herein as from ‘‘about” or “approximately” one particular value, and / or to “about” or “approximately” another particular value. When such a range is expressed, a further aspect includes from the one particular value and / or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent “about,” or “approximately,” it will be understood that the particular value forms a further aspect. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint and independently of the other endpoint. It is also understood that there are a number of values disclosed herein and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10” is also disclosed. It is also understood that each unit between two particular units is also disclosed. For example, if 10 and 15 are disclosed, then 11. 12. 13, and 14 are also disclosed.

[0033] As used herein, the terms “optional” or “optionally” mean that the subsequently described event or circumstance may or may not occur and that the description includes instances where said event or circumstance occurs and instances where it does not.

[0034] As used herein, the term “comprising” can include the aspects “consisting of’ and “consisting essentially of.”

[0035] The term “plant” is used herein to include any plant, tissues or organs (e.g., plant parts). Plant parts include, but are not limited to, cells, stems, roots, flowers, ovules, stamens, seeds, leaves, that can be cultured into a whole plant. A plant cell is a cell of a plant, either taken directly from a seed or plant, or derived through culture from a cell taken from a plant.

[0036] As used herein, the term “plant” further includes the whole plant or any parts or derivatives thereof, such as plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, embryos, pollen, ovules, fruit, flowers, leaves, seeds, roots, root tips and the like.

[0037] The exposed plants can be further assessed to isolate polynucleotides, amino acid sequences and / or genetic markers that are associated with, linked to, the desired trait. Further assessments include, but are not limited to, isolating polynucleotides, nucleic acids, or amino acids sequences from the exposed plant, carrying out an assay of the isolated polynucleotides or nucleic acids, for example, to detect one or more biological or molecular markers associated with one or more agronomic characteristics or traits, including but not limited to, reduced methane production or increased hydrogen production. The information gleaned from such methods can be used, for example, in a breeding program.

[0038] As used herein, the term “subject” refers to the target of administration, e.g., livestock. Thus the subject of the disclosed methods can be a vertebrate, such as a mammal, a fish, a bird, a reptile, or an amphibian. The term “subject” also includes domesticated animals (e.g., cats, dogs, etc.), livestock (e.g., cattle, horses, pigs, sheep, goats, etc.), and laboratory animals (e.g., mouse, rabbit, rat, guinea pig, fruit fly, etc ). In some aspects, a subject is a cow. The term does not denote a particular age or sex.

[0039] As used herein the terms “microorganism” or “microbe” are used interchangeably and include, but are not limited to, the two prokaryotic domains, Bacteria and Archaea, eukaryotic fungi and protozoa, as well as viruses. In some aspects, the disclosure refers to the “microbes” of Table 1, Table 2, and / or Table 3 or the “microbes” incorporated by reference. This characterization can refer to not only the predicted taxonomic microbial identifiers of the Tables, but also the identified strains of the microbes listed in the Tables.

[0040] The term “microbial consortia” or “microbial consortium” refers to a subset of a microbial community of individual microbial species, or strains of a species, which can be described as carry ing out a common function, or can be described as participating in, or leading to, or correlating with, a recognizable parameter or plant phenotypic trait. The community may comprise two or more species, or strains of a species, of microbes. In some instances, the microbes coexist within the community symbiotically.

[0041] The term “microbial community7” means a group of microbes comprising two or more species or strains. Unlike microbial ensemble, a microbial community' does not have to be carrying out a common function, or does not have to be participating in. or leading to, or correlating with, a recognizable parameter, such as a phenotypic trait of interest (e.g., decreased amount of methane in the rumen in cattle).

[0042] As used herein, “isolate,” “isolated,” “isolated microbe,” and like terms, are intended to mean that the one or more microorganisms has been separated from at least one of the materials with which it is associated in a particular environment (for example soil, water, animal tissue).

[0043] Thus, an “isolated microbe” does not exist in its naturally occurring environment; rather, it is through the various techniques described herein that the microbe has been removed from its natural setting and placed into a non-naturally occurring state of existence. Thus, the isolated strain or isolated microbe may exist as, for example, a biologically pure culture, or as spores (or other forms of the strain) in association with an acceptable carrier.

[0044] As used herein, “spore” or “spores” refer to structures produced by bacteria and fungi that are adapted for survival and dispersal. Spores are generally characterized as dormant structures; however, spores are capable of differentiation through the process of germination. Germination is the differentiation of spores into vegetative cells that are capable of metabolic activity, growth, and reproduction. The germination of a single spore results in a single fungal or bacterial vegetative cell. Fungal spores are units of asexual reproduction, and in some cases are necessary structures in fungal life cycles. Bacterial spores are structures for surviving conditions that may ordinarily be nonconductive to the survival or growth of vegetative cells.

[0045] As used herein, “microbial composition” refers to a composition comprising one or more microbes of the present disclosure, wherein a microbial composition, in some aspects, is administered to animals (e.g., ruminants) of the present disclosure.

[0046] As used herein, “carrier”, “acceptable carrier”, or “pharmaceutical carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the compound is administered. Such carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable, or synthetic origin; such as peanut oil, soybean oil, mineral oil, sesame oil, and the like. Water or aqueous solution saline solutions and aqueous dextrose and glycerol solutions are preferably employed as carriers, in some embodiments as injectable solutions. In some embodiments, gelling agents are employed as carriers. Alternatively, the carrier can be a solid dosage form carrier, including but not limited to one or more of a binder (for compressed pills), a glidant, an encapsulating agent, a flavorant, and a colorant. The choice of carrier can be selected with regard to the intended route of administration and standard pharmaceutical practice. See Hardee and Baggo (1998. Development and Formulation of Veterinary Dosage Forms. 2nd Ed. CRC Press. 504 pg.); E. W. Martin (1970. Remington's Pharmaceutical Sciences. 17th Ed. Mack Pub. Co.); and Blaser et al. (US Publication US20110280840A1).

[0047] In some aspects, carriers may be granular in structure, such as sand or sand particles. In some aspects, the carriers may be dry, as opposed to a moist or wet carrier. In some aspects, carriers can be nutritive substances and / or prebiotic substances selected from fructooligosaccharides, inulins, isomalto-oligosaccharides, lactitol, lactosucrose, lactulose, pyrodextrines, soy oligosaccharides, transgalacto-oligosaccharides, xylo-oligosaccharides, trace minerals, and vitamins. In some aspects, carriers can be in solid or liquid form. In some aspects, carriers can be zeolites, calcium carbonate, magnesium carbonate, silicon dioxide, ground com, trehalose, chitosan, shellac, albumin, starch, skim-milk powder, sweet-whey powder, maltodextrin, lactose, and inulin. In some aspects, a carrier is water or physiological saline.

[0048] The term “bioensemble,” “microbial ensemble,” or “synthetic ensemble” refers to a composition comprising one or more active microbes identified by methods, systems, and / or apparatuses of the present disclosure and that do not naturally exist in a naturally occurring environment and / or at ratios or amounts that do not exist in nature. A bioensemble is a subset of a microbial community of individual microbial species, or strains of a species, which can be described as carrying out a common function, or can be described as participating in, or leading to, or correlating with, a recognizable parameter, such as a phenotypic trait of interest (e.g. increased feed efficiency in feedlot cattle). The bioensemble may comprise two or more species, or strains of a species, of microbes. In some instances, the microbes coexist within the community symbiotically.

[0049] As used herein, “microbiome” refers to the collection of microorganisms that inhabit the digestive tract or gastrointestinal tract of an animal (including the rumen if said animal is a ruminant) and the microorganism's physical environment (i.e. the microbiome has a biotic and physical component). The microbiome is fluid and may be modulated by numerous naturally occurring and artificial conditions (e.g., change in diet, disease, antimicrobial agents, influx of additional microorganisms, etc.). The modulation of the microbiome of a rumen that can be achieved via administration of the compositions of the disclosure, can take the form of: (a) increasing or decreasing a particular Family, Genus, Species, or functional grouping of microbe (i.e., alteration of the biotic component of the rumen microbiome) and / or (b) increasing or decreasing volatile fatty acids in the rumen, increasing or decreasing rumen pH, increasing or decreasing any other physical parameter important for rumen health (i.e., temperature or alteration of the abiotic component of the rumen microbiome).

[0050] The term “growth medium” as used herein, is any medium which is suitable to support growth of a microbe. By way of example, the media may be natural or artificial including gastrin supplemental agar, LB media, blood serum, and tissue culture gels. It should be appreciated that the media may be used alone or in combination with one or more other media. It may also be used with or without the addition of exogenous nutrients.

[0051] The term “relative abundance” as used herein, is the number or percentage of a microbe present in the gastrointestinal tract or other organ system, relative to the number or percentage of total microbes present in said tract or organ system. The relative abundance may also be determined for particular types of microbes such as bacteria, fungi, viruses, and / or protozoa, relative to the total number or percentage of bacteria, fungi, viruses, and / or protozoa present. In one embodiment, relative abundance is determined by PCR. In another embodiment, relative abundance is determined by colony forming unit assays (cfu) or plaque forming unit assays (pfu) performed on samples from the gastrointestinal tract or other organ system of interest.

[0052] The medium for culturing any of the disclosed microbes or bacteria may be amended or enriched with additional compounds or components, for example, a component which may assist in the interaction and / or selection of specific groups of microorganisms. For example, antibiotics (such as penicillin) or sterilants (for example, quaternary ammonium salts and oxidizing agents) could be present and / or the physical conditions (such as salinity, nutrients (for example organic and inorganic minerals (such as phosphorus, nitrogenous salts, ammonia, potassium and micronutrients such as cobalt and magnesium), pH. and / or temperature), methionine, prebiotics, ionophores, and beta glucans could be amended.

[0053] As used herein, the term “ruminant” includes mammals that are capable of acquiring nutrients from plant-based food by fermenting it in a specialized stomach (rumen) prior to digestion, principally through microbial actions. Ruminants include cattle, goats, sheep, giraffes, yaks, deer, antelope, and others.

[0054] As used herein, the term “bovid” includes any member of family Bovidae, which include hoofed mammals such as antelope, sheep, goats, and cattle, among others.

[0055] As used herein, the term “steer” includes any member, species, variant, or hybrid of Bos indicus, Bos taurus indicus, or Bos taurus. The term “steer” further includes reference to cow (mature female), steer (castrated male), heifer (immature female not having bom offspring), bull (mature uncastrated male), and calve (immature males or females).

[0056] As used herein, the terms “beef cattle” and “feedlot cattle” are used synonymously to refer to cattle that are grown and utilized for the production of beef. Said cattle of the present disclosure include varieties such as the following: Africander, Angus, Aubrac, Barzona, Bazadaise, Beef Shorthorn, Beefalo, Beefmaster, Belgian Blue, Belmont Red, Belted Galloway, Black Angus, Blonde d'Aquitaine, Bonsmara, Boran, Bradford, Brahman, Brahmousin, Brangus, British White, Buelingo, Canchim, Caracu, Charolais, Chianina, Composite. Corriente. Devon, Dexter, Drakensberger. Droughtmaster, English Longhorn, Galloway, Gelbvieh, Gloucester, Hays Converter, Hereford, Highland, Holstein, Hybridmaster, Limousin, Lincoln Red, Lowline, Luing, Maine- Anjou, Rouge des Pres, Marchigiana. Miniature Hereford, Mirandesa, Mongolian, Murray Grey, Nelore, Nguni, Parthenais. Piemontese. Pinzgauer. Red Angus, Red Poll, Retinta. Romagnola. Salers, Sanganer, Santa Cruz, Santa Gertrudis, Senepol, Shetland, Simbrah, Simmental, South Devon, Speckle Park, Square Meaters, Sussex, Tarentaise, Texas Longhorn, Tuli, Wagyu. Watusi, Welsh Black, Whitebred Shorthorn, and Zebu; or hybrids and / or crosses thereof.

[0057] As used herein, “dairy cattle’’ or “dairy cows” are used synonymously to refer to cows that are grown and utilized for the production of milk.

[0058] As used herein, “performance” should be taken to be increased weight gain, improved feed efficiency, improved residual feed intake, improved feed intake.

[0059] As used herein, “improved” should be taken broadly to encompass improvement of a characteristic of interest, as compared to a control group, or as compared to a known average quantity associated with the characteristic in question. For example, “improved” feed efficiency associated with application of a beneficial microbe, or microbial ensemble, of the disclosure can be demonstrated by comparing the feed efficiency of beef cattle treated by the microbes taught herein to the feed efficiency of beef cattle not treated. In the present disclosure, “improved” does not necessarily demand that the data be statistically significant (i.e. p<0.05); rather, any quantifiable difference demonstrating that one value (e.g. the average treatment value) is different from another (e.g., the average control value) can rise to the level of “improved.”

[0060] As used herein, “inhibiting and suppressing” and like terms should not be construed to require complete inhibition or suppression, although this may be desired in some embodiments.

[0061] The term “marker” or “unique marker” as used herein is an indicator of unique microorganism type, microorganism strain or activity of a microorganism strain. A marker can be measured in biological samples and includes without limitation, a nucleic acid-based marker such as a ribosomal RNA gene, a peptide- or protein-based marker, and / or a metabolite or other small molecule marker.

[0062] The term “metabolite” as used herein is an intermediate or product of metabolism. A metabolite in one embodiment is a small molecule. Metabolites have various functions, including in fuel, structural, signaling, stimulatory and inhibitory effects on enzy mes, as a cofactor to an enzyme, in defense, and in interactions with other organisms (such as pigments, odorants and pheromones). A primary metabolite is directly involved in normal growth, development and reproduction. A secondary' metabolite is not directly involved in these processes but usually has an important ecological function. Examples of metabolites include but are not limited to antibiotics and pigments such as resins and terpenes, etc. Some antibiotics use primary metabolites as precursors, such as actinomycin which is created from the primary metabolite, try ptophan. Metabolites, as used herein, include small, hydrophilic carbohydrates; large, hydrophobic lipids and complex natural compounds.

[0063] As used herein, the term “trait’’ refers to a characteristic or phenotype. For example, in the context of some embodiments of the present disclosure; efficiency of feed utilization, particularly with com-intensive diets; amount of feces produced; susceptibility' to gut pathogens; and a decrease in mortality rates; among others. Desirable traits may also include other characteristics, including but not limited to: an increase in weight; an increase in average daily weight gain; an increase of musculature; an increase of fatty acid concentration in the gastrointestinal tract; an improved efficiency in feed utilization and digestibility; an increase in polysaccharide and lignin degradation; an increase in fat, starch, and / or protein digestion; an increase in fatty acid concentration in the rumen; pH balance in the rumen, an increase in vitamin availability'; an increase in mineral availability’; an increase in amino acid availability; a reduction in methane and / or nitrous oxide emissions; a reduction in manure production; an improved dry' matter intake; an improved efficiency of nitrogen utilization; an improved efficiency of phosphorous utilization; an increased resistance to colonization of pathogenic microbes that colonize cattle; reduced mortality; increased production of antimicrobials; increased clearance of pathogenic microbes; increased resistance to colonization of pathogenic microbes that colonize cattle; increased resistance to colonization of pathogenic microbes that infect humans; reduced incidence of acidosis or bloat; increased meat marbling, increased or decreased red coloring of meat, increased or decreased texture / coarseness of meat; increased amount of USDA Prime, USDA Choice, and USDA Select quality meat per animal, increased in the number of animals producing USDA Prime, USDA Choice, and USDA Select quality meat; increase or reduced concentration or presence of volatile compounds in the meat; reduced prevalence of acidosis or bloat; reduced body temperature; and any combination thereof; wherein said increase or reduction is determined by comparing against an animal not having been administered said composition.

[0064] A trait may be inherited in a dominant or recessive manner, or in a partial or incomplete-dominant manner. A trait may be monogenic (i.e. determined by a single locus) or polygenic (i.e., determined by more than one locus) or may also result from the interaction of one or more genes with the environment.

[0065] In the context of this disclosure, traits may also result from the interaction of one or more beef cattle genes and one or more microorganism genes.

[0066] In the present disclosure, “nucleic acid” refers to a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form, and unless otherwise limited, encompasses known analogues (e.g., peptide nucleic acids) having the essential nature of natural nucleotides in that they hybridize to single-stranded nucleic acids in a manner similar to naturally occurring nucleotides.

[0067] The terms “polypeptide,” “peptide,” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residues is an artificial chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers. Polypeptides of the present disclosure can be produced either from a nucleic acid disclosed herein, or by the use of standard molecular biology techniques. For example, a truncated protein of the present disclosure can be produced by expression of a recombinant nucleic acid of the embodiments in an appropriate host cell, or alternatively by a combination of ex vivo procedures, such as protease digestion and purification.

[0068] The term “encode” is used herein to mean that the nucleic acid comprises the required information, specified by the use of codons to direct translation of the nucleotide sequence into a specified protein. A nucleic acid encoding a protein can comprise non-translated sequences (e.g., introns) within translated regions of the nucleic acid or can lack such intervening non-translated sequences (e.g., as in cDNA).

[0069] Aspects of the disclosure encompass isolated or substantially purified polynucleotide or protein compositions. An “isolated” or “purified” polynucleotide or protein, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide or protein as found in its naturally occurring environment. Thus, an isolated or purified polynucleotide or protein is substantially free of other cellular material, or culture medium when produced by recombinant techniques (e.g. PCR amplification), or substantially free of chemical precursors or other chemicals when chemically synthesized. Optimally, an “isolated” polynucleotide is free of sequences (for example, protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5' and 3' ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived. For example, in some aspects of the disclosure, the isolated polynucleotide can contain less than about 5 kb, about 4 kb. about 3 kb. about 2 kb, about 1 kb, about 0.5 kb, or about 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived. A protein that is substantially free of cellular material includes preparations of protein having less than about 30%, about 20%. about 10%, about 5%, or about 1% (by dry weight) of contaminating protein. When the protein of the aspects, or a biologically active portion thereof, is recombinantly produced, optimally culture medium represents less than about 30%, about 20%. about 10%, about 5%, or about 1% (by dry weight) of chemical precursors or non- protein-of-interest chemicals.

[0070] The polynucleotides described herewith can be used to isolate corresponding sequences from other organisms, particularly other plants. In this manner, methods such as PCR or hybridization can be used to identify such sequences based on their sequence homology to the sequences set forth herein. Sequences isolated based on their sequence identity to the entire sequences set forth herein or to variants and fragments thereof are encompassed by the present disclosure. Such sequences include sequences that are orthologs of the disclosed sequences. The term "orthologs" refers to genes derived from a common ancestral gene and which are found in different species as a result of speciation. Genes found in different species are considered orthologs when their nucleotide sequences and / or their encoded protein sequences share at least about 60%, about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or greater sequence identity. Functions of orthologs are often highly conserved among species. Thus, isolated polynucleotides that encode for a protein that confers or enhances fungal plant pathogen resistance and that hybridize to the sequences disclosed herein, or to variants or fragments thereof, are encompassed by the present disclosure.

[0071] The terms “inhibit / ’ “inhibition,’7“inhibiting”, “reduced”, “reduction” and the like as used herein to mean any decrease in the amount of a composition (e.g., methane), including any relative decrease in concentration including complete abrogation of the composition.

[0072] The terms “increase,” “increasing,” “enhance,” “enhancing” and the like are used herein to mean any boost or gain or rise in the amount of a composition (e.g., methane). Further, the terms “induce” or “increase” as used herein can mean higher concentration of an amount of a composition (e.g., hydrogen), such that the level is increased 5% or more, 10% or more, 50% or more or 100% relative to a control subject or target.

[0073] The term “expression” as used herein in refers to the biosynthesis or process by which a polynucleotide, for example, is produced, including the transcription and / or translation of a gene product. For example, a polynucleotide of the present disclosure can be transcribed from a DNA template (such as into an mRNA or other RNA transcript) and / or the process by which a transcribed mRNA is subsequently translated into a polypeptide or protein. The term “gene product” can refer to for example, transcripts and encoded polypeptides. Inhibition of (or increase in) expression or function of a gene product (i.e., a gene product of interest) can be in the context of a comparison between any two plants, for example, expression or function of a gene product in a genetically altered plant versus the expression or function of that gene product in a corresponding, but susceptible wild-type plant or other susceptible plant. The expression level of a gene product in a wild-type plant can be absent.

[0074] Alternatively, inhibition of (or increase in) expression or function of the target gene product can be in the context of a comparison between plant cells, organelles, organs, tissues, or plant parts within the same plant or between plants, and includes comparisons between developmental or temporal stages within the same plant or between plants. Any method or composition that down-regulates expression of a target gene product, either at the level of transcription or translation, or down-regulates functional activity of the target gene product can be used to achieve inhibition of expression or function of the target gene product. Similarly, any method or composition that induces or up-regulates expression of a target gene product, either at the level of transcription or translation, or increases or activates or up- regulates functional activity of the target gene product can be used to achieve increased expression or function of the target gene or protein. Methods for inhibiting or enhancing gene expression are well known in the art.

[0075] As used herein “shelf-stable” refers to a functional attribute and new utility acquired by the microbes formulated according to the disclosure, which enable said microbes to exist in a useful / active state outside of their natural environment in the rumen (i.e. a markedly different characteristic). Thus, shelf-stable is a functional attribute created by the formulations / compositions of the disclosure and denoting that the microbe formulated into a shelf-stable composition can exist outside the rumen and under ambient conditions for a period of time that can be determined depending upon the particular formulation utilized, but in general means that the microbes can be formulated to exist in a composition that is stable under ambient conditions for at least a few days and generally at least one week. Accordingly, a “shelf-stable ruminant supplement” is a composition comprising one or more microbes of the disclosure, said microbes formulated in a composition, such that the composition is stable under ambient conditions for at least one week, meaning that the microbes comprised in the composition (e.g. whole cell, spore, or lysed cell) are able to impart one or more beneficial phenotypic properties to a ruminant when administered (e g. increased milk yield, improved milk compositional characteristics, improved rumen health, and / or modulation of the rumen microbiome).

[0076] “Percentage of sequence identity”, as used herein, is determined by comparing two optimally locally aligned sequences over a comparison window defined by the length of the local alignment between the two sequences. The amino acid sequence in the comparison window may comprise additions or deletions (e.g.. gaps or overhangs) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Local alignment between two sequences only includes segments of each sequence that are deemed to be sufficiently similar according to a criterion that depends on the algorithm used to perform the alignment (e. g. BLAST). The percentage of sequence identity is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100. Optimal alignment of sequences for comparison may be conducted by the local homolog}’ algorithm of Smith and Waterman (Add. APL. Math. 2:482, 1981), by the global homology alignment algorithm of Needleman and Wunsch (J Mol. Biol. 48:443, 1970), by the search for similarity method of Pearson and Lipman (Proc. Natl. Acad. Sci. USA 85:2444, 1988), by heuristic implementations of these algorithms (NCBI BLAST, WU-BLAST. BLAT, SIM, BLASTZ), or by inspection. Given that two sequences have been identified for companson. GAP and BESTFIT are preferably- employed to determine their optimal alignment. Typically, the default values of 5.00 for gap weight and 0.30 for gap weight length are used. The term “substantial sequence identity" between polynucleotide or polypeptide sequences refers to polynucleotide or polypeptide comprising a sequence that has at least 50% sequence identity, preferably at least 70%, preferably at least 80%>, preferably at least 85%, preferably at least 90%>, preferably at least 95%, and preferably at least 96%>, 97%, 98% or 99% sequence identity’ compared to a reference sequence using the programs. In addition, pairwise sequence homology or sequence similarity, as used, refers to the percentage of residues that are similar between two sequences aligned. Families of amino acid residues having similar side chains have been well defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g.. alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, try ptophan, histidine). Query’ nucleic acid and amino acid sequences can be searched against subject nucleic acid or amino acid sequences residing in public or proprietary databases. Such searches can be done using the National Center for Biotechnology Information Basic Local Alignment Search Tool (NCBI BLAST v 2.18) program. The NCBI BLAST program is available on the internet from the National Center for Biotechnology Information (blast.ncbi.nlm.nih.gov / Blast.cgi). Typically the following parameters for NCBI BLAST can be used: Filter options set to “default”, the Comparison Matrix set to “BLOSUM62”, the Gap Costs set to “Existence: 11, Extension: 1”, the Word Size set to 3, the Expect (E threshold) set to le-3, and the minimum length of the local alignment set to 50% of the query sequence length. Sequence identity and similarity may also be determined using GenomeQuest™ software (Gene-IT. Worcester Mass. USA).

[0077] A “control plant”, as used herein, provides a reference point for measuring changes in phenotype of the subject plant, and may be any suitable plant cell, seed, plant component, plant tissue, plant organ or whole plant which has not been exposed to a particular treatment such as, for example, an inoculant or combination of inoculants and / or other chemicals.

[0078] “Inoculant” as used herein refers to any culture or preparation that comprises at least one microorganism. In some aspects, an inoculant (sometimes as microbial inoculant, or soil inoculant) is an agricultural amendment that uses beneficial microbes (including, but not limited to endophytes) to promote plant health, growth and / or yield, animal health, growth or improvement of one or more traits. Many of the microbes suitable for use in an inoculant form symbiotic relationships with the target crops where both parties benefit (mutualism).

[0079] A bioreactor refers to any device or system that supports a biologically active environment. As described herein a bioreactor can be a vessel in which microorganisms including the microorganism of the aspects of this application can be grown.

[0080] COMPOSITIONS

[0081] Described herein are compositions comprising aquatic microbial species for application to terrestrial plants. In some aspects, the inoculant mixture also comprises a species that produces and / or maintains a microenvironment in the plant that is suitable for other microbes in the inoculant mixture to thrive.

[0082] Disclosed herein are compositions comprising a plant seed and one or more of the microbes listed in Table 1, Table 2, Table 3 or Table 4.

[0083] Disclosed herein are compositions comprising a plant seed and two or more bacterial strains. In some aspects, a first bacterial strain comprises Clostridium spp. In some aspects, the 16S sequence of Clostridium spp. comprises any one of the Clostridium spp. listed in Table 1 or Table 2. In some aspects, a second bacterial strain comprises an aquatic Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2. Disclosed herein are compositions comprising one or more of the microbes listed in Table 1, Table 2. Table 3 or Table 4. In some aspects, the compositions disclosed herein can further comprise one or more of the microbes listed in Table 1, Table 2, Table 3, or Table 4. In some aspects, the compositions disclosed herein can further comprise at least one different microbial strain. In some aspects, the 16S sequence of the one different microbial strain can comprise a 16S sequence that is at least about 97% identical to one or more of the 16S sequences listed in Table 1, Table 2. Table 3, or Table 4.

[0084] In some aspects, the compositions disclosed herein can further comprise an agriculturally effective amount of a compound or composition selected from the group consisting of a nutrient, a fertilizer, an acaricide, a bactericide, a fungicide, an insecticide, a microbicide, a nematicide, and a pesticide.

[0085] In some aspects, the compositions disclosed herein can further comprise a earner. In some aspects, the carrier can be peat, turf, talc, lignite, kaolinite, pyrophyllite, zeolite, montmorillonite, alginate, press mud, sawdust, perlite, mica, silicas, quartz powder, calcium bentonite, vermiculite or mixtures thereof.

[0086] In some aspects, the compositions disclosed herein can be prepared as a formulation selected from the group consisting of an emulsion, a colloid, a dust, a granule, a pellet, a powder, a spray, and a solution.

[0087] In some aspects, compositions disclosed herein can be mixed with animal feed. In some aspects, the animal feed can be present in various forms such as pellets, capsules, granulated, powdered, mash, liquid, semi-liquid, or mixed rations(s).

[0088] In some aspects, the plant seed can be a transgenic plant seed.

[0089] Disclosed herein are plant seeds. In some aspects, the plants seeds can have a coating comprising any of the compositions disclosed herein. In some aspects, the plant seeds can have a coating comprising two or more bacterial strains, wherein a first bacterial strain comprises Clostridium spp., and w herein the 16S sequence of Clostridium spp. comprises any one of the Clostridium spp. listed in Table 1 or Table 2 and a second bacterial strain comprising an aquatic Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2. In some aspects, the plant seeds can have a coating comprising two or more bacterial strains, wherein a first bacterial strain comprises Clostridium spp., and wherein the 16S sequence of Clostridium spp. comprises any one of the Clostridium spp. listed in Table 1 or Table 2, a second bacterial strain comprising an aquatic Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2 and one or more of the microbes listed in Table 1, Table 2 or Table 3. In some aspects, the plant seeds can have a coating comprising two or more bacterial strains, wherein a first bacterial strain comprises Clostridium spp., and wherein the 16S sequence of Clostridium spp. comprises any one of the Clostridium spp. listed in Table 1 or Table 2, a second bacterial strain comprising an aquatic Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2 and one or more of the microbes listed in Table 1 , Table 2 or Table 3. In some aspects, the plant seeds can a coating further comprise a composition that has at least one different microbial strain, wherein the 16S sequence of the one different microbial strain comprises a 16S sequence that is at least about 97% identical to one or more of the 16S sequences listed in Table 1, Table 2 or Table 3.

[0090] The primary structure of major rRNA subunit 16S comprise a particular combination of conserved, variable, and hypervariable regions that evolve at different rates and enable the resolution of both very ancient lineages such as domains, and more modem lineages such as genera. The secondary structure of the 16S subunit include approximately 50 helices which result in base pairing of about 67% of the residues. These highly conserved secondary- structural features are of great functional importance and can be used to ensure positional homology7in multiple sequence alignments and phylogenetic analysis. Over the previous few decades, the 16S rRNA gene has become the most sequenced taxonomic marker and is the cornerstone for the cunent systematic classification of bacteria and archaea (Yarza et al. 2014. Nature Rev. Micro. 12:635-45).

[0091] A sequence identify of 94.5% or lower for two 16S rRNA genes is strong evidence for distinct genera, 86.5% or lower is strong evidence for distinct families, 82% or lower is strong evidence for distinct orders, 78.5% is strong evidence for distinct classes, and 75% or lower is strong evidence for distinct phyla. The comparative analysis of 16S rRNA gene sequences enables the establishment of taxonomic thresholds that are useful not only for the classification of cultured microorganisms but also for the classification of the many environmental sequences. Yarza et al. 2014. Nature Rev. Micro. 12:635-45).

[0092] A loss of biodiversify within a soil matrix can lead to yield depression of agricultural crops. Microbial inoculants can increase solubilization, uptake, and / or assimilation of nutrients such as, for example, carbon, nitrogen, potassium, phosphorus, selenium, cobalt, zinc, and copper. Microbial inoculants also can reduce plant pathogen damage to crops by stimulating plant production of a stable and continuous source of plant hormones that enhance growth. While microorganisms capable of promoting plant growth and plant production can occur naturally in soil, the mere presence of the microbes does not guarantee the successful integration of the microbes.

[0093] In some aspects, the composition can function endophytically within at least one plant to maintain an available electron state that is available for use within the plant's metabolic process. That is, the composition can act as an ionic catalyst to either accept or remove an electron to make the electron available to or remove the electron from the plant. This process can occur, in the absence of such a composition, when a plant switches from photosynthesis during the day to respiration at night and vice versa. The composition, when applied to the plant, supports the plant by making nutrients chemically available so the plant can produce hormones at a sufficient level to promote grow th.

[0094] The composition can inoculate the plant by being in close proximity and / or direct physical contact with the plant. As an example, a droplet of water including the composition can be deposited on the plant, and thereby not deposited in the soil and not absorbed by the roots.

[0095] Described herein are compositions isolated from an aquatic environment for application to terrestrial plants. In some aspects, the inoculant mixture also comprises a species that produces and / or maintains a microenvironment in the plant that is suitable for other microbes in the inoculant mixture to thrive.

[0096] Generally, the composition includes a. Pseudomonas spp. and a Clostridium spp., such as, for example, P. fluorescens and C. saccharobutylicum.

[0097] In some aspects, the composition further comprises one or more of Agrobacterium tume aciens (TPD7005), Bacillus megaterium (TPD7007), Bacillus megaterium (TPD 7008), Agrobacterium rhizogenes (1713117 009), Microbacterium testaceum (TPD7010), Bacillus megaterium (TPD7011), Microbacterium spp. (TPD7012), Pedobacier kribbensis (TPD70013), Janthinobacterium lividum (TPD7014), Bacillus racemilacticus (TPD7015), Bacillus megaterium (TPD 7018), Delftia spp. (TPD3002), Chryseobacterium spp. (TPD3003), Bacillus licheniformis, Brevundimonas kwangchunensis (TPD3004), Fictibacillus barbaricus / Bacillus barbaricus (TPD3005). Prosthecobacter spp. (TPD3006), Lactobacillus plantarum (TPD3007). Sphingobacterium multivorum, Sphingomonas spp. (TPD3009), Sphingosinicella microcystinivorans (TPD3010), Pseudomonas chlororaphis. Pseudomonas mandelii, Pseudomonas umsongensis, Clostridium saccharobutylicum (TPD3014), Arthrobacter ramosus (TPD3015), Streptomyces yogyakartensis (TPD3016), Arthrobacter spp. (TPD3017), Xanthomonas spp.. Chryseobacterium tndologenes (TPD3019), or Lactobacillus plantarum. Table 1 shows 16S RNA analysis and / or whole genome shotgun sequencing project data for exemplary members of the composition.

[0098] Table 1. Microbes

[0099] Table 2 shows bacterial strains useful in the compositions and methods disclosed herein.

[0100] Table 2. Microbes.

[0101] Table 3 shows bacterial strains useful in the compositions and methods disclosed herein. Table 3. Microbes.

[0102]

[0103] Table 4 shows bacterial strains useful in the compositions and methods disclosed herein.

[0104] Table 4. Microbes.

[0105] In some aspects, the compositions further comprise one or more of yeast strain TAH3020 or yeast strain TAH3021.

[0106] The compositions disclosed herein can promote plant growth (e.g., increase leaf size, increase root mass), decrease the impact of stress, decrease water consumption, increase solubility and / or assimilation of nutrients, increase feed value, increase decay of carbon- containing molecules so that the organic molecules are more readily available to the plant, increase production of hormones in plants, and / or increase plant metabolism (thereby decreasing the time to fruit). Moreover, in legumes, the composition can increase pod numbers, increase root growth, increase nodulation, and / or increase the number of branches per plant. In some aspects, the composition can be applied to contact and / or interact endophytically with the plant.

[0107] In some aspects, bacteria in the composition can produce 1- aminocyclopropane-l-carboxylate (ACC) deaminase. ACC can lower plant ethylene levels, often a result of various stresses such as, for example, stress to heat and / or drought. ACC can interact synergistically with the plant and bacterial auxin, indole-3-acetic acid (IAA). ACC- producing bacteria not only can directly promote plant grow th, but also can protect plants against flooding, drought, salt, flower wilting metals, organic contaminants, bacterial pathogens, and fungal pathogens.

[0108] In some aspects, decreasing water consumption can increase solubilization of minerals and / or fertilizers so that water requirements are reduced to transport the minerals and / or fertilizers from the roots, increase root development so that soil nutrients can be obtained from a greater area and / or water can be obtained from deeper in the soil, and / or reduce daily heat stress. Reducing daily heat stress allows the plant to better acquire CO2, thereby metabolize more sugars and increase yield, regulate pH, and / or produce more energy’ during daylight hours.

[0109] The compositions can include additional microbial species or other additives to induce the plant to perform desired physiological, metabolic, or other activity. For example, in some aspects, the compositions can include one or more of the following microbial species: anAcetobacteraceae, spp. (e.g.,Acidisphaera spp.). an Acetivibrio spp. (e.g., Acetlvibrio cellulolyticus), an Acidiphilium spp.. an Acidimicrobiaceae spp. (e.g., an Acidimicrobium spp., an Aciditerrimonas spp.), an Acidobacteriales spp. (e.g., an Acidobacteriaceae spp. [e.g., an Acidobacterium spp.]), an Acidothermus spp.. an Acidovor ax spp. (e.g.. Acidovorax citrulli), an Acinetobacter spp. (e.g., Acinetobacter hvojfii), an Actinoallomurus spp. (e.g., Actinoallomurus iriomotensis), an Actinocat enispor a spp. (e.g., Actinocatenispora rupis). an Actinomadura spp., an Actinomycetales spp. (e.g., an Actinomyces spp ), an Actinoplanes spp. (e.g., Actinoplanes auranlicolor), an Actinopolymorpha spp. (e.g., Actinopoly mor pha pittospori), an Actinotalea spp. (e.g., Actinotalea fermentans), an Adhaeribacter spp. (e.g., Adhaeribacter terreus), an Aeromicrobium spp. (e.g., Aeromicrobium fastidiosum), an Afipia spp., an Agromyces spp. (e.g., Agromyces ulmi, Agromyces subbeticus), anAlcaligenaceae spp., an Algor iphagus spp., an Alkaliflexus spp., an Alphaproteobacteria spp., an Alsobacter spp. (e.g., Alsobacter metallidurans), an Alter erythrobacter spp., an Alteromonadaceae spp., an Amaricoccus spp., anAminobacter spp., an Amycolatopsis spp. (e.g., Amy colat opsis iriomotensis,Amycolatopsis vancoresmycina), an Anaeromyxobacteraceae sp\r (e.g., an Anaeromyxobacter spp. [e.g., Anaeromyxobacter dehalogenans]), an Ancylobacter spp., an Angustibacter spp. (e.g., Angustibacter peucedani), an Aquabacterium spp., an Aquicella spp., an Armatimonadetes spp., an Arenimonas spp. (e.g., Arenimonas oryziterrae), an Arsenicicoccus spp. (e.g., Arsenicicoccus dermatophilus), an Arthrobacter spp. (e.g., Arthrobacter pascens, Arthrobacter tumbae), an Asanoa spp. (e.g., Asanoa ishikariensis), an Azohydromonas spp. (e.g., Azohydromonas australica), an Azonexus spp.. anAzospira spp. (e.g., Azospira oryzae), an Azospirillum spp. (e.g., Azospirillum lipqferum), an Azotobacter spp. (e.g., Azotobacter chroococcum), a Bacillaceae spp. (e.g., a Bacillus spp. [e.g., Bacillus acidiceler, Bacillus aphidicola, Bacillus senegalensis , Bacillus megaterium, Bacillus subtilis]), a Bacteroidetes spp. (e.g., a Bacteroidales spp. [e.g., a Bacteroides spp.]), a Bauldia spp. (e.g., Bauldia consociate), a Bdellovibrionaceae spp., a Beijerinckia spp., a Blastococcus spp. (e.g., Blastococcus saxobsidens), a Blastomonas spp., a Bordetella spp. (e.g., Bordetella hinzii), a Bosea spp., a Bradyrhizobiaceae, spp. (e.g., Bradyrhizobium spp. [e.g., Bradyrhizobium elkanii, Bradyrhizobium yuanmingense]), a Brevibacteriaceae spp., a Brevundimonas spp. (e.g., Brevundimonas lenta), a Bryobacter spp., a Burkholderiales spp. (e.g., a Burkholderiaceae spp. [e.g.. a Burkholderia spp. ). a Brucellaceae spp.. a Buttiauxella spp. (e.g., Buttiauxella izardii), a Byssovorax, spp., a Caldilineales spp. (e.g., a Caldilineaceae spp. [e.g., a Caldilinea spp.]), a Caloramator spp., a Candidatus spp. (e.g., Candidatus brocadiaceae, Candidatus entotheonella, Candidatus koribacter, Candidatus nitrosoarchaeum, Candidatus phytoplasma, Candidatus saccharibacteria, Candidatus solibacter), a Carnobacterium spp., a Catenuloplanes spp., a Catellatospora spp., (e.g.. Catellatospora citrea), a Caulobacteraceae spp. (e.g., a Caulobacter spp. [e.g., Caulobacter tundrae]), a Cellulosimicrobium spp. (e.g., Cellulosimicrobium cellulans). a Cellvibrio spp. (e.g.. Cellvibrio vulgaris), a Cellulomonas spp. (e.g., Cellulomonas terrae). a Chelatococcus spp. (e.g., Chelatococcus asaccharovorans, a Chitinophagaceae spp., a Chromobacteriaceae spp., a Chloroflexales spp. (e.g., a Chloroflexaceae spp. [e.g., a Chloroflexus spp.} , a Chthoniobacter spp. (e.g., Chthoniobacter flavus), a Chryseobacterium spp., a Cilrobacter spp., a Clavibacter spp. (e.g., Clavibacter michiganensis), a Clostndiaceae spp. (e.g.. a Clostridium spp. [e.g., Clostridium bowmanii, Clostridium gasigenes, Clostridium uliginosum, Clostridium vincentii}), a Comamonadaceae spp. (e.g., a Comamonas, spp. [e.g., Comamonas koreensis}), a Conexibacteraceae spp. (e.g., a Conexibacter spp. [e.g., Conexibacter woesei}), a Coxiellaceae spp.. a Crenotrichaceae spp. a Cryomorphaceae spp., a Cryobacterium spp. (e.g.. Cryobacterium mesophilum), a Cupriavidus spp. (e.g., Cupriavidus campinensis), aCurtobacterium spp., aCyanobacteria spp., aCyclobacteriaceae spp., a Cystobacteraceae spp. (e.g., a Cystobacter spp ), a Cytophagaceae spp. (e.g., a Cytophaga spp I). a Defluviicoccus spp., a Dehalococcoidales spp. (e.g., a Dehalogenimonas spp., a Dehalococcoides spp.). aDenitratisoma spp., aDerxia spp.. a Desulfovibrionales spp. (e.g., a Desulfobacteraceae spp. [e.g., a Desulfocapsa spp., a Desulfatiglans spp., a Desulforegula spp. ]), a Desulfoglaeba spp., a Desulfosporosinus spp. (e.g., Desulfosporosinus meridiei), a Desulfotomaculum spp., a Desulfuromonadales spp. (e.g., a Desulfuromonas spp.). a Devosia spp. (e.g.. Devosia insulae), a Dickeya spp. (e.g., Dickeya zeae), a Dyadobacter spp., an Ectothiorhodospiraceae spp., an Elusimicrobia spp. (e.g., an Elusimicrobiaceae spp. [e.g., an Elusimicrobium spp.}), an Endomicrobia spp., an Enhygromyxa spp. (e.g., Enhygromyxa salina), an Epilithonimonas spp.. an Erwinia spp. (e.g., Erwinia persicina), an Exiguobacterium spp. (e.g., Exiguobacterium undae), a Ferrimicrobium spp., a Fictibacillus spp., a Flavobacteriales spp. (e.g., aFlavobacteriaceae, [e.g., aFlavobacterium spp. such as, for example, Flavobacterium arsenatis, Flavobacterium columnare, Flavobacterium hauense, Flavobacterium johnsoniae, Flavobacterium terrigena]), a Flavisolibacter spp.. aFlexibacter spp., aFlindersiella spp., aFodinicola spp., a Frankia spp., Frigoribacterium spp., a Gaiellales spp. (e.g.. a Gaiella spp. [e.g.. Gaiella occulta}), a Gallionellaceae spp. (e.g., a Gallionella spp ), a Gemmatimonadales spp. (e.g., a Gemmatimonadaceae spp. [a Gemmatimonas spp.}), a Gemmata spp., a Geoalkalibacter spp., a Geobacillus spp., a Geobacteraceae spp. (e.g., a Geobacter spp ). a Gillisia spp., a Glycomyces spp. (e.g., Glycomyces harbinensis), a Halomonas spp. (e.g., Halomonas muralis), a Haliangium spp., a Herbaspirillum spp. (e.g., Herbaspirillum huttiense), a Holophagales spp. (e.g., a Holophagaceae spp. [e.g., aHolophaga spp.]), a Humibacillus spp. (e.g., Humibacillus xanthopallidus), a Hydrogenophaga spp. (e.g., Hydrogenophaga palleronu). a Hydrogenophilaceae spp., a Hyphomicrobiaceae spp. (e.g., a Hyphomicrobium spp. [e.g., Hyphomicrobium methylovorum]), aHyphomonas spp., an Icimiaceae spp. (e.g., an lamia spp ), an Ideonella spp., an Ignavibacteriales spp. (e.g., an Ignavibacteriaceae spp. such as, for example, an Ignavibacterium spp ), an Ilumatobacter spp., an Intrasporangiaceae spp. (e.g., an Intrasporangium spp. [e.g.. Intrasporangium oryzae]). aJiangella spp., aKaistia spp., a Kaistobacter spp., a Kallotenuales spp., a Kineococcus spp., a Kineosporia spp. (e.g., Kineosporia mikuniensis), a Knoellia spp., a Kofleriaceae spp. (e.g., a Kofleria spp ), a Kribbella spp. (e.g., Kribbella karoonensis, Kribbella swartbergensis), a Labedella spp., a Labilitrichaceae spp. (e.g., a Labilithrix spp. [e.g., Labilithrix luteola]), a Lactobacillus spp., a Ixictococcus spp. (e.g.. Lactococcus garvieae), a Lapillicoccus spp. (e.g., Lapillicoccus jejuensis), a Legionellaceae spp., a Leifsonia spp., a Lentzea spp. (e.g., Lentzea albida), a Leptospira spp., aLeptothrix spp., aLeucobacter spp. (e.g., Leucobacter tardus), aLongilinea spp., a Lysinibacillus spp. (e.g., Lysinibacillus sphaericus), a Lysobacter spp., a Marinimicrobium spp., a Marinobacter spp., a Marmoricola spp.. a Massilia spp. (e.g., Massilia timonae), a Melioribacteraceae spp. (e.g., a Melioribacter spp.), a Mesorhizobium spp. (e.g., Mesorhizobium loti, Mesorhizobium plurifarium), a Methylibium spp., a Methylobacillus spp. (e.g.. Methylobacillus flagellates), a Methylobacteriaceae spp. (e.g., a Methylobacterium spp. [e.g.. Methylobacterium adhaesivum]), a Methylocella spp., a Methyl ococcaceae spp. (e.g., a Methylobacter spp ), a Methyl ocystaceae spp. (e.g., a Methylocystis spp. [e.g., Methylocystis echinoides]), aMethylosinus spp., aMethyloversatilis spp., a Microbacteriaceae spp. (e.g., a Microbacterium spp. [e.g., Microbacterium kitamiense], a Microcella spp. [e.g.. Microcella alkaliphile]), a Micrococcaceae spp.. a Microlunatus spp., a Microvirga spp. (e.g., Microvirga aerilata, Microvirga subterranean), a Mycobacteriaceae spp. (e.g., a Mycobacterium spp. [e.g., Mycobacterium sacrum, Mycobacterium salmoniphilum, Mycobacterium septicum]), a Micromonosporaceae spp. (e.g., a Micromonospora spp. [e.g., Micromonospora rhodorangea]), a Modestobacter spp. (e.g.. Modestobacter multiseptatus). a Moorella spp., a Myxococcales spp.. a Nakamurella spp., a Nannocystaceae spp. (e.g., a Nannocystis spp. [e.g., Nannocystis exedens]), a Neorhizobium spp. (e.g., Neorhizobium huautlense), a Niastella spp., a Nitriliruptor spp., a Nitrosomonadaceae spp. (e.g., a Nitrosomonas spp. [e.g., Nitrosomonas communis, Nitrosomonas ureae]), a Nitrosopumilales spp. (e.g., a Nitrosopumilaceae sppl), a Nitrosospira spp., a Nitrosovibrio spp. (e.g.. Nitrosovibrio tenuis), aNitrospirales spp. (e.g.. a Nitrospira spp.). a Nocardiaceae spp. (e.g., a Nocardia spp. [e.g., Nocardia anaemiae]), a Nocardioidaceae spp. (e.g., a Nocardioides spp. [e.g., Nocardioides albus. Nocardioides iriomotensis , Nocardioides islandensis. Nocardioides marilimus. Nocardioides penllae. Nocardia pneumoniae]'), a Nocardiopsis spp. (e.g., Nocar diopsis synnemataf ormans), a Nonomuraea spp. (e.g., Nonomuraea kuesteri), aNordella spp., aNovosphingobium spp., an Ochrobactrum spp. (e.g., Ochrobaclrum haematophllum), an Ohtaekwangia spp.. an Olivibacter spp. (e.g., Olivibacter soli), an Opitutaceae spp., an Oryzihumus spp., an Oxalobacteraceae spp., an Oxalophagus spp. (e.g., Oxalophagus oxalicus), a Paenibacillus spp., (e.g., Paenibacillus graminis, Paenibacillus chondr oitinus, Paenibacillus validus), a Pantoea pp. (e.g.. Pantoea agglomerans), a Paracoccus spp., a Paracraurococcus spp., a Parastreptomyces spp., a Pasteuriaceae spp., (e.g., a Pasteuria spp.), a Pedosphaera spp. (e.g., Pedosphaera parvula), aPedobacter spp. (e.g., Pedobacter tournemirensis, Pedobacter kribbensis, Pedobacter kwangyangensis), a Pelagibacterium spp. (e.g., Pelagibacterium halotolerans), a Pelobacteraceae spp. (e.g., aPelobacter spp ), aPeptoclostridium spp. (e.g., Peptoclostridium Clostridium sordellii), a Peredibacter spp., a Phaselicystidaceae spp.. a Phenylobacterium spp., a Phycicoccus spp., a Phycisphaerae spp., a Phyllobacterium spp. (e.g., Phyllobacterium trifolii), aPigmentiphaga spp., a Pianococcus spp., a Planomicrobium spp., (e.g., Planomicrobium novatatis), a Planctomycetes spp. (e.g., a Pirellula spp., such as Pirella staleyi), a Plesiocystis spp., a Polaromonas spp., a Polyangiaceae spp., a Procabacteriacae spp., a Prolixibacter spp., a Promicromonospora spp., (e.g., Promicromonospora sukumoe), a Prosthecobacter spp., a Prosthecomicrobium spp., a Pseudoalteromonas spp., a Pseudoclavibacter spp., (Pseudoclavibacter helvohis), a Pseudolabrys spp., (e.g., Pseudolabrys taiwanensis), a Pseudomonadaceae spp. (e.g., Pseudomonas fluorescens. Pseudomonas flavescens, Pseudomonas protegens, Pseudomonas veronii. Pseudomonas rhodesiae. Pseudomonas koreensis. Pseudomonas moorei. Pseudomonas baetica), a Pseudonocardia spp., (e.g., Pseudonocardia zijingensis, Pseudonocardia carboxydivorans), a Pseudorhodoferax spp., a Pseudoxanthobacter spp., a Pseudoxanthomonas spp., a Ralstonia spp., a Ramlibacter spp., a Reyranella spp. (e.g., Reyranella massiliensis), a Rheinheimera spp., a Rhizobiales spp. (e.g., a Rhizobiaceae spp., a Rhodobiaceae spp ), a Rhizobium spp. (e.g., Rhizobium etli), a Rhizomicrobium spp., a Rhodobacterales spp. (e.g., a Rhodobacter spp ), a Rhodococcus spp. (e.g., Rhodococcus gordoniae, Rhodococcus kroppensiedlii. Rhodococcus wratislaviensis). a Rhodocyclales spp. (e.g.. a Rhodocyclaceae spp.), a Rhodomicrobium spp., a Rhodoplanes spp. (e.g., Rhodoplanes elegans), a Rhodopseudomonas spp., a Rhodospirillales spp. (e.g., a Rhodospirillaceae spp.). a Rhodothermus spp., a Rickettsiaceae spp., a Roseateles spp., a Roseomonas spp., a Rubrivivax spp. (e.g., Rubrivivax gelatinosus), a Rubrobacterales spp. (e.g., a Rubrobacter spp.), a Ruminococcaceae spp., a Saccharopolyspora spp. (e.g., Saccharopolyspora gloriosa), a Sandar acinus spp., a Saprospiraceae spp., a Serratia spp. (e.g., Serratia proteamaculans), a Shimazuella spp. (e.g., Shimazuella kribbensis), a Shinella spp. (e.g., Shinella granuli), a Sideroxydans spp. (e.g., Sideroxydans lilhotrophicus, Sideroxydans paludicola), a Smobacteraceae spp. (e.g., a Steroidobacter spp.), a Sinorhizobium spp., a Solibacteraceae spp. (e.g., a Solibacter spp.), a Solirubrobacteraceae spp. (e.g., a Solirubrobacter spp ), a Sorangium spp. (e.g., Sorangium cellulosum), a Sphaerobacterales spp. (e.g., a Sphaerobacteraceae spp. such as, for example, a Sphaerobacter spp I), a Sphingobacteriales spp. (e.g., a Sphingobacteriaceae spp. such as, for example, a Sphingobacterium spp.), a Sphingobium spp. (e.g., Sphingobium herbicidovorans), a Sphingomonadaceae spp. (e.g., a Sphingobium spp. [e.g., S. xenophagum], a Sphingomonas spp. [e.g., S. wittichii]), a Sphingopyxis spp. (e.g., Sphingopyxis macrogoltabida), a Sphingosinicella spp., a Spirochaetales spp. (e.g., a Spirochaeta spp.). a Sporichthyaceae spp. (e.g., a Sporichthya spp.), a Stackebrandtia spp. (e.g., Stackebrandtia nassauensis, a Stella spp., a Stenotrophomonas spp. (e.g., Stenotrophomonas maltophilia), a Stigmatella spp. (e.g., Stigmatella erecta), a Streptacidiphilus spp., a Streptoalloteichus spp., a Streptomycelaceae spp. (e.g., a Streptomyces spp. [e.g., Streptomyces aculeolatus, Streptomyces clavuligerus . Streptomyces fradiae, Streptomyces ghanaensis, Streptomyces glauciniger, Streptomyces hebeiensis, Streptomyces heteromorphus , Streptomyces mashuensis , Streptomyces microflavus , Streptomyces netropsis, Streptomyces phaeochromogenes, Streptomyces roseogriseolus, Streptomyces variabilis. Streptomyces vayuensis, Streptomyces viridodiastaticus , Streptomyces viridochromogenes , Streptomyces xylophagus, Streptomyces xinghaiensis]), a Sulfuricella spp., a Syntrophobacterales spp. (e.g., a Syntrophorhabdaceae spp. such as, for example, Syntrophobacter spp. [e.g., S. wolinii], Syntrophorhabdus spp., a Syntrophaceae spp., a Syntrophus sppl), a Taibaiella spp., a Tepidamorphus spp., a Terrabacter spp.. a Terriglobus spp., a Terrimonas spp.. a Tetrasphaera spp. (e.g.. Tetrasphaera elongate), a Thermoanaerobacterales spp. (e.g., a Thermoanaerobacteraceae spp.), a Thermoflavimicrobium spp., a Ihermoleophilaceae spp., a Thermomonosporaceae spp., a Thioalkalivibrio spp., a Thiobacillus spp., (e.g., Thiobacillus denitriflcans), a Thiobacter spp., a Thiomonas spp.. a Thiorhodovibrio spp.. a Tolumonas spp.. (e.g., Tolumonas auensis) a Variovorax spp., (e.g., Variovorax paradoxus), a Verrucomicrobiales spp., (e.g., a Verrucomicrobia subdivision 3 spp.). a Vibrionales spp., a Woodsholea spp., (e.g., Woodsholea maritima), a Xanthomonadaceae spp.. (e.g.. a Xanthomonas spp ), a Zoogloea spp., or a Zooshikella spp.

[0110] In some aspects, the following can act as an antagonist to at least one of the microbial species listed above, e.g., such as Pseudomonas fluor escens, Pseudomonas Streptornyces hygroscopicus, Mycobacterium vaccae, Agrobacterium turnefaciens, Bacillus megaterium, Bacillus amyloliquifaciens , Bacillus subtilus, Bacillus pumtlus. a Shingomonas spp., Sphingomonas melonis, an Arthrobacter spp.. Agrobacterium rhizogenes, Serratia proteatnaculans Microbacterium testaceum, a Pseudomonas spp., an Erwinia spp., Pantoea agglomerans, Pseudomonas inandelii, a Microbacterium spp., Clostridium saccharobutylicum, Pseudomonas moraviensis, Pantoea vagans, Serratia liquefaciens , Pedobacter kribbensis, Tolumonas auensis, Janthinobacterium lividum. Bacillus racemilacticus , Sporolactoba cillus laevolacticus, Brevundimonas mediterranea, Pantoea cloacae, Clostridium acidisoli, Erwinia aphidicola, Bacillus arbutinivorans , Paenibacillus grarninis Pseudomonas veronii, Pseudomonas rhodesiae, Pseudomonas koreensis, Tolumonas auensis. Pseudomonas moorei, Pseudomonas baetica, and / or Pseudomonas protegens.

[0111] In some aspects, a microbial species that provides insecticidal activity can be added to the microbial inoculant. Suitable microbes can include bacteria or fungi that produce phytochemicals that have insecticidal or insect repelling properties. In some aspects, the microbial species can be a bacterium such as, for example, B. thuringiensis, B. pipilliae, Photohabdus luminescens, Pseudomonas entomohpilia, Envinia aphidicola, etc., or a fungus such as, for example, Beaveria bassiana, Lagenidium giganteum, etc.

[0112] The composition also can include one or more non-microbial additives. For example, the composition can include one or more macronutrients or one or more micronutrients such as, for example, carbon, nitrogen, potassium, phosphorus, zinc, magnesium, selenium, chromium, tin, manganese, cobalt, zinc, and / or copper.

[0113] Suitable macronutrients or micronutrients may enhance the longevity of the bacteria and microbes leading to a longer shelf life. Also, adding a slow growth supporting carbon source (e.g., glycerol, a vegetable oil, lignin, etc.) may be beneficial. This can also function as a stratification media for more anaerobic and aerobic microbes in a single package.

[0114] In some aspects, the composition can include one or more plant hormones such as, for example, an auxin. Exemplary suitable plant hormones include but are not limited to auxins such as indole-3 -acetic acid (IAA), 4-chloroindole-3-acetic acid (4-CI-IAA), 2-phenylacetic acid (PAA), indole-3 -butyric acid (IB A), indole-3 -propionic acid (IP A), naphthaleneacetic acid (NAA). Adding a plant hormone to the inoculant composition can provide an initial boost of plant growth and / or establish a faster growth pattern in a field that has, for example, sustained crop damage and is replanted so that the replanted crops need to mature faster than usual.

[0115] In some aspects, the composition can include a fertilizing agent. A fertilizing agent may include an organic fertilizing agent or an inorganic fertilizing agent. Exemplary inorganic fertilizing agents may include, for example, nitrogen, phosphorus, potassium, zinc, and / or magnesium. Exemplary organic fertilizers may include, for example, compost, manure, agricultural w aste, bone meal, humic extract of peat, and the like or other as known by persons skilled in the art.

[0116] In some aspects, the composition can include one or more adhesive agents to promote the composition adhering to a plant once it is applied to a plant or crop field. In some aspects, the adhesive agent can include any biocompatible adhesive agent that can be mixed with the composition and dried onto a seed. As used herein, “biocompatible” refers to an agent that is compatible with the other components of the composition, and not deleterious to the seed or plant to which a formulation that includes the biocompatible component is applied. Suitable adhesive agents include talc, graphite, gum agar, cane sugar, dextrin, commercial potato shellac, starch, or other as known by persons skilled in the art.

[0117] In some aspects, this disclosure describes a plant to which any embodiment of the composition described above is applied. Suitable plants include but are not limited to terrestrial plants, such as, for example, crop plants, trees (deciduous or coniferous), feed plants (e.g., alfalfa), biomass crops, or horticultural plants.

[0118] Exemplary crop plants can include wheat, oats, barley, cotton, sugar beets, flax, peanuts, beans, soybeans, potatoes, tomatoes, peppers, com (especially following sugar beet syndrome), cucumbers, lettuce, cabbage, cauliflower, broccoli, radishes, carrots, celery, jalapeno peppers, okra, Brussels sprouts, watermelon, musk melon, apples, pears, grapes, peaches, oranges, grapefruit, plums, apricots, lemons, avocados, bananas, cassava, sweet potato, pineapple, dates, figs, almonds, walnuts, hazel nuts, pecans, cashews, tobacco, cannabis, oregano, cilantro, sage, saffron, cinnamon, agave, other herbs, or other as known by persons skilled in the art.

[0119] Exemplary biomass crop plants can include, poplar trees, switch grass, duck weed, elephant grass, moringa, or other as known by persons skilled in the art. Exemplary trees to which any embodiment of the composition can be applied include, for example, cottonwood, willow, birch, poplar, or other as known by persons skilled in the art.

[0120] Exemplary horticultural plants can include roses, vines, tubered perennials, petunias, hollyhocks, daffodils, reed sedge, tulips, chry santhemums, or other as known by persons skilled in the art.

[0121] The effect of the composition can be mitigated to some extent if used in combination with certain fungicides such as, for example, propi conazole. If the fungicide is applied at the manufacturer recommended rate, the efficacy of the composition can be reduced. For example, when applied to wheat before jointing, the fungicide kills bacteria in the composition and the effects of the composition can be negated. If the fungicide is applied to wheat after jointing, one can still see an increase in head count, but increases in leaf size, kernel size, protein ratio, etc. are mitigated.

[0122] In some aspects, the composition can be co-fermented. In some aspects, the composition can comprise a mixture of at least one aerobic species and at least one anaerobic species. During co-fermentation. the aerobic microbes typically grow more quickly than anaerobic microbes at first. Eventually, fermentation by the aerobes depletes the fermentation broth of oxygen and produces CO2. Depletion of oxygen in the broth promotes growth of the anaerobic microbes, while accumulation of CO2 in the broth slows growth of the aerobic microbes. In this way. a composition comprising an aerobic species and an anaerobic species can be prepared in a single co-fermentation. In some aspects, the composition can be aerated to facilitate growth of the Pseudomonas spp. The composition may be prepared by incubating the microbes in a suitable culture medium at any suitable temperature. A suitable culture medium can include a carbon source (e.g., cane sugar or sucrose), sufficient white vinegar to adjust the pH of the culture medium to no higher than 7.0 (e.g., no higher than 6.8), iron, and a source of potassium (e.g., potassium nitrate).

[0123] The microbes of the disclosed compositions may be incubated at a minimum temperature of at least 5°C, such as, for example, at least 10°C, at least 15°C at least 20°C, at least 25°C, at least 30°C. or at least 40°C. The microbes may be incubated at a maximum temperature of no more than 50°C, such as, for example, no more than 45°C, no more than 45°C, no more than 40°C, no more than 35°C, or no more than 30°C. The microbes may be incubated at a temperature characterized by any range that includes, as endpoints, any combination of a minimum temperature identified above and any maximum temperature identified above that is greater than the minimum temperature. For example, in some aspects, the microbes may be incubated at a temperature of from 10°C to 40°C.

[0124] The composition may be prepared by incubating the microbes in a suitable culture medium for a sufficient time to allow growth of both aerobic and anaerobic microbes in the fermentation culture. When a mixture of aerobic microbes and anaerobic microbes are cofermented, the microbes may be incubated for a minimum of at least 48 hours, such as, for example, at least 72 hours, at least 96 hours, at least 120 hours, at least 144 hours, or at least 1 8 hours. The microbes may be incubated for a maximum of no more than 240 hours, no more than 216 hours, no more than 192 hours, no more than 168 hours, no more than 144 hours, no more than 120 hours, or no more than 96 hours. The microbes may be incubated for a period characterized by a range having, as endpoints, any combination of a minimum incubation time listed herein and any maximum incubation time listed herein that is greater than the minimum incubation time.

[0125] METHODS

[0126] Disclosed herein are methods of producing plants. In some aspects, the methods can comprise: applying an isolated bacterial species to a plant, plant seed, or to a growth medium in which the plant is located; culturing the plant under conditions suitable for plant growth; and harvesting the plant. In some aspects, the isolated bacterial species can one or more of the microbes listed in Table 1, Table 2, Table 3 or Table 4. In some aspects, the plant produced comprises one or more of the microbes listed in Table 1, Table 2, Table 3 or Table 4. In some aspects, when consumed by a subject, the plant comprising the one or more of the microbes listed in Table 1, Table 2, Table 3 or Table 4 can decrease the amount of methane in the rumen of the subject. In some aspects, when consumed by a subject, the plant comprising the one or more of the microbes listed in Table 1, Table 2, Table 3, or Table 4 can decrease the amount of ammonia in the rumen of the subject. In some aspects, when consumed by a subject, the plant comprising the one or more of the microbes listed in Table 1 , Table 2, Table 3, or Table 4 can increase the amount of hydrogen in the rumen of the subject. In some aspects, the subj ect can have a single stomach. In some aspects, the methods can comprise: applying an isolated bactenal species to a plant, plant seed, or to a growth medium in which the plant is located; culturing the plant under conditions suitable for plant growth; and harvesting the plant. In some aspects, the isolated bacterial species can be a Clostridium spp. In some aspects, the plant produced comprises the Clostridium spp. In some aspects, when consumed by a subject, the plant comprising the Clostridium spp. can decrease the amount of methane in the rumen of the subject. In some aspects, when consumed by a subject, the plant comprising the Clostridium spp. can decrease the amount of ammonia in the rumen of the subject. In some aspects, when consumed by a subject, the plant comprising the Clostridium spp. can increase the amount of hydrogen in the rumen of the subject. In some aspects, the subject can have a single stomach.

[0127] In some aspects, the methods of producing plants can comprise: applying a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 to a plant, plant seed, or to a growth medium in which the plant is located; culturing the plant under conditions suitable for plant growth; and harvesting the plant. In some aspects, the plant produced comprises the Clostridium spp. In some aspects, when consumed by a subject, the plant comprising the Clostridium spp. can decrease the amount of methane in the rumen of the subject. In some aspects, when consumed by a subject, the plant comprising the Clostridium spp. can decrease the amount of ammonia in the rumen of the subject. In some aspects, when consumed by a subject, the plant comprising the Clostridium spp. can increase the amount of hydrogen in the rumen of the subject. In some aspects, the subject can have a single stomach. In some aspects, the composition can comprise one or more of the microbes listed in Table 1, Table 2, Table 3, or Table 4.

[0128] Disclosed herein are method of enhancing plant fiber digestion in a ruminant. In some aspects, the methods can comprise: administering to a ruminant an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1. Table 2 or Table 3; and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to enhance the plant fiber digestion in the ruminant administered the composition, as compared to a ruminant that was not administered the composition. In some aspects, the ruminant can be a bovine, goat, sheep, giraffe, deer, gazelle, or antelope. In some aspects, the bovine can be a bison, brown Swiss, a Ayrshire cattle, shorthorn, Holstein cow, or jersey cow. In some aspects, the bovine can be a lactating bovine animal. In some aspects, the composition can be administered to the ruminant during the grow th phase of the ruminant. In some aspects, the methods can further comprise feeding the ruminant a diet comprising complex carbohydrates. In some aspects, the composition can further comprise a carrier suitable for ruminant administration. In some aspects, the carrier suitable for ruminant administration is selected from the group consisting of peat, turf, talc, lignite, kaolinite, pyrophyllite, zeolite, montmorillonite, alginate, press mud, sawdust, perlite, mica, silicas, quartz powder, calcium bentonite, vermiculite and mixtures thereof. In some aspects, the carrier suitable for ruminant administration can comprise a feed additive. In some aspects, the feed additive is selected from the group consisting of grains, silage, and pellets. In some aspects, the carrier suitable for ruminant administration can comprise a liquid suspension suitable for application to forage material. In some aspects, when the composition, feedstock or foodstuff is administered to the ruminant, milk production is increased in the ruminant. In some aspects, when the composition, feedstock or foodstuff is administered to the ruminant, meat production in the ruminant is increased.

[0129] Disclosed herein are methods of enhancing plant protein digestion in a ruminant. In some aspects, the methods can comprise: administering to a ruminant an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1. Table 2 or Table 3; and optionally, b) a earner suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to enhance the digestibility of plant protein in the ruminant administered the composition, as compared to a ruminant that was not administered the composition. In some aspects, the ruminant can be a bovine, goat, sheep, giraffe, deer, gazelle, or antelope. In some aspects, the bovine can be a bison, brow n Swiss, a Ayrshire cattle, shorthorn, Holstein cow, or jersey cow. In some aspects, the bovine can be a lactating bovine animal. In some aspects, the composition can be administered to the ruminant during the growth phase of the ruminant. In some aspects, the methods can further comprise feeding the ruminant a diet comprising complex carbohydrates. In some aspects, the composition can further comprise a carrier suitable for ruminant administration. In some aspects, the carrier suitable for ruminant administration is selected from the group consisting of peat. turf. talc, lignite, kaolinite, pyrophyllite, zeolite, montmorillonite, alginate, press mud, sawdust, perlite, mica, silicas, quartz powder, calcium bentonite, vermiculite and mixtures thereof. In some aspects, the carrier suitable for ruminant administration can comprise a feed additive. In some aspects, the feed additive is selected from the group consisting of grains, silage, and pellets. In some aspects, the carrier suitable for ruminant administration can comprise a liquid suspension suitable for application to forage material. In some aspects, when the composition, feedstock or foodstuff is administered to the ruminant, milk production is increased in the ruminant. In some aspects, when the composition, feedstock or foodstuff is administered to the ruminant, meat production in the ruminant is increased.

[0130] Disclosed herein are methods of enhancing digestibility of fiber in a ruminant. In some aspects, the methods can comprise: administering to a ruminant an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1. Table 2 or Table 3. and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the feedstock or foodstuff in an amount effective to enhance the digestibility- of fiber in the ruminant administered the feedstock or foodstuff, as compared to a ruminant that was not administered the feedstock or foodstuff. In some aspects, the ruminant can be a bovine, goat, sheep, giraffe, deer, gazelle, or antelope. In some aspects, the bovine can be a bison, brown Swiss, a Ayrshire cattle, shorthorn, Holstein cow, or jersey cow. In some aspects, the bovine can be a lactating bovine animal. In some aspects, the feedstock or foodstuff can be administered to the ruminant during the growth phase of the ruminant. In some aspects, the feedstock or foodstuff can comprise a carrier suitable for ruminant administration. In some aspects, the carrier suitable for ruminant administration is selected from the group consisting of peat. turf, talc, lignite, kaolinite, pyrophyllite, zeolite, montmorillonite, alginate, press mud, sawdust, perlite, mica, silicas, quartz powder, calcium bentonite, vermiculite and mixtures thereof. In some aspects, the carrier suitable for ruminant administration can comprise a feed additive. In some aspects, the feed additive is selected from the group consisting of grains, silage, and pellets. In some aspects, the carrier suitable for ruminant administration can comprise a liquid suspension suitable for application to forage material. In some aspects, when the composition, feedstock or foodstuff is administered to the ruminant, milk production is increased in the ruminant. In some aspects, when the composition, feedstock or foodstuff is administered to the ruminant, meat production in the ruminant is increased.

[0131] Disclosed herein are methods of enhancing digestibility of protein in a ruminant. In some aspects, the methods can comprise: administering to a ruminant an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1. Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the feedstock or foodstuff in an amount effective to enhance the digestibility' of protein in the ruminant administered the feedstock or foodstuff, as compared to a ruminant that was not administered the feedstock or foodstuff. In some aspects, the ruminant can be a bovine, goat, sheep, giraffe, deer, gazelle, or antelope. In some aspects, the bovine can be a bison, brown Swiss, a Ayrshire cattle, shorthorn, Holstein cow, or jersey cow. In some aspects, the bovine can be a lactating bovine animal. In some aspects, the feedstock or foodstuff can be administered to the ruminant during the grow th phase of the ruminant. In some aspects, the feedstock or foodstuff can comprise a carrier suitable for ruminant administration. In some aspects, the carrier suitable for ruminant administration is selected from the group consisting of peat, turf, talc, lignite, kaolinite, pyrophyllite, zeolite, montmorillonite, alginate, press mud, sawdust, perlite, mica, silicas, quartz powder, calcium bentonite, vermiculite and mixtures thereof. In some aspects, the carrier suitable for ruminant administration can comprise a feed additive. In some aspects, the feed additive is selected from the group consisting of grains, silage, and pellets. In some aspects, the carrier suitable for ruminant administration can comprise a liquid suspension suitable for application to forage material. In some aspects, when the composition, feedstock or foodstuff is administered to the ruminant, milk production is increased in the ruminant. In some aspects, when the composition, feedstock or foodstuff is administered to the ruminant, meat production in the ruminant is increased.

[0132] Disclosed herein are methods of increasing milk production in a dairy cow. In some aspects, the methods can comprise: administering to the dairy cow an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the milk production from the daily7cow administered the composition, as compared to a dairy7cow not administered the composition. In some aspects, the methods can further comprise at least one improved trait is selected from the group consisting of: an increase on overall milk production by the dairy cow. an increase of fat in milk, an increase of carbohydrates in milk, an increase of protein in milk, an increase of vitamins in milk, an increase of minerals in milk, an increase in milk volume, an improved efficiency in feed utilization and digestibility7, an increase in polysaccharide and lignin degradation, an increase in fatty acid concentration in the rumen, pH balance in the rumen, a reduction in methane emissions, a reduction in carbon dioxide production, a reduction in manure production, improved dry matter intake, an increase in energy corrected milk (ECM) by weight and / or volume, and an improved efficiency of nitrogen utilization; wherein the increase or reduction is determined by comparing against an animal not having been administered the composition. In some aspects, the amount of the milk produced can be increased at least 5% relative prior to administering the composition, feedstock or foodstuff to the ruminant.

[0133] Disclosed herein are methods of increasing milk production in a dairy cow. In some aspects, the methods can comprise: administering to the dairy cow an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the milk production from the dairy cow administered the composition, as compared to a dairy cow not administered the composition. In some aspects, the methods can further comprise at least one improved trait is selected from the group consisting of: an increase on overall milk production by the dairy cow, an increase of fat in milk, an increase of carbohydrates in milk, an increase of protein in milk, an increase of vitamins in milk, an increase of minerals in milk, an increase in milk volume, an improved efficiency in feed utilization and digestibility, an increase in polysaccharide and lignin degradation, an increase in fatty acid concentration in the rumen, pH balance in the rumen, a reduction in methane emissions, a reduction in carbon dioxide production, a reduction in manure production, improved dry matter intake, an increase in energy corrected milk (ECM) by weight and / or volume, and an improved efficiency of nitrogen utilization; wherein the increase or reduction is determined by comparing against an animal not having been administered the composition. In some aspects, the amount of the milk produced can be increased at least 5% relative prior to administering the composition, feedstock or foodstuff to the ruminant.

[0134] Disclosed herein are methods of increasing meat production in beef cattle. In some aspects, the methods can comprise: administering to the beef cattle an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the meat production from the beef cattle administered the composition, as compared to a beef cattle not administered the composition. In some aspects, the amount of the meat produced can be increased at least 5% relative prior to administering the composition, feedstock or foodstuff is administered to the ruminant. Disclosed herein are methods of increasing meat production in a beef cattle. In some aspects, the methods can comprise: administering to the beef cattle an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the meat production from the beef cattle administered the composition, as compared to a beef cattle not administered the composition. In some aspects, the amount of the meat produced can be increased at least 5% relative prior to administering the composition, feedstock or foodstuff is administered to the ruminant.

[0135] Disclosed herein are methods of enhancing plant fiber digestion in a ruminant. In some aspects, the methods can comprise: administering to the rumen of the ruminant an effective amount of a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; wherein the purified population of bacteria is present in the composition in an amount effective to enhance the fiber digestion in the ruminant administered the composition, as compared to a ruminant not administered the composition. In some aspects, the purified population of bacteria can comprise a combination of microbial strains that can inhibit or reduce methane-producing microbes and promote the growth of non-methane producing microbes. In some aspects, the combination of microbial strains is capable of modulating the oxidation-reduce potential (ORP) inside the rumen. In some aspects, wherein the ORP is modulated inside the rumen of the ruminant. In some aspects, the composition can provide buffering capacity in the rumen of the ruminant and can maintain the pH at above about 6.5 and below about 7.8. In some aspects, the combination of microbial strains can modulate the temperature inside the rumen of ruminant. In some aspects, the methods can further comprise administering a feed additive or a supplement to the ruminant. In some aspects, the feed additive or the supplement can be a prebiotic, a probiotic, an enzy me or direct-fed microbial. In some aspects, the methods can further comprise applying a composition comprising a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 to a feed, a forage, or a concentrate; and administering the feed, the forage or the concentrate to the ruminant.

[0136] Disclosed herein are methods of enhancing plant protein digestion in a ruminant. In some aspects, the methods can comprise: administering to the rumen of the ruminant an effective amount of a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2. (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; wherein the purified population of bacteria is present in the composition in an amount effective to enhance the digestibility of protein in the ruminant administered the composition, as compared to a ruminant not administered the composition. In some aspects, the purified population of bacteria can comprise a combination of microbial strains that can inhibit or reduce methane-producing microbes and promote the growth of non-methane producing microbes. In some aspects, the combination of microbial strains is capable of modulating the oxidation-reduce potential (ORP) inside the rumen. In some aspects, wherein the ORP is modulated inside the rumen of the ruminant. In some aspects, the composition can provide buffering capacity in the rumen of the ruminant and can maintain the pH at above about 6.5 and below about 7.8. In some aspects, the combination of microbial strains can modulate the temperature inside the rumen of ruminant. In some aspects, the methods can further comprise administering a feed additive or a supplement to the ruminant. In some aspects, the feed additive or the supplement can be a prebiotic, a probiotic, an enzyme or direct-fed microbial. In some aspects, the methods can further comprise applying a composition comprising a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 to a feed, a forage, or a concentrate; and administering the feed, the forage or the concentrate to the ruminant.

[0137] Disclosed herein methods of modulating the microbiome of a ruminant. In some aspects, the methods can comprise: administering to the rumen of the ruminant an effective amount of a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3: wherein the purified population of bacteria is present in the composition in an amount effective to impart at least one improved trait upon the ruminant. In some aspects, the at least one improved trait is selected from the group consisting of: an increase on overall milk production by the ruminant, an increase of fat in milk, an increase of carbohydrates in milk, an increase of protein in milk, an increase of vitamins in milk, an increase of minerals in milk, an increase in milk volume, an improved efficiency in feed utilization and digestibility, an increase in polysaccharide and lignin degradation, an increase in fatty acid concentration in the rumen, pH balance in the rumen, a reduction in methane emissions, a reduction in carbon dioxide production, a reduction in manure production, improved dry matter intake, an increase in energy corrected milk (ECM) by weight and / or volume, and an improved efficiency of nitrogen utilization; wherein the increase or reduction is determined by comparing against an animal not having been administered the composition. In some aspects, the purified population of bacteria can comprise a combination of microbial strains that can inhibit or reduce methane-producing microbes and promote the growth of non-methane producing microbes. In some aspects, the combination of microbial strains is capable of modulating the oxidation-reduce potential (ORP) inside the rumen. In some aspects, wherein the ORP is modulated inside the rumen of the ruminant. In some aspects, the composition can provide buffering capacity in the rumen of the ruminant and can maintain the pH at above about 6.5 and below about 7.8. In some aspects, the combination of microbial strains can modulate the temperature inside the rumen of ruminant. In some aspects, the methods can further comprise administering a feed additive or a supplement to the ruminant. In some aspects, the feed additive or the supplement can be a prebiotic, a probiotic, an enzy me or direct-fed microbial. In some aspects, the methods can further comprise applying a composition comprising a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 to a feed, a forage, or a concentrate; and administering the feed, the forage or the concentrate to the ruminant.

[0138] In any of the methods disclosed herein, the composition, feedstock or foodstuff can be a plant or derived from a plant, wherein a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 is applied to a plant, plant seed, or to a growth medium in which the plant is located; culturing the plant under conditions suitable for plant growth; and harvesting the plant, and subsequently processing the plant into the composition feedstock or foodstuff.

[0139] In any of the methods disclosed herein, the composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 can be in a dried, freeze-dried, in powder, lyophilized, or in a liquid form.

[0140] Disclosed herein are methods of increasing the digestibility of a plant. In some aspects, the methods can comprise: applying a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria w ith a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 to a plant, plant seed, or to a growth medium in which the plant is located; culturing the plant under conditions suitable for plant growth; and harvesting the plant, wherein the digestibility of the plant is increased. In some aspects, the purified population of bacteria can comprise a combination of microbial strains that can inhibit or reduce methane-producing microbes and promote the growth of non-methane producing microbes. In some aspects, the methods can further comprise feeding the plant to a ruminant.

[0141] In some aspects, the composition described herein can be administered through the ingestion of a feedstock or foodstuff comprising the disclosed compositions. In some aspects, the dose of the composition can be administered such that there exists 102to 1012, 103to 1012, 104to 1012, 105to 1012, 106to 1012, 107to 1012, 108to 1012, 109to 1012, 1010to 1012, 10nto 1012, 102to 1011, 103to 1011, 104to 1011, 105to 1011, 106to 1011, 107to 1011, 108to 1011, 109to 1011, 1010to 1011, 102to IO10, 103to IO10, 104to IO10, 105to IO10, 106to IO10. 107to IO10, 108to IO10. 109to IO10. 102to 109, 103to 109, 104to 109, 105to 109, 106to 109. 107to 109, 108to 109, 102to 108, 102to 108, 104to 108, 105to 108, 106to 108, 107to 108, 102to 107, 103to 105, 104to IO5, 102to 104, 103to 104, 102to 103, 1012, IO11, IO10, 109, 108, 107, 106, IO5, 104, IO3, or 102total microbial cells per gram or milliliter of the composition.

[0142] In some aspects, the composition can be administered 1 or more times per day. In some aspects, the composition is administered with food each time the animal is fed. In some aspects, the composition can be administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to

[0143] 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to

[0144] 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5. 5 to 10, 5 to 9, 5 to

[0145] 8, 5 to 7, 5 to 6, 6 to 10. 6 to 9, 6 to 8. 6 to 7, 7 to 10, 7 to 9, 7 to 8. 8 to 10. 8 to 9, 9 to 10. 1,

[0146] 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per day.

[0147] In some aspects, the composition can be administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4. 4 to 10, 4 to 9, 4 to 8, 4 to 7. 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per week.

[0148] Inn some aspects, the composition can be administered 1 to 10, 1 to 9. 1 to 8, 1 to 7, 1 to 6, 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8. 2 to 7, 2 to 6, 2 to 5, 2 to 4, 2 to 3, 3 to 10, 3 to 9. 3 to 8, 3 to 7, 3 to 6. 3 to 5, 3 to 4. 4 to 10, 4 to 9. 4 to 8, 4 to 7. 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per month.

[0149] In some aspects, the composition can be administered 1 to 10, 1 to 9, 1 to 8, 1 to 7, 1 to 6. 1 to 5, 1 to 4, 1 to 3, 1 to 2, 2 to 10, 2 to 9, 2 to 8. 2 to 7, 2 to 6, 2 to 5. 2 to 4, 2 to 3, 3 to 10, 3 to 9, 3 to 8, 3 to 7, 3 to 6, 3 to 5, 3 to 4, 4 to 10, 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 10, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 10, 6 to 9, 6 to 8, 6 to 7, 7 to 10, 7 to 9, 7 to 8, 8 to 10, 8 to 9, 9 to 10. 1, 2, 3. 4, 5, 6, 7, 8, 9, or 10 times per year.

[0150] In some aspects, the composition can be administered to animals throughout the entire time they are on the feedlot. In some aspects, the composition can be administered to animals only during a portion of time while they are on the feedlot. In some aspects, the composition can be administered only during the grower phase. In some aspects, the composition can be administered only during the time when animals are in the receiving pen. In some aspects, the composition can administered only when the animals are receiving vaccinations and / or treatments. In some aspects, the composition can administered only when the animals are on a step up diet or when being adapted to a high grain diet. In some aspects, the composition can be administered only when the animals are on a finisher diet or a high grain diet.

[0151] In some aspects, the microbial composition can be administered during the grower phase, when animals are in the receiving pen, when animals are receiving vaccinations and / or treatments, when animals are being adapted to a high grain diet or are on a step up diet, and / or when the animals are on a finisher diet or a high grain diet.

[0152] In some aspects, an animal entering the feed lot receives at least one composition prior to entering the feed lot. In some aspects, an animal on the feed lot receives a composition that is different from the first at least one composition. In further aspects, an animal on the feed lot receives a composition that is different from the first and second at least one microbial composition.

[0153] In some aspects, the type of diet fed to the animal corresponds with the type of composition administered to the animal. In some aspects, a grazing or grass / hay-fed animal will receive a first composition. In further aspects, the same animal fed a different diet will receive a second composition, wherein the first composition can be different from the second composition. In some aspects, the same animal fed yet a different diet will receive a third composition, wherein the first composition can be different from the second and third compositions. In some aspects, the same animal fed yet a different diet will receive a fourth composition, wherein the first composition can be different from the second, third, and fourth compositions. In some aspects, the same animal fed yet a different diet will receive a fifth composition, wherein the first composition is different from the second, third, fourth, and fifth compositions.

[0154] In some aspects, the feed can be uniformly coated with one or more layers of the microbes and / or microbial compositions disclosed herein, using conventional methods of mixing, spraying, or a combination thereof through the use of treatment application equipment that is specifically designed and manufactured to accurately, safely, and efficiently apply coatings. Such equipment uses various types of coating technology such as rotary coaters, drum coaters, fluidized bed techniques, spouted beds, rotary mists, or a combination thereof. Liquid treatments such as those of the present disclosure can be applied via either a spinning “atomizer” disk or a spray nozzle, which evenly distributes the microbial composition onto the feed as it moves though the spray pattern. In some aspects, the feed can then be mixed or tumbled for an additional period of time to achieve additional treatment distribution and drying.

[0155] In some aspects, the feed coats of the present disclosure can be up to 10 pm, 20 pm, 30 pm, 40 pm, 50 pm, 60 pm, 70 pm, 80 pm, 90 pm, 100 pm, 110 pm, 120 pm, 130 pm, 140 pm, 150 pm, 160 pm, 170 pm, 180 pm, 190 pm, 200 pm. 210 pm, 220 pm. 230 pm, 240 pm,

[0156] 250 pm, 260 pm, 270 pm, 280 pm, 290 pm, 300 pm, 310 pm, 320 pm, 330 pm, 340 pm, 350 pm, 360 pm, 370 pm, 380 pm, 390 pm, 400 pm, 410 pm, 420 pm, 430 pm, 440 pm, 450 pm,

[0157] 460 pm, 470 pm, 480 pm, 490 pm, 500 pm, 510 pm, 520 pm, 530 pm, 540 pm, 550 pm, 560 pm, 570 pm, 580 pm, 590 pm, 600 pm, 610 pm, 620 pm, 630 pm, 640 pm. 650 pm, 660 pm,

[0158] 670 pm. 680 pm, 690 pm. 700 pm, 710 pm. 720 pm, 730 pm, 740 pm. 750 pm, 760 pm. 770 pm, 780 pm, 790 pm, 800 pm, 810 pm, 820 pm, 830 pm, 840 pm, 850 pm, 860 pm, 870 pm,

[0159] 880 pm, 890 pm, 900 pm, 910 pm, 920 pm, 930 pm, 940 pm, 950 pm, 960 pm, 970 pm, 980 pm, 990 pm, 1000 pm, 1010 pm, 1020 pm, 1030 pm, 1040 pm, 1050 pm, 1060 pm, 1070 pm, 1080 pm. 1090 pm, 1100 pm, 1110 pm. 1120 pm, 1130 pm, 1140 pm. 1150 pm, 1160 pm, 1170 pm, 1180 pm, 1190 pm, 1200 pm, 1210 pm, 1220 pm, 1230 pm, 1240 pm, 1250 pm, 1260 pm, 1270 pm, 1280 pm, 1290 pm, 1300 pm, 1310 pm, 1320 pm, 1330 pm, 1340 pm, 1350 pm, 1360 pm, 1370 pm, 1380 pm, 1390 pm, 1400 pm, 1410 pm, 1420 pm, 1430 pm, 1440 pm. 1450 pm, 1460 pm, 1470 pm. 1480 pm, 1490 pm, 1500 pm. 1510 pm, 1520 pm, 1530 pm, 1540 pm, 1550 pm, 1560 pm, 1570 pm, 1580 pm, 1590 pm, 1600 pm, 1610 pm, 1620 pm, 1630 pm, 1640 pm, 1650 pm, 1660 pm, 1670 pm, 1680 pm, 1690 pm, 1700 pm, 1710 pm, 1720 pm, 1730 pm, 1740 pm, 1750 pm, 1760 pm, 1770 pm, 1780 pm, 1790 pm, 1800 pm, 1810 pm, 1820 pm, 1830 pm, 1840 pm, 1850 pm, 1860 pm, 1870 pm, 1880 pm, 1890 pm. 1900 pm, 1910 pm, 1920 pm. 1930 pm, 1940 pm, 1950 pm. 1960 pm, 1970 pm, 1980 pm, 1990 pm, 2000 pm, 2010 pm, 2020 pm, 2030 pm, 2040 pm, 2050 pm, 2060 pm, 2070 pm, 2080 pm, 2090 pm, 2100 pm, 2110 pm, 2120 pm, 2130 pm, 2140 pm, 2150 pm, 2160 pm, 2170 pm, 2180 pm, 2190 pm, 2200 pm, 2210 pm, 2220 pm, 2230 pm, 2240 pm, 2250 pm. 2260 pm, 2270 pm, 2280 pm. 2290 pm, 2300 pm, 2310 pm. 2320 pm, 2330 pm, 2340 pm, 2350 pm, 2360 pm, 2370 pm, 2380 pm, 2390 pm, 2400 pm, 2410 pm, 2420 pm, 2430 pm, 2440 pm, 2450 pm, 2460 pm, 2470 pm, 2480 pm, 2490 pm, 2500 pm, 2510 pm, 2520 pm, 2530 pm, 2540 pm, 2550 pm, 2560 pm, 2570 pin, 2580 pm, 2590 pm, 2600 pm, 2610 pm, 2620 pm, 2630 pm, 2640 pm, 2650 pm, 2660 pm, 2670 pm, 2680 pm, 2690 pm, 2700 pm, 2710 pm, 2720 pm, 2730 pm, 2740 pm, 2750 pm, 2760 pm, 2770 pm, 2780 pm, 2790 pm, 2800 pm, 2810 pm, 2820 pm, 2830 pm, 2840 pm, 2850 pm, 2860 pm, 2870 pm, 2880 pm, 2890 pm, 2900 pm, 2910 pm, 2920 pm, 2930 pm, 2940 pm, 2950 pm, 2960 pm, 2970 pm. 2980 pm. 2990 pm, or 3000 pm thick.

[0160] In some aspects, the microbial cells can be coated freely onto any number of compositions or they can be formulated in a liquid or solid composition before being coated onto a composition. For example, a solid composition comprising the microorganisms can be prepared by mixing a solid carrier with a suspension of the spores until the solid carriers are impregnated with the spore or cell suspension. This mixture can then be dried to obtain the desired particles.

[0161] In some other aspects, it is contemplated that the solid or liquid compositions of the present disclosure further contain functional agents e.g.. activated carbon, minerals, vitamins, and other agents capable of improving the quality of the products or a combination thereof.

[0162] Methods of coating and compositions in use of said methods that are known in the art can be particularly useful when they are modified by the addition of one of the embodiments of the present disclosure. Such coating methods and apparatus for their application are disclosed in. for example: U.S. Pat. Nos. 8.097,245 and 7,998.502; and PCT Pat. App. Pub. Nos. WO 2008 / 076975, WO 2010 / 138522, WO 2011 / 094469, WO 2010 / 111347, and WO 2010 / 111565 each of which is incorporated by reference herein.

[0163] In some aspects, the microbes or microbial compositions of the present disclosure exhibit a synergistic effect, on one or more of the traits described herein, in the presence of one or more of the microbes or microbial compositions coming into contact with one another.

[0164] The microbial inoculant may be applied to seeds, plants, or a field of plants by any suitable method. As described above, the composition may be formulated with a biocompatible adhesive agent that allows the composition to be applied to, and adhere to, a seed. Such a formulation can be a folair liquid, seed coating, seed coating hydrogel, etc. The formulation can be mixed into a seeder at planting or can be mixed prior to planting. Alternatively, the composition may be formulated into with one or more biocompatible agents that can be applied to seeds and dried. Suitable agents include but are not limited to, for example, dried tapioca, powdered milk, or gum arabic. Other application methods can involve applying the composition to one or more tissues of plant, such as, for example, the root, the stem, one or more leaves, or a seedproducing pod. In such cases, the composition may be applied by any suitable method including but not limited to, for example, spraying or ampule delivery. The formulation may be sprayed using, for example, a portable spraying unit, hand-held spraying device, irrigation equipment, or aerial spraying. Ampule delivery may be performed manually or using an automated system.

[0165] Still other application methods can involve applying the composition to the soil or seed bed into which seeds will be planted. In some aspects, the composition may be applied by spraying or ampule delivery as described immediately above. Alternatively, the composition may be applied by drip. In some aspects, the composition can be applied, whether by spray or by drip, while the soil is being seeded.

[0166] Still other application methods can include application as a foliar spray, through an irrigation pivot, and as a seed coat. In some aspects, a seed coat media that can hold water can be used to allow the bacteria to live without drying out. In some aspects, the bacteria can include primarily non-sporulating bacteria that may die when desiccated.

[0167] In some aspects, a formulation of the composition can comprise a predetermined moisture content. In some aspects, the minimum moisture content can be at least 5% such as, for example, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 15%, at least 20%. at least 25%. at least 30%. or at least 50%.

[0168] In some aspects, a formulation of the composition can comprise a sugar (e.g., cane sugar or sucrose) and vinegar (e.g., white vinegar). The sugar can provide a metabolic carbon source. The vinegar can provide an acidic pH and / or an alternative carbon source. As an alternative to. or in addition to, the use of vinegar to regulate pH, the composition can comprise Lactobacillus plantarum, as described herein, to help maintain an acidic pH once the composition is applied to the plant.

[0169] In some aspects, a formulation of the composition can comprise lactic acid media to provide an acidic pH.

[0170] In some aspects, a formulation of the composition can comprise glycerol as a dispersion medium. EXAMPLES

[0171] Example 1: Rumen fluid from cows consuming corn silage treated with biological seed treatment improves rumen metabolism measures and reduces methane emissions in vitro

[0172] It was determined whether com grown for silage and treated with a biological seed treatment, and fed to dairy cows, affected rumen metabolism and greenhouse gas emission measures in vitro.

[0173] Long term dairy and beef producers increasingly need to adopt both economic and environmentally sustainable practices or technologies. A composition comprising a first bacterial strain comprising Clostridium spp. with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Clostridium spp. listed in Table 1 or Table 2 and a second bacterial strain comprising aquatic Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 was applied to a com seed and the seed-treated com silage was fed to cannulated cows and the rumen fluid from these donor cows was compared to rumen fluid inoculum from cows consuming untreated com silage. The inoculum from cows consuming the composition treated com silage significantly increased in vitro total mixed ration sample digestion, microbial protein production and diet digestion efficiency while lessening methane emissions and intensity.

[0174] Whole-plant com silage is a principal feed in dairy and beef cattle diets throughout the world. Based upon recent economic evaluation, com silage value can annually eclipse $350,000 for even' 500 dairy cows. Optimizing the com silage economic impact and dairyherd performance are focal points with growers, dairy farmers, agronomists and nutritionists. Microbial based biological seed treatments are a technology which can affect com silage agronomic measures such as seedling vigor and emergence, dry matter yield, nutritional quality and microbial characteristics following ensiling. Com silage nutritional value and microbial characteristics following ensiling are known to affect daily' cow performance in numerous ways.

[0175] The nutritional value associated with com silage is primarily attributed to digestible fiber and starch and energy contributions from these nutrients. Com silage microbial characteristics are attributed to soil, field, fermentation and feed-out microbial interactions. The microbial characteristics associated with com silage are known to interact with rumen bacteria, protozoa and fungi and subsequently affect dairy cattle performance. A composition comprising a first bacterial strain comprising Clostridium spp. with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Clostridium spp. listed in Table 1 or Table 2 and a second bacterial strain comprising aquatic Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 was applied to a com seed and the seed- treated com silage was harvested following seed treatment to affect agronomic performance, nutritional quality and greenhouse gas emissions in ruminants. Com silage treated with the composition is thought to differ in microbial attributes relative to untreated silage, thus positively affecting dairy cow rumen metabolism and performance. Hence, the objective of this study was to determine if rumen fluid inoculum collected from cows consuming the composition treated com silage improved in vitro mmen digestion and gas production measures relative to that with cows consuming untreated com silage.

[0176] Methodology’. Ten non-lactating cannulated Holstein dairy cows were enrolled in this study. Each dairy cow was used as a rumen fluid inoculum donor for in vitro mmen metabolism and greenhouse gas measures. The 10 cows were separated into two different groups, with 5 cows in each group housed in a pen. The two groups were housed in adjacent pens and fed a mixed ration, consisting of 4.5 kg com silage (Treated or Control), 2.3 kg grass silage and 2.3 kg pelleted supplement feed per cow'. The rations w ere blended within a Ritchie mixer and fed to the cows once daily in a concrete feed bunk. The diets were formulated to meet or exceed the cows' energy protein, energy, vitamin and mineral requirements for nonlactating cows.

[0177] The treated silage was collected from a commercial dairy. This silage was grown following seed treatment, harvested and ensiled by a commercial dairy. During collection at the commercial dairy’, the silage was removed from the silage pile with a loading tractor and packed into 2,000 pound tote bags, anaerobically sealed and placed within a refrigerated semitractor trailer for transported. In total, approximately’ 20 tote bags were packed, sealed and trucked to for this research project. The control (CTL) com silage was collected on an as needed basis from a commercial dairy.

[0178] In summary', com silage was introduced into treated and untreated control (CTL) pen diets. After the silage was introduced into the treatment diets for each of the two pens, four in vitro rumen measure observation periods were conducted. The in vitro mmen gas production technique has been extensively used to quantify rumen metabolism and digestion efficiency gains associated with various nutrition technologies. In vitro gas production was measured. During this study, mmen metabolism was assessed and greenhouse gas observation periods corresponded to treated and CTL silages fed to cannulated cows for 7 days (Period 1), 14 days (Period 2), 21 days (Period 3), or 28 days (Period 4).

[0179] On the collection day for each period, rumen fluid inoculum was collected from each of the five cows on the treated and CTL diets, processed and immediately used to inoculate two in vitro TMR samples (A or B), in duplicate. The batch culture system involves incubating 400 mg dried and 6 mm ground TMR samples, for 24 hours. After 24 hours, rumen in vitro metabolism and greenhouse gas measures were summarized and reported for each period. The in vitro gas, pH and greenhouse gas measurements were recorded. The microbial protein yield and organic matter digestion were measured following the 24h digestion.

[0180] In sum, 40 sets of data and observations were collected at each period, corresponding to: 2 Treatment silages fed; 5 donor cows per treatment; 2 in vitro TMR samples digested per inoculum source (cow); and 2 sets of data and observations per in vitro TMR sample digestion.

[0181] Rumen metabolism measures following 24h incubations included: apparent organic matter digestion (OMD, %); total gas production, ml; microbial protein production (MBP, mg / g organic matter); partitioning factor (PF; truly degraded organic matter / total gas production; an efficiency measure as suggested by Blummel et al., 1997); and in vitro rumen pH.

[0182] Greenhouse gas measures collected following 24h incubations included: methane emissions, ml; carbon dioxide emissions, ml; hydrogen concentration, ppm; ammonia-N concentration, ppm; and methane emission intensity as a function of methane emissions per mg OM digested, ml / g organic matter.

[0183] Statistical analysis. The in vitro rumen metabolism and greenhouse gas measures were modeled with a multiple linear regression approach. The final model was fit using backward stepwise elimination model selection, with significant effects declared at P < 0.05 and trends at P < 0.10. The fixed effects of inoculum source (treated or CTL silage fed cows), in vitro TMR sample (A or B), sampling period and two way interactions were evaluated.

[0184] The impact associated with rumen fluid inoculum corresponding to cows fed either treated or untreated com silages is grouped into either rumen metabolism or greenhouse gas measures within this section. The rumen metabolism measures, including organic matter digestion, microbial biomass production, total in vitro gas production, partitioning factor and other measures are reported. The greenhouse gas measurements include methane, carbon dioxide, ammonia-N, hydrogen and methane intensity measures. In both groups, notable and economically or environmentally impactful nutrition and greenhouse gas observations are found. Rumen metabolism. Organic matter digestion. Increased organic matter digestion is thought to correspond to increased animal performance by way of increased nutrient digestion and more efficient diet utilization. Apparent organic matter digestion corrects for microbial protein produced during digestion, and this measure was significantly increased when using rumen fluid inoculum from cows consuming treated silage (Table 4). The 5-unit increase in organic matter digestion corresponds to approximately 10% increase in diet digestion within the in vitro rumen system. The two TMR samples digested were also significantly different, demonstrating that two different diets were evaluated within this project (Table 5). The organic matter digestion differed by period, which is to be expected within in vitro batch culture systems.

[0185] 'fable 4. Least square means for 24 hour in vitro rumen digestion and gas production observations, following an incubation conducted with rumen fluid from donor cows consuming either treated com silage or a CTL com silage in a total mixed ration Table 5. Least square means for in vitro rumen digestion and gas production observations for two total mixed ration samples following a 24 h in vitro rumen digestion.

[0186] A significant treatment and TMR interaction was noted, with TMR sample. A responding to treated inoculum to a greater extent than TMR B (Table 6). This observation is consistent with commercial dairy experience where different diets and farms respond differently to nutrition technologies or ingredients. A treatment by period interaction was also observed, with the most notable response and increased organic matter digestion observed for period 1 and 2 with treated inoculum. Table 6. Least square means for 24 hour in vitro rumen digestion and gas production observations corresponding to rumen fluid from donor cows consuming either treated com silage or a control (CTL) com silage in a total mixed ration, and applied to two different total mixed ration samples.

[0187] Total gas production. Gas produced during digestion can be interpreted in different ways, understanding that gas production represents carbon, nitrogen or hydrogen that are not incorporated into microbial grow th. In general, the in vitro gas production observations should be interpreted relative to the organic matter digested. The partitioning factor discussed herein expands upon this concept, and better relates to potential efficiency gains associated with treatment.

[0188] The total gas production did not differ between treated or CTL (Table 4). The gas production did differ for the TMR samples, with greater total gas yield for TMR B (Table 5). A treatment and TMR interaction was observed for total gas production, with treated decreasing gas production for TMR A but numerically increasing gas production for TMR B (Table 6). There was also a treatment and period interaction observed, with treated gas production equivalent to or lower than CTL for all periods except Period 2.

[0189] Microbial biomass production (aMBP). Dairy and beef cattle performance and production is attributed to both diet nutrient absorption and microbial biomass production. Roughly 50% of the metabolizable protein needs for milk production are attributed to microbial growth and biomass. Hence, microbial biomass production is an important rumen nutrition measure. In this study, the microbial biomass yield associated with treated inoculum was significantly increased relative to CTL (Table 4). This difference agrees with the increased organic matter digestion attributed to the treatment, suggesting that increased organic matter digestion corresponds to increased microbial productivity.

[0190] The two TMR samples also different in microbial protein yield, with TMR B being greater in protein yield relative to TMR A (Table 5). This observation is supported by the organic matter digestion differences noted for TMR A and B, with greater organic matter digestion for TMR B also yielding greater microbial protein. There were differences in microbial protein yield for the four periods (Table 7) and a significant treatment and period interaction was observed. The treatment inoculum increased aMBP for the periods tested except period 2, leading to the significant interaction.

[0191] Table 7. Least square means for 24 hour in vitro rumen digestion and gas production observations corresponding to rumen fluid donor cow-s consuming treatment com silages for 7 (Period 1), 14 (Period 2), 21 (Period 3) and 28 days (Period 4).

[0192] Recognizing that microbial protein is related to milk production, an equation to predict milk yield has been used to assess potential performance impact associated with different treatments within the in vitro batch culture system. The following equation was applied to the microbial biomass yield observations to project milk production potential in pounds per cow: [(aMBP yield mg / g substrate x 0.41) x 1.35] x 25 kg dry matter intake / 70 x 2.204. The milk production potential predicted from in vitro microbial protein yield through this equation was 88.9 and 85. 1 pounds per cow. for treated and CTL. respectively.

[0193] Partitioning factor. Blummel et al. (1997) proposed a partitioning factor as an indicator of diet digestion efficiency. This observation is calculated as the truly degraded organic matter divided by total gas production. In theory', a numerically increased partitioning factor suggests an increase in diet digestion with relatively less in gaseous losses. The partitioning factor was significantly increased with treated inoculum at 3.64 relative to 3.29 for CTL, respectively (Table 4). There were no differences between the TMR samples for partitioning factor (Table 5); however the efficiency indicator did differ between periods (Table 6).

[0194] There was a significant interaction observed between treatment and TMR sample (Table 6), with TMR A responding to a much greater extent to treatment relative to TMR B. This observation agrees with the interaction observed with these parameters for organic matter digestion, and shows that some diets respond differently to treatment. A treatment by period interaction was also evident, with periods 1 and 2 presenting the greatest difference in partitioning factor between treated and CTL.

[0195] Greenhouse gas emissions. Methane gas yield and intensity). Enteric methane emissions by dairy' and beef cattle have become an increasingly important topic; however assessing gaseous emissions is time consuming and capital intensive. The in vitro rumen digestion and greenhouse gas measurement system can provide an efficient approach to determine and project environmental impact associated with agronomic inputs such as biological seed treatments or nutrition technologies.

[0196] Within the system, across 4 periods, the methane emissions were significantly decreased with inoculum from cows consuming treated com silage (Table 4). The 5.88 ml CH4 emissions after 24 h was roughly 11% less than the 6.62 ml emissions with CTL treatment. There were no differences in methane yield for the two TMR samples digested or among the four periods. There were also no interactions evident between treatment and TMR or period. In general, inoculum from donor cows consuming treated com silage was associated with decreased methane emissions in vitro.

[0197] The dairy and beef industry also interpret methane emissions per unit animal protein produced. For example, methane intensity per hundredweight milk produced is one metric to assess environmental impact. Recognizing that organic matter digestion is related to milk production, the methane emission intensity was calculated as: total methane emissions (ml) divided by organic matter digested (g). This methane emission intensity metric was found to be significantly improved with treatment inoculum, with 25.4 vs 31.0 ml methane produced per g TMR sample digested for treated and CTL, respectively.

[0198] Interpreting the data through this CH4 intensity' metric, the treatment is associated with a roughly 18% reduction in CH4 emissions relative to feed digested relative to CTL treatment.

[0199] Other gasses. Insignificant or minor significant differences in carbon dioxide, hydrogen and ammonia nitrogen were evident within the data shown in Tables 4, 5, 6, and 7. Aside from the methane emission observations, these additional gaseous measures and observations were not deemed substantial.

[0200] In sum, throughout this feeding and in vitro rumen metabolism study, inoculum harvested from non-lactating cows consuming treated com silage affected in vitro rumen metabolism and greenhouse gas emission measures. While numerous interactions were observed, the treatment generally equated to increased diet digestion, microbial protein yield, greater efficiency as indicated by the partitioning factor, and less in methane emissions and intensity. The observations demonstrate that treated com silage can have a synergistic effect within a cow’s rumen relative to an untreated com silage.

[0201] References

[0202] Blummel, M., H.P.S. Makkar, and K. Becker. 1997. In vitro gas production: A technique revisited. J. Anim. Physiol, and Anim. Nutr. 77:24-34. Example 2: Rumen fluid microbiota analysis

[0203] FIG. 1 shows the microbial analysis results. FIG. 2 shows the principal component analysis.

[0204] The results show that rumen methanogens and bacteria appeared to be reduced at day 1 vs day 14, while ciliate protozoa counts increased. The methanogen reduction can be considered desired. On the other hand, the reduction of beneficial fiber-degrading bacteria is not desired.

[0205] Increase of ciliate protozoa and reduction of methanogens rumen fluid can generally be considered beneficial. Ciliate protozoa help in fiber digestion, breakdown of complex carbohydrates, and increase the overall efficiency of feed utilization. By increasing ciliate protozoa, the rumen's ability to digest and efficiently utilize feed can be improved.

[0206] A possible explanation for the simultaneous increase in protozoa and decrease in methanogens and bacteria could be an indirect effect. The test product may contain certain components that inhibit the methanogen and bacterial growth by altering the rumen environment.

[0207] Consequently, an increased protozoa population might result in a higher removal rate of excess hydrogen, which would have otherwise been utilized by methanogens to increase methane production and by propionate-producing bacteria. This can consequently reduce the availability of hydrogen for methanogens and propionigenic bacteria, hampering their growth and activity.

[0208] For these studies, the rumen of a ruminant was administration a biological treatment. The biological treatment refers to a composition comprising a first bacterial strain comprising Clostridium spp. with a 16S nucleic acid sequence that is at least about 97% identical to anyone of the Clostridium spp. listed in Table 1 or Table 2 and a second bacterial strain comprising aquatic Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2 that is fermented.

Claims

CLAIMSWHAT IS CLAIMED IS:

1. A method of enhancing plant fiber digestion in a ruminant, the method comprising: administering to a ruminant an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to enhance the plant fiber digestion in the ruminant administered the composition, as compared to a ruminant that was not administered the composition.

2. A method of enhancing plant protein digestion in a ruminant, the method comprising: administering to a ruminant an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to enhance the digestibility of plant protein in the ruminant administered the composition, as compared to a ruminant that was not administered the composition.

3. A method of enhancing digestibility of fiber in a ruminant, the method comprising: administering to a ruminant an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 orTable 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the feedstock or foodstuff in an amount effective to enhance the digestibility of fiber in the ruminant administered the feedstock or foodstuff, as compared to a ruminant that was not administered the feedstock or foodstuff.

4. A method of enhancing digestibility of protein in a ruminant, the method comprising: administering to a ruminant an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the feedstock or foodstuff in an amount effective to enhance the digestibility of protein in the ruminant administered the feedstock or foodstuff, as compared to a ruminant that was not administered the feedstock or foodstuff.

5. The method of any of the preceding claims, wherein the ruminant is a bovine goat, sheep, giraffe, deer, gazelle, or antelope.

6. The method of claims 1 or 2, wherein the composition is administered to the ruminant during the growth phase of the ruminant.

7. The method of claims 3 or 4, wherein the feedstock or foodstuff is administered to the ruminant during the growth phase of the ruminant.

8. The method of claim 5, wherein the bovine animal is a bison, brown Swiss, a Ayrshire cattle, shorthorn, Holstein cow, or jersey cow.

9. The method of claim 5. wherein the bovine is a lactating bovine animal.

10. The method of claim 7, further comprising feeding the ruminant a diet comprising complex carbohydrates.

11. The method of claims 1 or 2, wherein the composition further comprises a carrier suitable for ruminant administration.

12. The method of claims 3 or 4, wherein the feedstock or foodstuff comprises a carrier suitable for ruminant administration.

13. The method of claims 11 or 12. wherein the carrier suitable for ruminant administration is selected from the group consisting of peat, turf, talc, lignite, kaolinite, pyrophyllite, zeolite, montmorillonite, alginate, press mud, sawdust, perlite, mica, silicas, quartz powder, calcium bentonite, vermiculite and mixtures thereof.

14. The method of claim 13, wherein the carrier suitable for ruminant administration comprises a feed additive.

15. The method of claim 14. wherein the feed additive is selected from the group consisting of grains, silage, and pellets.

16. The method of claims 11 or 12, wherein the carrier suitable for ruminant administration comprises a liquid suspension suitable for application to forage material.

17. The method of any of the preceding claims, wherein when the composition, feedstock or foodstuff is administered to the ruminant, milk production is increased in the ruminant.

18. The method of any of the preceding claims, wherein when the composition, feedstock or foodstuff is administered to the ruminant, meat production in the ruminant is increased.

19. A method of increasing milk production in a dairy cow, the method comprising: administering to the dairy cow an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or(iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the milk production from the dairy cow administered the composition, as compared to a dairy7cow not administered the composition.

20. A method of increasing milk production in a dairy cow, the method comprising: administering to the dairy cow an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2. (ii) a Pseudomonas spp. bacteria with a 1 S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the milk production from the dairy cow administered the composition, as compared to a dairy cow not administered the composition.

21. The method of claims 19 or 20, further comprising at least one improved trait is selected from the group consisting of: an increase on overall milk production by the dairy cow, an increase of fat in milk, an increase of carbohydrates in milk, an increase of protein in milk, an increase of vitamins in milk, an increase of minerals in milk, an increase in milk volume, an improved efficiency in feed utilization and digestibility, an increase in polysaccharide and lignin degradation, an increase in fatty acid concentration in the rumen, pH balance in the rumen, a reduction in methane emissions, a reduction in carbon dioxide production, a reduction in manure production, improved dry matter intake, an increase in energy corrected milk (ECM) by weight and / or volume, and an improved efficiency of nitrogen utilization; wherein the increase or reduction is determined by comparing against an animal not having been administered the composition.

22. The method of claims 20 or 21. wherein the amount of the milk produced is increased at least 5% relative prior to administering the composition, feedstock or foodstuff to the ruminant.

23. A method of increasing meat production in beef cattle, the method comprising: administering to the beef cattle an effective amount of a composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1 , Table 2 or Table 3: and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the meat production from the beef cattle administered the composition, as compared to a beef cattle not administered the composition.

24. A method of increasing meat production in a beef cattle, the method comprising: administering to the beef cattle an effective amount of a feedstock or foodstuff comprising a population of bacteria selected from one or more bacteria comprising a) a purified population of bacteria selected from: (i) a Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3, and optionally, b) a carrier suitable for ruminant administration; wherein the purified population of bacteria of a) is present in the composition in an amount effective to increase the meat production from the beef cattle administered the composition, as compared to a beef cattle not administered the composition.

25. The method of claims 23 or 24, wherein the amount of the meat produced is increased at least 5% relative prior to administering the composition, feedstock or foodstuff is administered to the ruminant.

26. A method of enhancing plant fiber digestion in a ruminant, the method comprising: administering to the rumen of the ruminant an effective amount of a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; wherein the purified population of bacteria is present in the composition in an amount effective to enhance the fiber digestion in the ruminant administered the composition, as compared to a ruminant not administered the composition.

27. A method of enhancing plant protein digestion in a ruminant, the method comprising: administering to the rumen of the ruminant an effective amount of a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a. Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; wherein the purified population of bacteria is present in the composition in an amount effective to enhance the digestibility of protein in the ruminant administered the composition, as compared to a ruminant not administered the composition.

28. A method of modulating the microbiome of a ruminant, the method comprising: administering to the rumen of the ruminant an effective amount of a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2. and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3; wherein the purified population of bacteria is present in the composition in an amount effective to impart at least one improved trait upon the ruminant.

29. The method of claim 28, wherein the at least one improved trait is selected from the group consisting of: an increase on overall milk production by the ruminant, an increase of fat in milk, an increase of carbohydrates in milk, an increase of protein in milk, an increase of vitamins in milk, an increase of minerals in milk, an increase in milk volume, an improved efficiency in feed utilization and digestibility, an increase in polysaccharide and lignin degradation, an increase in fatty acid concentration in the rumen, pH balance in the rumen, areduction in methane emissions, a reduction in carbon dioxide production, a reduction in manure production, improved dry matter intake, an increase in energy corrected milk (ECM) by weight and / or volume, and an improved efficiency of nitrogen utilization; wherein the increase or reduction is determined by comparing against an animal not having been administered the composition.

30. The method of any of claims 26, 27 or 28, wherein the purified population of bacteria comprise a combination of microbial strains that can inhibit or reduce methane- producing microbes and promote the grow th of non-methane producing microbes.

31. The method of claim 30, wherein the combination of microbial strains is capable of modulating the oxidation-reduce potential (ORP) inside the rumen.

32. The method of any of claims 26, 27, or 28, wherein the ORP is modulated inside the rumen of the ruminant.

33. The method of any of claims 26, 27, or 28, wherein the composition provides buffering capacity in the rumen of the ruminant and can maintain the pH at above about 6.5 and below about 7.8.

34. The method of any of claims 26, 27, or 28, wherein the combination of microbial strains modulates the temperature inside the rumen of ruminant.

35. The method of any of claims 26 to 34, further comprising administering a feed additive or a supplement to the ruminant.

36. The method of claim 35, wherein the feed additive or the supplement is a prebiotic, a probiotic, an enzyme or direct-fed microbial.

37. The method of any of claims 26 to 36, further comprising applying a composition comprising a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3to a feed, a forage, or a concentrate; and administering the feed, the forage or the concentrate to the ruminant.

38. The method of any of the preceding claims, wherein the composition, feedstock or foodstuff is a plant or derived from a plant, wherein a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria w ith a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 is applied to a plant, plant seed, or to a growth medium in which the plant is located; culturing the plant under conditions suitable for plant growth; and harvesting the plant, and subsequently processing the plant into the composition feedstock or foodstuff.

39. The method of any of the preceding claims, wherein the composition comprising: a) a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 is in a dried, freeze-dried, in powder, lyophilized, or in a liquid form.

40. A method of increasing the digestibility of a plant, the method comprising: applying a composition comprising: a purified population of bacteria selected from: (i) Clostridium spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical any of the Clostridium spp. listed in Table 1 or Table 2, (ii) a Pseudomonas spp. bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any one of the Pseudomonas spp. bacteria listed in Table 1 or Table 2, and / or (iii) a bacteria with a 16S nucleic acid sequence that is at least about 97% identical to any of the bacteria listed in Table 1, Table 2 or Table 3 to a plant, plant seed, or to a growth medium in which the plant is located; culturing the plant under conditions suitable for plant growth; and harvesting the plant, wherein the digestibility of the plant is increased.

41. The method of claim 40, wherein the purified population of bacteria comprise a combination of microbial strains that can inhibit or reduce methane-producing microbes and promote the growth of non-methane producing microbes.

42. The method of any of claims 40 or 41, further comprising feeding the plant to a ruminant.

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