Bile acid modifying engineered bacteria to prevent or treat colon cancer

Abstract

The present disclosure provides methods for treating colorectal cancer (CRC) or methods for reducing the risk of occurrence or delaying the occurrence of CRC in a subject by administering to the subject engineered native bacteria cells, wherein the engineered native bacteria cells are generated by transforming cultured population of native bacteria cells with one or more heterologous polynucleotides encoding bile salt hydrolase (BSH), and wherein the engineered native bacteria cells colonize in or on the subject and expresses BSH, thereby treating CRC or reducing the risk of occurrence or delaying the occurrence of CRC in the subject. Also described are populations of bacteria cells that are transformed with one or more heterologous polynucleotides encoding BSH, and compositions comprising such populations.

Description

[0001]Attorney Docket No.15670-0408WO1 BILE ACID MODIFYING ENGINEERED BACTERIA TO PREVENT OR TREAT COLON CANCER CLAIM OF PRIORITY This application claims the benefit of U.S. Provisional Application Serial No. 63 / 644,001, filed on May 8, 2024. The entire contents of the foregoing are incorporated herein by reference. FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT This invention was made with Government support under Grant Nos. CA265719 and EB030134 awarded by the National Institutes of Health. The Government has certain rights in the invention. TECHNICAL FIELD The present disclosure relates to engineered bacteria and use of the same in prevention and treatment of cancer. BACKGROUND Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the third most common cause of cancer deaths in the U.S. Though overall incidence of CRC is decreasing, epidemiological studies demonstrate an alarming increase of incidence in adults younger than the age of 50. Patients with a genetic predisposition (e.g., familial adenomatous polyposis), disease traits (e.g., inflammatory bowel disease), or demographics account for a large percentage of individuals in this category. Despite the vigilance and cost of yearly exams, CRC detection is difficult in these high-risk groups. Thus, there is a significant need for innovative solutions for early detection of CRC and the prevention of adenoma-to-CRC conversion. SUMMARY Described herein are methods for treating colorectal cancer (CRC) in a subject in need thereof, the methods comprising: a) culturing or having cultured an isolated native bacteria cell from a donating subject to yield a cultured population of the isolated bacteria cell; b) transforming or having transformed the cultured population with one or more polynucleotides heterologous to the bacteria cell to generate a Attorney Docket No.15670-0408WO1 population of transformed bacteria cells comprising the heterologous polynucleotide(s), wherein the one or more polynucleotides encode bile salt hydrolase (BSH); and c) administering or having administered at least a portion of the population of transformed bacteria cells comprising the heterologous polynucleotide(s) to a receiving subject, wherein the population of transformed bacteria cells colonizes in or on the receiving subject and expresses BSH, thereby treating CRC in the receiving subject. In some embodiments, the method further comprises administering to the subject one or more additional therapeutic agents. In some embodiments, the one or more additional therapeutic agents is an immunotherapeutic agent, a chemotherapeutic agent, and / or a radiotherapeutic agent. Also described herein are methods for reducing the risk of occurrence or delaying the occurrence of colorectal cancer (CRC) in a subject, the methods comprising: a) culturing or having cultured an isolated native bacteria cell from a donating subject to yield a cultured population of the isolated bacteria cell; b) transforming or having transformed the cultured population with one or more polynucleotides heterologous to the bacteria cell to generate a population of transformed bacteria cells comprising the heterologous polynucleotide(s), wherein the one or more polynucleotides encode bile salt hydrolase (BSH); and c) administering or having administered at least a portion of the population of transformed bacteria cells comprising the heterologous polynucleotide(s) to a receiving subject, wherein the population of transformed bacteria cells colonizes in or on the receiving subject and expresses BSH, thereby reducing the risk of occurrence or delaying the occurrence of CRC in the receiving subject. In some embodiments, the subject is at risk for developing CRC. In some embodiments, the subject has genetic predisposition for CRC. In some embodiments, the subject has familial adenomatous polyposis syndrome or Lynch syndrome. In some embodiments, the subject has a disease that increases the risk for CRC. In some embodiments, the disease is inflammatory bowel disease (IBD). In some embodiments, the receiving subject is same as the donating subject. In some embodiments, the receiving subject is different from the donating subject and is of the same species as the donating subject. Attorney Docket No.15670-0408WO1 In some embodiments, the native bacteria cell is isolated from a biological sample from the donating subject. In some embodiments, the method further comprises obtaining the biological sample from the donating subject. In some embodiments, the biological sample is selected from the group consisting of a bodily excretion, a biopsy or swab of a surface, and a pathological specimen. In some embodiments, the biological sample comprises a fecal sample, a colon biopsy, and / or a CRC tissue. In some embodiments, the bacteria cell is not from a laboratory adapted bacterial strain. In some embodiments, the bacteria cell is derived from a bacteria genus selected from the group consisting of Bacteroides, Clostridium, Streptococcus, Lactococcus, Eubacterium rectale, Escherichia coli, Enterobacter sp., Klebsiella sp., Bifidobacterium, Staphylococcus, Lactobacillus, Veillonella, Haemophilus, Moraxella, Corynebacterium and Propionibacterium. In some embodiments, the bacteria cell is derived from Escherichia coli. In some embodiments, the bacteria cell does not comprise one or more polynucleotides encoding for one or more pathogenic toxins selected from the group consisting of AB toxin, Alpha toxin, Anthrax toxin, Botulinum toxin, Cereulide, Cholesterol-dependent cytolysin, Clostridial Cytotoxin family, Clostridium botulinum C3 toxin, Clostridium difficile toxin A, Clostridium difficile toxin B, Clostridium enterotoxin, Clostridium perfringens alpha toxin, Clostridium perfringens beta toxin, Cry1Ac, Cry6Aa, Cry34Ab1, Delta endotoxin, Diphtheria toxin, Enterotoxins, Enterotoxin type B, Erythrogenic toxin, Exfoliatin, Fragilysin, Haemolysin E, Heat- labile enterotoxin, Heat-stable enterotoxin, Hemolysin, HrpZ Family, Leukocidin, Listeriolysin O, Panton–Valentine leucocidin, intact Pathogenicity island, Phenol- soluble modulin, Pneumolysin, Pore-forming toxin, Pseudomonas exotoxin, Pyocyanin, anti-eukaryotic Rhs toxins, RTX toxin, Shiga toxins, Shiga-like toxin, Staphylococcus aureus alpha toxin, Staphylococcus aureus beta toxin, Staphylococcus aureus delta toxin, Streptolysin, Tetanolysin, Tetanospasmin, Toxic shock syndrome toxin, Tracheal cytotoxin, and Verocytotoxin. In some embodiments, the bacteria cell is antibiotic sensitive or transformed with one or more polynucleotides to be antibiotic sensitive to one or more antibiotic agents used for selection of transformed bacteria cells. In some embodiments, the one Attorney Docket No.15670-0408WO1 or more antibiotic agents used for selection of transformed bacteria cells comprises kanamycin, chloramphenicol, carbenicillin, hygromycin, or trimethoprim. In some embodiments, the bacteria cell is not antibiotic resistant to one or more clinically used antibiotic agents. In some embodiments, the one or more clinically used antibiotic agents comprises antibiotic macrolides, rifamycins, polymyxins, quinolone antibiotics, beta-lactams, aminoglycosides, cephalosporins, monobactams, carbapenems, or tetracyclines. In some embodiments, the one or more polynucleotides encode Lactobacillus salivarius BSH (LsBSH). In some embodiments, the one or more heterologous polynucleotides encoding LsBSH is engineered into a native E. coli chassis. In some embodiments, the one or more polynucleotides encode Dubosiella newyorkensis–A0A1U7NKD7 BSH (DnBSH1). In some embodiments, the one or more heterologous polynucleotides encoding DnBSH1 is engineered into a native E. coli chassis. In some embodiments, the one or more heterologous polynucleotides comprise codon bias configured to improve or enhance expression of BSH in the transformed bacteria cells. In some embodiments, the one or more heterologous polynucleotides are integrated into the chromosome of the transformed bacteria cells. In some embodiments, the one or more heterologous polynucleotides are integrated into the attB and / or yfgG genes of the bacterial genome. In some embodiments, the one or more heterologous polynucleotides are episomally introduced into the transformed bacteria cells in a plasmid. In some embodiments, the transformed bacteria cells further comprise a plasmid retention or maintenance system. In some embodiments, the plasmid retention or maintenance system comprises a partitioning system or a toxin-antitoxin module or system. In some embodiments, the one or more heterologous polynucleotides are integrated into an expression cassette and are expressed under the control of a Ptrc promoter. In some embodiments, the population of transformed bacteria cells colonizes in or on the receiving subject permanently or long-term. In some embodiments, the population of transformed bacteria cells colonizes in or on the receiving subject for at least 48 hours. In some embodiments, the method further comprises determining Attorney Docket No.15670-0408WO1 and / or measuring the colonization or presence of the administered population of transformed bacteria cells in or on the receiving subject. In some embodiments, the one or more heterologous polynucleotides further encode a fluorescent protein. In some embodiments, the fluorescent protein comprises green fluorescent protein, yellow fluorescent protein, red fluorescent protein (mCherry, mEos2, mRuby2, mRuby3, mClover3, mApple, mKate2, mMaple, mCardinal, mNeptune), mTurquoise, or mVenus. In some embodiments, the population of transformed bacteria cells is administered to the receiving subject multiple times. In some embodiments, the population of transformed bacteria cells is administered to the receiving subject at daily, weekly, biweekly, or monthly intervals. In some embodiments, administration of the population of transformed bacteria cells do not substantially alter the microbiome of the receiving subject. In some embodiments, expression of BSH by the population of transformed bacteria cells results in deconjugation of one or more bile acids in the receiving subject. In some embodiments, expression of BSH by the population of transformed bacteria cells results in activation of farnesoid X receptor (FXR) signaling in the receiving subject. In some embodiments, the donating subject and / or the receiving subject is a human. Also described herein are populations of bacteria cells transformed with one or more polynucleotides heterologous to the bacteria cells, wherein the one or more polynucleotides encode bile salt hydrolase (BSH), and wherein the bacteria cells are obtained from and adapted to or configured for the microbiome of a mammalian subject, and are not adapted for or configured for culture in a laboratory environment. In some embodiments, the one or more polynucleotides encode Lactobacillus salivarius BSH (LsBSH). In some embodiments, the one or more heterologous polynucleotides encoding LsBSH is engineered into a native E. coli chassis. In some embodiments, the one or more polynucleotides encode Dubosiella newyorkensis–A0A1U7NKD7 BSH (DnBSH1). In some embodiments, the one or more heterologous polynucleotides encoding DnBSH1 is engineered into a native E. coli chassis. Attorney Docket No.15670-0408WO1 In some embodiments, the bacteria cell is isolated from a biological sample from a donating mammalian subject. In some embodiments, the biological sample is selected from the group consisting of a bodily excretion, a biopsy or swab of a surface, and a pathological specimen. In some embodiments, the biological sample comprises a fecal sample, a colon biopsy, and / or a CRC tissue. In some embodiments, the bacteria cell is not from a laboratory adapted bacterial strain. In some embodiments, the bacteria cell is derived from a bacteria genus selected from the group consisting of Bacteroides, Clostridium, Streptococcus, Lactococcus, Eubacterium rectale, Escherichia coli, Enterobacter sp., Klebsiella sp., Bifidobacterium, Staphylococcus, Lactobacillus, Veillonella, Haemophilus, Moraxella, Corynebacterium and Propionibacterium. In some embodiments, the bacteria cell is derived from Escherichia coli. In some embodiments, the bacteria cell does not comprise one or more polynucleotides encoding for one or more pathogenic toxins selected from the group consisting of AB toxin, Alpha toxin, Anthrax toxin, Botulinum toxin, Cereulide, Cholesterol-dependent cytolysin, Clostridial Cytotoxin family, Clostridium botulinum C3 toxin, Clostridium difficile toxin A, Clostridium difficile toxin B, Clostridium enterotoxin, Clostridium perfringens alpha toxin, Clostridium perfringens beta toxin, Cry1Ac, Cry6Aa, Cry34Ab1, Delta endotoxin, Diphtheria toxin, Enterotoxins, Enterotoxin type B, Erythrogenic toxin, Exfoliatin, Fragilysin, Haemolysin E, Heat- labile enterotoxin, Heat-stable enterotoxin, Hemolysin, HrpZ Family, Leukocidin, Listeriolysin O, Panton–Valentine leucocidin, intact Pathogenicity island, Phenol- soluble modulin, Pneumolysin, Pore-forming toxin, Pseudomonas exotoxin, Pyocyanin, anti-eukaryotic Rhs toxins, RTX toxin, Shiga toxins, Shiga-like toxin, Staphylococcus aureus alpha toxin, Staphylococcus aureus beta toxin, Staphylococcus aureus delta toxin, Streptolysin, Tetanolysin, Tetanospasmin, Toxic shock syndrome toxin, Tracheal cytotoxin, and Verocytotoxin. In some embodiments, the bacteria cell is antibiotic sensitive or transformed with one or more polynucleotides to be antibiotic sensitive to one or more antibiotic agents used for selection of transformed bacterial cells. In some embodiments, the one or more antibiotic agents used for selection of transformed bacterial cells comprises kanamycin, chloramphenicol, carbenicillin, hygromycin, or trimethoprim. Attorney Docket No.15670-0408WO1 In some embodiments, the bacteria cell is not antibiotic resistant to one or more clinically used antibiotic agents. In some embodiments, the one or more clinically used antibiotic agents comprises antibiotic macrolides, rifamycins, polymyxins, quinolone antibiotics, beta-lactams, aminoglycosides, cephalosporins, monobactams, carbapenems, or tetracyclines. In some embodiments, the population of bacteria cells expresses BSH when administered to a receiving mammalian subject. In some embodiments, the population of bacteria cells is capable of colonizing or is configured to colonize in or on the receiving mammalian subject permanently or long-term. Also described herein are compositions comprising the populations of bacteria cells of the present disclosure. In some embodiments, the composition is an edible composition. In some embodiments, the edible composition comprises a gel capsule. In some embodiments, the edible composition comprises a beverage. In some embodiments, the edible composition is selected from the group consisting of yogurt, milk, ice cream, vegetable puree, fruit puree, sorbet, and oatmeal. Also described herein are kits comprising one or more containers comprising the compositions of the present disclosure. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims. DESCRIPTION OF DRAWINGS FIGs.1A-1I. Time-restricted feeding (TRF) identified BSHs have an increased capacity for amidation. (FIG.1A) BSHs chosen and successfully Attorney Docket No.15670-0408WO1 engineered based on the diet and feeding condition its expression was most enriched in. (FIG.1B) Design of the culture experiment performed on the various BSH ENBs. (FIG.1C) Change from baseline of the BA supplemented into the cultures, a measurement of the deconjugative activity of BSH, for each of the BSH ENBs (n = 3 cultures / timepoint / BA supplement / BSH ENB; Student’s t-test, ***: p < 0.001, **: p < 0.01, *: p < 0.05). (FIG.1D) Protein sequence alignment using CLUSTAL Omega, highlighting the selectivity loop region containing motifs associated with taurine or glycine preference. (FIG.1E) Difference in the normalized abundance of amidated BAs between 0h and 48h in the cultures of BSH ENBs, faceted by the different BAs supplemented in the cultures. Amidated BAs with significant normalized abundance differences between 0h and 48h for EcAZ-2BSH+and EcAZ-1DnBSH1in the (FIG.1F- 1G) GUDCA and TUDCA and (FIG.1H-1I) other BAs supplemented cultures (n = 3 cultures / timepoint / BA supplement / BSH ENB; Student’s t-test, ***: p < 0.001, **: p < 0.01, *: p < 0.05). BSH+ = EcAZ-2BSH+; DnBSH1 = EcAZ- 1DnBSH1; DnBSH2 = EcAZ-1DnBSH2; LgBSH = EcAZ-1LgBSH; LCAG95BSH = EcAZ-1LCAG95BSH; EpBSH = EcAZ-1EpBSH. GCA = glycocholic acid; GCDCA = glycochenodeoxycholic acid; GDCA = glycodeoxycholic acid; GLCA = glycolithocholic acid; GUDCA = glycoursodeoxycholic acid; TCA = taurocholic acid; TCDCA = taurochenodeoxycholic acid; TDCA = taurodeoxycholic acid; TLCA = taurolithocholic acid; TUDCA = tauroursodeoxycholic acid. BlonBSH = Bifidobacterium longum BSH; BspBSH = Bacteroidales sp. BSH; BtheBSH = Bacteroides thetaiotaomicron BSH; CspBSH = Clostridiales sp. BSH; EfaeBSH = Enterococus faecalis BSH; FspBSH = Faecalibacterium sp. BSH; LaciBSHa = Lactobacillus acidophilus BSHa; LaciBSHb = Lactobacillus acidophilus BSHb; LaviBSH = Ligilactobacillus aviarius BSH; LcolBSH = Limosilactobacillus coleomonis BSH; LcriBSHa = Lactobacillus crispatus BSHa; LcriBSHb = Lactobacillus crispatus BSHb; LgasBSHa = Lactobacillus gasseri BSHa; LgasBSHb = Lactobacillus gasseri BSHb; LgigBSH = Lactobacillus gigeriorum BSH; LingBSH = Limosilactobacillus ingluveiei BSH; LjohBSHa = Lactobacillus johnsonii BSHa; LjohBSHb = Lactobacillus johnsonii BSHb; LjohBSHc = Lactobacillus johnsonii BSHc; LmurBSH = Ligilactobacillus murinus BSH; LplaBSH = Lactiplantibacillus plantarum BSH; LreuBSH = Limosilactobacillus reuteri; LrogBSH = Lactobacillus rogoseae BSH; LsalBSH = Ligilactobacillus salivarius BSH. Ile / Leu-UDCA = Attorney Docket No.15670-0408WO1 Isoleucine / Leucine-conjugated ursodeoxycholic acid; Ala-UDCA = Alanine- conjugated ursodeoxycholic acid; Lys-CA = Lysine-conjugated cholic acid; Lys- CDCA = Lysine-conjugated chenodeoxycholic acid. FIGs.2A-2I show that engineered E. coli with the NKD7 D. newyorkensis BSH has a more pronounced phenotypic effect than other BSHs. (FIG.2A) Experimental design and sample collection protocol. (FIG.2B) Colonization of the BSH ENBs 6 weeks post single gavage (n = 10 mice / group; pairwise Student’s t-test, n.s. = not significant at α < 0.05). (FIG.2C) Plating of fecal samples from mice gavaged with the BSH ENBs on LB containing TDCA plates. White precipitate around colonies indicate BSH is deconjugating TDCA to DCA, qualitatively indicating enzyme functionality. (FIG.2D) Average cumulative food intake and (FIG. 2E) body weight of mice after single gavage (n = 10 mice / group; pairwise Student’s t- test, n.s. = not significant at α < 0.05). Postprandial (FIG.2F) blood glucose and (FIG.2G) serum insulin concentrations of mice 6 weeks post single gavage (n = 10 mice / group; pairwise Student’s t-test, * : p < 0.05). Percent change in (FIG.2H) fat and (FIG.2I) lean mass from Wk 0 to Wk 6 (n = 10 mice / group; pairwise Student’s t- test, **: p < 0.01, *: p < 0.05). FIGs.3A-3C. EcAZLsBSH+prevent polyp formation in ApcF / WT;Cdx2- Cre+ / +mice. (FIG.3A) Schematic showing the experimental design. Six-week-old ApcF / WT;Cdx2-Cre+ / +mice were gavaged with EcAZ or EcAZLsBSH+, and tumor formation and colonization were assessed after 13 weeks. (FIG.3B) Tumor-bearing vs. tumor-free mice. (3C) Colonization in ileum, cecum, colon, and tumors. Data presented as mean ± SEM, with each dot representing an individual mouse. LOD: limit of detection. FIGs.4A-4B. EcAZ-2LsBSH+engrafts in ApcF / F;Cdx2-CreER+ mice. (FIG. 4A) Schematic showing the experimental design. Six-week-old ApcF / F;Cdx2-CreER+ mice were gavaged with EcAZ or EcAZLsBSH+. One week later, mice received tamoxifen injections and were euthanized 15 weeks post-gavage. (FIG.4B) Stool colonization over time. Data shown as mean ± SEM; dots represent individual mice. Statistics: two-way ANOVA. LOD: limit of detection. FIG.5. BSH-expressing EcAZ strains differentially activate FXR signaling in the ileum. Mice received a single gavage of EcAZ, EcAZLsBSH+, EcAZDnBSH+, or EcAZLgBSH+. Ileal FXR target gene expression (Nr0b2, Fgf15, Slc51a, Slc51b) was Attorney Docket No.15670-0408WO1 measured by qRT-PCR 15 weeks later. EcAZLsBSH+and EcAZDnBSH+significantly upregulated FXR signaling; EcAZLgBSH+had little effect. Mean ± SEM shown; * p < 0.05, ** p < 0.01 by one-way ANOVA. DETAILED DESCRIPTION Described herein are methods for prevention and / or treatment of colorectal cancer (CRC). Diets rich with red meat and saturated fatty acids are strongly associated with CRC risks. These diets have elevated levels of fecal secondary bile acids (BAs), particularly deoxycholic acid (DCA). The role of BAs as tumor promoters has been tested using a variety of experimental settings. More than 85% of CRC arise from a mutation in the adenomatous polyposis coli (APC) gene. Recent studies show a relationship between the BA receptor farnesoid X receptor (FXR) and APC. FXR is the master regulator of BA homeostasis, but also influences cholesterol, glucose, and lipid metabolism. FXR expression is inversely correlated with CRC progression; loss of FXR in the APCMin / +mouse model of CRC leads to the development of intestinal tumors. Suppression of FXR with its antagonist tauro-β-muricholic acid (TbMCA) leads to CRC progression; reduction of TbMCA leads to FXR activation and CRC suppression. TbMCA can be reduced by increasing luminal bile salt hydrolase (BSH) activity, a bacterial enzyme that deconjugates BAs. The present disclosure addresses these hurdles by developing BSH-expressing engineered native bacteria (ENB). Engineered Native Bacteria (ENB) Described herein are engineered native bacteria (ENB) for use in the methods of the present disclosure. For example, described herein are BSH-expressing ENB for use in prevention and / or treatment of CRC. ENB described herein can be produced by the methods of the present disclosure and the methods described in WO 2018 / 195097, the entire contents of which are incorporated herein by reference. Each specific tumor microenvironment is a niche for a particular bacterial community. In particular, CRC tumors select for bacterial taxa that may contribute to carcinogenesis. Serendipitously, one of the most commonly associated bacteria with CRC is E. coli both in humans and in mice, for which there are many synthetic Attorney Docket No.15670-0408WO1 biology tools. There is concern that E. coli may contribute to CRC development. For example, enterotoxigenic Bacteroides fragilis and pks+ E. coli are known to be associated with CRC and their colocalization leads to increased tumor burden compared to mono-colonization. However, commonly, non-pathogenic E. coli are found in the normal microbiome. Thus, native E. coli isolated from a subject can be used to produce ENB of the present disclosure. For example, native E. coli isolated from stool sample of a subject can be used to generate ENB of the present disclosure. Since gut microflora can sense and manipulate the luminal environment, they have become an attractive avenue for engineered, cell-based therapeutics. However, engineered, live bacterial therapies have been tested only under non-colonizing conditions (i.e., gnotobiotic, antibiotic-treated mice) and have failed to provoke functional changes in hosts with an intact microbiome, including humans. There are multiple barriers to the survival of an engineered probiotic in the luminal environment, including those from the host (e.g., innate and adaptive immunity) and other native microorganisms (e.g., competition, niche availability). To address the inability of engineered bacteria to colonize the host, several strategies have been outlined by different groups, including developing tools to manipulate families of bacteria that are commonly found in the gut microbiome, specifically Bifidobacteria, Bacteroides, Lactococci, and Lactobacilli to determine whether they can outcompete native microorganisms and engraft in the intestinal lumen. However, there are only few synthetic biology tools available to recombineer these genera of bacteria, severely limiting the types of functional manipulations that can be performed. The study described herein (e.g., as described in Examples 1-3) overcomes these limitations by recombineering native bacteria isolated from a subject (e.g., from fecal sample of a subject) to generate the ENB of the present disclosure. Accordingly, the present disclosure describes isolation and development of native bacteria (e.g., native E. coli) as long-residing synthetic biology vectors in fully conventional hosts to sense, compute, report, and treat diseases, such as cancers (e.g., CRC). So far, the field simply did not have the capable tools to perform advanced mechanistic studies on the gut microbiome and its relationship with CRC. The ENB described herein can serve as a much-needed, programmable platform for introducing specific functions, allowing scientists to determine how the gut microbiome can affect host physiology. There are a practically unlimited number of functions that await Attorney Docket No.15670-0408WO1 proper vectors, for being introduced into the gut microbiome. Furthermore, the ENB described here can be used in different organ systems (e.g., skin, lungs, and vagina), fundamentally expanding the ability to perform mechanistic studies (e.g., the roles of cysteine proteases in the progression of CRC) and to create therapeutic ENBs for microbiome mediated / modulated disease. Current synthetic biology approaches to using engineered bacteria for the treatment of CRC suffer from limitations. To understand whether a bacterial function in the gut lumen can sense or treat a malignancy, better tools to functionally manipulate the gut microbiome are needed. The inability of engineered bacteria to colonize conventionally raised wild-type (WT) hosts has thus far limited their use in mechanistic, biosensor applications, and therapeutic studies. Described herein are techniques that have advanced the ability to use engineered bacteria to effectively manipulate the gut microbiome and better understand how these changes affect host physiology in a fully conventional host. This has been accomplished by identifying tractable, native bacteria (e.g., E. coli) from a host, genetically modifying these bacteria to express a potentially therapeutic gene, and then reintroducing the engineered native bacteria (ENB) to the host (either to the same host (e.g., same subject) from whom the native bacteria is isolated (e.g., autologous), or to a different host (e.g., different subject) who is of the same species as the host from whom the native bacteria is isolated (e.g., allogeneic)). By choosing native bacteria as the vector for function delivery, the present methods select organisms that are already maximally adapted to the luminal environment of the host, thereby bypassing nearly all the barriers to colonization. Native bacteria, e.g., native E. coli, are easily culturable, common in human stool and the tools to engineer them have existed for decades. Moreover, E. coli are particularly well-adapted to the CRC tumor environment. Though E. coli are common in the gut lumen, many have assumed that they are not good colonizers due to so much disappointment with commensal laboratory strains (e.g., E. coli Nissle, E. coli MG1655). Moreover, this work allows investigators to use commensal laboratory strains like E. coli Nissle or E. coli MG1655 for in vitro testing of their synthetic biology biosensors or therapeutics prior to recombineering into native E. coli for in vivo use, which is not possible for other commensal bacterial families currently used for synthetic biology approaches. Attorney Docket No.15670-0408WO1 Thus, described herein are ENB that are produced by engineering, e.g., genetically modifying (e.g., transforming) native bacteria cells with one or more heterologous polynucleotides. Native Bacteria Cells For the purpose of the present disclosure, the terms “bacteria”, “bacteria cells” and “bacterial cells” can be used interchangeably. Native bacteria cells for use in the present methods are described in the present disclosure and in WO 2018 / 195097, the entire contents of which are incorporated herein by reference. To generate ENB of the present disclosure, native bacteria cells can be isolated from a subject. Additionally, or alternatively, native bacteria cells isolated (e.g., previously isolated) from a subject can be used to generate ENB of the present disclosure. A subject from whom native bacteria cells are isolated (or has been isolated) can be referred to herein as a donating subject. For example, a mammalian subject from whom native bacteria cells are isolated (or has been isolated) can be referred to herein as a donating mammalian subject. A subject to whom the ENB are administered can be referred to herein as a receiving subject. For example, a mammalian subject to whom the ENB are administered can be referred to herein as a receiving mammalian subject. The bacteria cells used in the present methods can be native to a subject (e.g., native to a donating subject and / or a receiving subject) and are not from a laboratory adapted bacterial strain. The term “native bacteria” can refer to a bacteria cell or population of bacteria cells obtained from and adapted to or configured for the microbiome of a subject (e.g., a donating subject and / or a receiving subject). For example, native bacteria can refer to a bacteria cell or population of bacteria cells obtained from and adapted to or configured for the microbiome of a mammalian subject (e.g., a donating mammalian subject and / or a receiving mammalian subject). Native bacteria are adapted to colonize or configured for colonization of a subject and are not adapted for or configured for culture in a laboratory environment. In some embodiments, native bacteria are commensal to a host organism. As used herein, “commensal” when used in reference to an association between two organisms, is a particular association in which one member of the association benefits from the association while the other member is essentially unaffected. In a Attorney Docket No.15670-0408WO1 commensal association of organisms, none of the members of the association is significantly harmed by the presence of the other member. Two organisms can form a commensal association under particular, but not necessarily all, conditions. In such cases, as long as an organism is capable of forming a commensal association with the other organism under at least one set of conditions, the organism is considered to be one that can form a commensal association with the other organism. However, commensal bacteria are not necessarily native, and can be a laboratory strain (e.g., a commensal laboratory strain).  Examples of commensal laboratory strains include E. coli Nissle and E. coli MG1655. As described herein, subjects can include, without limitation, vertebrates, including any member of the class mammalia, including humans, non-human veterinary subjects including experimental animals, domestic and farm animals, and zoo, sports or pet animals, such as mouse, rat, rabbit, dogs, cats, pig, sheep, goat, horse, cattle, and higher primates. Thus, the subjects can be mammals, e.g., primates (e.g., humans or non-human primates) or non-primate mammals (e.g., mouse, rat, rabbit, dogs, cats, pig, sheep, goat, horse, and cattle). For example, the subjects can be humans. The subjects can be male or female. The subjects can be adults (18 years or above) or children (below 18 years, e.g., 0-17 years). For preparation of ENB, native bacteria cells can be isolated from a subject, or native bacteria cells previously isolated from a subject can be used. The native bacteria cells can be isolated from one or more biological samples of a subject. Biological samples can comprise bodily excretions (e.g., saliva, mucus, urine, stool, tear, and / or semen). For example, a biological sample can comprise a stool sample (i.e., a fecal sample). Biological samples can also comprise biopsy or swab of a surface (e.g., biopsy or swab of mucosal GI tract, biopsy or swab of mouth / pharynx / nares, biopsy or swab of urogenital track, biopsy or swab of skin, biopsy or swab of anus / rectum, biopsy or swab of cheek / mouth, and / or biopsy or swab of eye). For example, a biological sample can comprise a colon biopsy sample. Biological samples can also comprise pathological specimen (e.g., tumor tissues). For example, a biological sample can comprise a CRC tissue sample. The native bacteria cells can be derived from one or more of the following genus: Bacteroides, Clostridium, Streptococcus, Lactococcus, Eubacterium (e.g., Eubacterium rectale), Escherichia (e.g., Escherichia coli), Enterobacter (e.g., Attorney Docket No.15670-0408WO1 Enterobacter sp.), Klebsiella (e.g., Klebsiella sp.), Bifidobacterium, Staphylococcus, Lactobacillus, Veillonella, Haemophilus, Moraxella, Corynebacterium, and / or Propionibacterium. For example, the native bacteria cells can be derived from E. coli. Thus, native bacteria cells derived from E. coli can be engineered by the present methods (e.g., as described in Examples 1-3) to generate ENB of the present disclosure. For example, one or more heterologous polynucleotides can be engineered into native Escherichia coli chassis, EcAZ, to produce ENB of the present disclosure. In some instances, native bacteria cells used in the present methods do not comprise one or more polynucleotides encoding for one or more pathogenic toxins. The pathological toxins can be one or more of: AB toxin, Alpha toxin, Anthrax toxin, Botulinum toxin, Cereulide, Cholesterol-dependent cytolysin, Clostridial Cytotoxin family, Clostridium botulinum C3 toxin, Clostridium difficile toxin A, Clostridium difficile toxin B, Clostridium enterotoxin, Clostridium perfringens alpha toxin, Clostridium perfringens beta toxin, Cry1Ac, Cry6Aa, Cry34Ab1, Delta endotoxin, Diphtheria toxin, Enterotoxins, Enterotoxin type B, Erythrogenic toxin, Exfoliatin, Fragilysin, Haemolysin E, Heat-labile enterotoxin, Heat-stable enterotoxin, Hemolysin, HrpZ Family, Leukocidin, Listeriolysin O, Panton–Valentine leucocidin, intact Pathogenicity island, Phenol-soluble modulin, Pneumolysin, Pore-forming toxin, Pseudomonas exotoxin, Pyocyanin, anti-eukaryotic Rhs toxins, RTX toxin, Shiga toxins, Shiga-like toxin, Staphylococcus aureus alpha toxin, Staphylococcus aureus beta toxin, Staphylococcus aureus delta toxin, Streptolysin, Tetanolysin, Tetanospasmin, Toxic shock syndrome toxin, Tracheal cytotoxin, and Verocytotoxin. Thus, described herein are native bacteria cells that do not comprise polynucleotides encoding for one or more of the following pathogenic toxins: AB toxin, Alpha toxin, Anthrax toxin, Botulinum toxin, Cereulide, Cholesterol-dependent cytolysin, Clostridial Cytotoxin family, Clostridium botulinum C3 toxin, Clostridium difficile toxin A, Clostridium difficile toxin B, Clostridium enterotoxin, Clostridium perfringens alpha toxin, Clostridium perfringens beta toxin, Cry1Ac, Cry6Aa, Cry34Ab1, Delta endotoxin, Diphtheria toxin, Enterotoxins, Enterotoxin type B, Erythrogenic toxin, Exfoliatin, Fragilysin, Haemolysin E, Heat-labile enterotoxin, Heat-stable enterotoxin, Hemolysin, HrpZ Family, Leukocidin, Listeriolysin O, Panton–Valentine leucocidin, intact Pathogenicity island, Phenol-soluble modulin, Attorney Docket No.15670-0408WO1 Pneumolysin, Pore-forming toxin, Pseudomonas exotoxin, Pyocyanin, anti-eukaryotic Rhs toxins, RTX toxin, Shiga toxins, Shiga-like toxin, Staphylococcus aureus alpha toxin, Staphylococcus aureus beta toxin, Staphylococcus aureus delta toxin, Streptolysin, Tetanolysin, Tetanospasmin, Toxic shock syndrome toxin, Tracheal cytotoxin, and Verocytotoxin Native bacteria cells used in the present methods can be antibiotic sensitive or transformed with one or more polynucleotides to be antibiotic sensitive to one or more antibiotic agents used for selection of transformed bacterial cells. Antibiotics used for selection of transformed bacterial cells can comprise one or more of: kanamycin, chloramphenicol, carbenicillin, hygromycin, and trimethoprim. Thus, described herein are native bacteria cells that are antibiotic sensitive (or are transformed with one or more polynucleotides to be antibiotic sensitive) to one or more of kanamycin, chloramphenicol, carbenicillin, hygromycin, and trimethoprim. Native bacteria cells used in the present methods can be antibiotic resistant to one or more clinically used antibiotic agents. Clinically used antibiotic agents can comprise one or more of: macrolide antibiotics, rifamycins, polymyxins, quinolone antibiotics, beta-lactams, aminoglycosides, cephalosporins, monobactams, carbapenems, and tetracyclines. Thus, described herein are native bacteria cells that are antibiotic resistant to one or more of macrolide antibiotics, rifamycins, polymyxins, quinolone antibiotics, beta-lactams, aminoglycosides, cephalosporins, monobactams, carbapenems, and tetracyclines. Isolated native bacteria cells can be cultured by techniques known in the art to generate a population (e.g., a cultured population) of the native bacteria cells. The population (e.g., cultured population) of the native bacteria cells can then be genetically modified by methods described herein (e.g., as described in Examples 1-3) to generate ENB of the present disclosure. Briefly, isolated native bacteria cells and / or cultured population of native bacteria cells can be transformed with one or more heterologous polynucleotides. For transformation of native bacteria cells and / or cultured population of native bacteria cells, one or more polynucleotides can be transferred to (i.e., introduced into) the bacteria cells and / or cultured population thereof, resulting in genetically-stable inheritance. Host native bacteria cells (or cultured population thereof) comprising the transferred polynucleotides can be Attorney Docket No.15670-0408WO1 referred to as “recombinant” or “transgenic” or “transformed” or “engineered” or “genetically modified” native bacteria cells (or cultured population thereof). Native bacteria cells (or cultured population thereof) can be transformed using techniques known in the art. Such techniques are described, e.g., in Green and Sambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press; 4th edition (2012). Clinical microbiology differentiation manuals to guide selection and identification of bacterial species of interest include, e.g., Medical Microbiology, 8th Edition by Murray, Rosenthal, and Pfaller, Elsevier, 2015; and Medical Microbiology: A Guide to Microbial Infections: Pathogenesis, Immunity, Laboratory Investigation and Control, 19th Edition, by Barer, Irving, Swann and Perera, Elsevier, 2018. Isolated native bacteria cells (or cultured population thereof) can be transformed with one or more heterologous polypeptides to generate ENB of the present disclosure, and the ENB can express one or more heterologous polypeptides of interest. In order to maintain the ability for long-term or permanent colonization of a mammalian subjection (e.g., the ability for successful reintroduction into a mammalian microbiome), populations of native bacteria cells transformed to express one or more heterologous polypeptides are not adapted for laboratory or in vitro culture environments. The ENB can be cultured in vitro in a laboratory environment for as few divisions as possible. For example, the ENB can be cultured in vitro in a laboratory environment outside of the donating subject for 30 or fewer days, e.g., 25, 20, 15, 10, 7, 5 or fewer days before administration to the receiving subject. The ENB have an overall in vitro growth time of about 14 or fewer days, e.g., 13, 12, 11, 10, 9, 8, 7 or fewer days between collection from the donating subject and administration to the receiving subject. Such calculations of in vitro growth time or culture time generally do not include time the bacteria cells are stored (e.g., cryopreserved or lyophilized), and include time for transformation or introduction of the one or more heterologous polynucleotides. Heterologous Polynucleotides Heterologous polynucleotides can refer to polynucleotides that are heterologous to the bacteria cells. Heterologous polynucleotides can also refer to Attorney Docket No.15670-0408WO1 polynucleotides that are heterologous to the mammalian subject (e.g., donating subject and / or receiving subject). The heterologous polynucleotide can be one or more transgenes described in Table 1. For example, isolated native bacteria cells and / or cultured population of native bacteria cells can be transformed with one or more of the following heterologous polynucleotides: a polynucleotide encoding a fluorescent protein, a polynucleotide encoding bile salt hydrolase (BSH), a polynucleotide encoding cytosine deaminase, a polynucleotide encoding thymidylate synthase (ThyA), a polynucleotide encoding 4-hydroxytetrahydrodipicolinate synthase (DapA), a polynucleotide encoding histone-like protein A (HlpA), a polynucleotide encoding protease biosensor FRET pair (e.g., tagGFP-tagRFP), and / or a polynucleotide encoding a protease inhibitor. Table 1. Assessment of Specific Transgenes Gene(s) Source Function Clinical Purpose In Vitro Utility measure 9 ci U ti ti Attorney Docket No.15670-0408WO1 Gene(s) Source Function Clinical Purpose In Vitro Utility measure th g p y p g , g encoding a therapeutic protein. Such heterologous polynucleotides can include a polynucleotide encoding BSH and / or a polynucleotide encoding cytosine deaminase. Thus, isolated native bacteria cells and / or cultured population of native bacteria cells can be transformed with one or more of the following heterologous polynucleotides: a polynucleotide encoding BSH, and / or a polynucleotide encoding cytosine deaminase. The heterologous polynucleotide can encode a fluorescent protein. The fluorescent protein can be one or more of the following: green fluorescent protein, yellow fluorescent protein, red fluorescent protein (e.g., mCherry, mEos2, mRuby2, mRuby3, mClover3, mApple, mKate2, mMaple, mCardinal, mNeptune), mTurquoise, and / or mVenus. Thus, isolated native bacteria cells and / or cultured population of native bacteria cells can be transformed with one or more of the following heterologous polynucleotides: a polynucleotide encoding green fluorescent protein, a polynucleotide encoding yellow fluorescent protein, a polynucleotide encoding red fluorescent protein (e.g., one or more of mCherry, mEos2, mRuby2, mRuby3, mClover3, mApple, mKate2, mMaple, mCardinal, and mNeptune), a polynucleotide encoding mTurquoise, and / or a polynucleotide encoding mVenus. Attorney Docket No.15670-0408WO1 The heterologous polynucleotide can be selected based on function of the encoded protein. For example, for tracking the ENB, isolated native bacteria cells and / or cultured population of native bacteria cells can be transformed with a heterologous polynucleotide that encodes a fluorescent protein. For delivering therapeutic payloads (e.g., a therapeutic protein, such as BSH, cytosine deaminase), isolated native bacteria cells and / or cultured population of native bacteria cells can be transformed with a heterologous polynucleotide that encodes that therapeutic protein. For improving CRC specificity, isolated native bacteria cells and / or cultured population of native bacteria cells can be transformed with a heterologous polynucleotide that encodes HlpA. For ensuring bioconfinement, isolated native bacteria cells and / or cultured population of native bacteria cells can be transformed with a heterologous polynucleotide that encodes ThyA or DapA. The heterologous polynucleotides can comprise codon bias configured to improve or enhance expression of the encoded protein in the transformed bacteria cells. The heterologous polynucleotides can be integrated into the chromosome of the transformed bacterial cells. Thus, in some ENB, one or more heterologous polynucleotides can be integrated into the genome of the native bacteria. For example, one or more heterologous polynucleotides can be integrated into attB and / or yfgG genes of the bacterial genome. Alternatively, the heterologous polynucleotides can be episomally introduced into the transformed bacteria cells. For example, one or more heterologous polynucleotides can be introduced into the native bacteria cells in a plasmid. Such transformed bacteria cells (e.g., such ENB) can further comprise a plasmid retention or maintenance system. The plasmid retention or maintenance system can comprise a partitioning system or a toxin-antitoxin module or system. In the ENB, the expression of the heterologous polynucleotides can be under one or more promoters. For example, one or more heterologous polynucleotides can be integrated into an expression cassette and can be expressed under the control of a promoter. The use of these promoters can ensure proper expression of the heterologous polynucleotides (e.g., only in the microenvironment of precancerous and cancerous tumors). The promoters can be constitutive. The promoters can be inducible. The promoters can comprise one or more of the following: a Ptrc promoter, an anaerobic-inducible promoter (e.g., the E. coli endogenous promoter Pfnrs), a Attorney Docket No.15670-0408WO1 microaerobic-inducible promoter (e.g., the PVHb), and / or a lac operon promoter (e.g., lacP or lacO). For example, expression of the heterologous polynucleotides can be under the control of a lac operon. Expression of the heterologous polynucleotides can be under the control of an anaerobic-inducible promoter (e.g., the E. coli endogenous promoter Pfnrs). Expression of the heterologous polynucleotides can be under the control of a microaerobic-inducible promoter (e.g., the PVHb). Expression of the heterologous polynucleotides can be under the control of a Ptrc promoter. Bile Salt Hydrolase (BSH) In some embodiments, the heterologous polynucleotide encodes bile salt hydrolase (BSH). Thus, isolated native bacteria cells (or cultured population thereof) can be transformed with one or more heterologous polynucleotides that encode BSH. Transformation of isolated native bacteria cells (or cultured population thereof) with such heterologous polynucleotides can produce ENB-expressing ENB (i.e., ENB that can express BSH when administered into a receiving subject). Heterologous polynucleotides encoding one or more of the following BSH can be used in the present methods: Dubosiella newyorkensis–A0A1U7NKD7 BSH (DnBSH1), D. newyorkensis–A0A1U7NP31 BSH (DnBSH2), L. gasseri BSH (LgBSH), E. plexicaudatum BSH (EpBSH), Lachnospiraceae CAG-95 sp009917455 BSH (LCAG95BSH), Lachnospiraceae 14-2 sp000403315 BSH, B. uniformis– A0A3E5F5J9 BSH, and Lactobacillus salivarius BSH (LsBSH). For example, a heterologous polynucleotide encoding Lactobacillus salivarius BSH (LsBSH) can be used in the present methods. Additionally, or alternatively, a heterologous polynucleotide encoding D. newyorkensis–A0A1U7NKD7 BSH (DnBSH1) can be used in the present methods. Heterologous polynucleotides encode BSH, thus producing BSH-expressing ENB. BSH-expressing ENB produced by the present methods can express BSH when administered into a receiving subject. BSH expressed by the BSH-expressing ENB can help in prevention and / or treatment of CRC by promoting deconjugation of one or more bile acids (BAs). BSH expressed by the BSH-expressing ENB can also help in prevention and / or treatment of CRC by activating FXR signaling. BSH expressed by the BSH-expressing ENB can activate FXR signaling by reducing the expression of FXR antagonists (e.g., TbMCA). BSH expressed by the BSH-expressing ENB can Attorney Docket No.15670-0408WO1 also activate FXR signaling by increasing the expression of one or more FXR targets, including Nr0b2 (Shp), Fgf15, Slc51a, and Slc51b. For example, one or more heterologous polynucleotides encoding L. salivarius BSH (LsBSH) can be engineered into native E. coli chassis, EcAZ, to produce BSH- expressing ENB, EcAZLsBSH+. EcAZLsBSH+can express BSH when administered into a receiving subject. BSH expressed by EcAZLsBSH+can help in prevention and / or treatment of CRC by promoting deconjugation of one or more bile acids (BAs). BSH expressed by EcAZLsBSH+can also help in prevention and / or treatment of CRC by activating FXR signaling. BSH expressed by EcAZLsBSH+can activate FXR signaling by reducing the expression of FXR antagonists (e.g., TbMCA). BSH expressed by EcAZLsBSH+can also activate FXR signaling by increasing the expression of one or more FXR targets, including Nr0b2 (Shp), Fgf15, Slc51a, and Slc51b. Also, one or more heterologous polynucleotides encoding D. newyorkensis– A0A1U7NKD7 BSH (DnBSH1) can be engineered into native E. coli chassis, EcAZ, to produce BSH-expressing ENB, EcAZDnBSH1. EcAZDnBSH1can express BSH when administered into a receiving subject. BSH expressed by EcAZDnBSH1can help in prevention and / or treatment of CRC by promoting deconjugation of one or more bile acids (BAs). BSH expressed by EcAZDnBSH1can also help in prevention and / or treatment of CRC by activating FXR signaling. BSH expressed by EcAZDnBSH1can activate FXR signaling by reducing the expression of FXR antagonists (e.g., TbMCA). BSH expressed by EcAZDnBSH1can also activate FXR signaling by increasing the expression of one or more FXR targets, including Nr0b2 (Shp), Fgf15, Slc51a, and Slc51b. Also, one or more heterologous polynucleotides encoding L. gasseri BSH (LgBSH) can be engineered into native E. coli chassis, EcAZ, to produce BSH- expressing ENB, EcAZLgBSH. EcAZLgBSHcan express BSH when administered into a receiving subject. BSH expressed by EcAZLgBSHcan help in prevention and / or treatment of CRC by promoting deconjugation of one or more bile acids and / or by activating FXR signaling. Also, one or more heterologous polynucleotides encoding D. newyorkensis– A0A1U7NP31 BSH (DnBSH2) can be engineered into native E. coli chassis, EcAZ, to produce BSH-expressing ENB, EcAZDnBSH2. EcAZDnBSH2can express BSH when administered into a receiving subject. BSH expressed by EcAZDnBSH2can help in Attorney Docket No.15670-0408WO1 prevention and / or treatment of CRC by promoting deconjugation of one or more bile acids and / or by activating FXR signaling. Also, one or more heterologous polynucleotides encoding E. plexicaudatum BSH (EpBSH) can be engineered into native E. coli chassis, EcAZ, to produce BSH- expressing ENB, EcAZEpBSH. EcAZEpBSHcan express BSH when administered into a receiving subject. BSH expressed by EcAZEpBSHcan help in prevention and / or treatment of CRC by promoting deconjugation of one or more bile acids and / or by activating FXR signaling. Also, one or more heterologous polynucleotides encoding Lachnospiraceae CAG-95 sp009917455 BSH (LCAG95BSH) can be engineered into native E. coli chassis, EcAZ, to produce BSH-expressing ENB, EcAZLCAG95BSH. EcAZLCAG95BSHcan express BSH when administered into a receiving subject. BSH expressed by EcAZLCAG95BSHcan help in prevention and / or treatment of CRC by promoting deconjugation of one or more bile acids and / or by activating FXR signaling. Methods of Treatment and / or Prevention Described herein are methods for treating and / or preventing colorectal cancer (CRC) in a subject in need thereof by administering to the subject ENB of the present disclosure or a population (or at least a part of the population) thereof. Subjects who are administered ENB of the present disclosure or a population (or at least a part of the population) thereof can be receiving subjects. For use in the present methods, “ENB” and “population of ENB” and “a part of the population of ENB” and “at least a part of the population of ENB” can be used interchangeably. Thus, described herein are methods for treating CRC in a subject by administering to the subject ENB of the present disclosure. A subject who is treated by the present methods can be a subject with CRC (e.g., a subject who is diagnosed with CRC, a subject who has been previously diagnosed with CRC, and / or a subject who shows one or more symptoms of CRC). For example, described herein are methods for treating CRC in a subject, the method comprising one or more of the following steps: culturing or having cultured an isolated native bacteria cell from a donating subject to yield a cultured population of the isolated bacteria cell; transforming or having transformed the cultured population with one or more polynucleotides heterologous to the bacteria cell to generate a population of Attorney Docket No.15670-0408WO1 transformed bacteria cells comprising the heterologous polynucleotide(s); and administering or having administered at least a portion of the population of transformed bacteria cells comprising the heterologous polynucleotide(s) to a receiving subject, and wherein the population of transformed bacteria cells colonizes in or on the receiving subject and expresses a heterologous protein (e.g., the protein that is encoded by the heterologous polynucleotide(s)), thereby treating CRC in the receiving subject. In some of these methods, the one or more heterologous polynucleotides encode bile salt hydrolase (BSH). For example, the one or more heterologous polynucleotides can encode L. salivarius BSH (LsBSH) or D. newyorkensis–A0A1U7NKD7 BSH (DnBSH1). Also described herein are methods for preventing CRC in a subject by administering to the subject ENB of the present disclosure. Preventing CRC can include reducing the risk of occurrence of CRC and / or delaying the occurrence of CRC. For example, described herein are methods for reducing the risk of occurrence of CRC and / or delaying the occurrence of CRC in a subject by administering to the subject ENB of the present disclosure. The present methods can be used for preventing CRC in a subject who is at risk for developing CRC. Subjects at risk for developing CRC can include subjects with genetic predisposition for CRC (e.g., subjects with familial adenomatous polyposis syndrome or Lynch syndrome) and / or subjects with a disease that increases the risk for CRC (e.g., subjects with inflammatory bowel disease (IBD)). Thus, described herein are methods for reducing the risk of occurrence or delaying the occurrence of CRC in a subject, the method comprising one or more of the following steps: culturing or having cultured an isolated native bacteria cell from a donating subject to yield a cultured population of the isolated bacteria cell; transforming or having transformed the cultured population with one or more polynucleotides heterologous to the bacteria cell to generate a population of transformed bacteria cells comprising the heterologous polynucleotide(s); and administering or having administered at least a portion of the population of transformed bacteria cells comprising the heterologous polynucleotide(s) to a receiving subject, wherein the population of transformed bacteria cells colonizes in or on the receiving subject and expresses a heterologous protein (e.g., the protein that is encoded by the heterologous polynucleotide(s)), thereby reducing the risk of occurrence or delaying the occurrence of CRC in the Attorney Docket No.15670-0408WO1 receiving subject. In some of these methods, the one or more heterologous polynucleotides encode bile salt hydrolase (BSH). For example, the one or more heterologous polynucleotides can encode L. salivarius BSH (LsBSH) or D. newyorkensis–A0A1U7NKD7 BSH (DnBSH1). Methods for treating CRC and / or preventing CRC (e.g., methods for reducing the risk of occurrence or delaying the occurrence of CRC), as described herein, can further comprise isolating native bacteria cells from a donating subject. For preparation of ENB, native bacteria cells can be isolated from a subject, or native bacteria cells previously isolated from a subject can be used. The native bacteria cells can be isolated from one or more biological samples of a donating subject. Thus, methods for treating CRC and / or preventing CRC (e.g., methods for reducing the risk of occurrence or delaying the occurrence of CRC), as described herein, can further comprise obtaining one or more biological samples from a subject (e.g., from a donating subject). Biological samples can comprise bodily excretions (e.g., saliva, mucus, urine, stool, tear, and / or semen), biopsy or swab of a surface (e.g., biopsy or swab of mucosal GI tract, mouth / pharynx / nares, urogenital track, skin, anus / rectum, cheek / mouth, and / or eye), and / or pathological specimen (e.g., tumor tissues). ENB prepared from native bacteria cells isolated from one or more of these biological samples can be administered to a receiving subject for use in the present methods. For example, ENB prepared from native bacteria cells isolated from stool sample of a donating subject can be administered to a receiving subject. Autologous In some instances of the present methods, autologous ENB are administered to a subject. For example, ENB produced by the present methods can be introduced to the same subject (i.e., same individual) from whom the native bacteria cells are / were isolated. In such instances, the receiving subject is the same (i.e., same individual) as the donating subject. Thus, ENB generated from native bacteria cells isolated from a human subject can be administered to the same human subject. For example, described herein are methods for treating CRC in a subject, the method comprising one or more of the following steps: culturing or having cultured an isolated native bacteria cell from a donating subject to yield a cultured population of the isolated bacteria cell; transforming or having transformed the cultured population with one or Attorney Docket No.15670-0408WO1 more polynucleotides heterologous to the bacteria cell to generate a population of transformed bacteria cells comprising the heterologous polynucleotide(s); and administering or having administered at least a portion of the population of transformed bacteria cells comprising the heterologous polynucleotide(s) to a receiving subject, wherein the receiving subject is the same as the donating subject, and wherein the population of transformed bacteria cells colonizes in or on the receiving subject and expresses a heterologous protein (e.g., the protein that is encoded by the heterologous polynucleotide(s)), thereby treating CRC in the receiving subject. Also described herein are methods for reducing the risk of occurrence or delaying the occurrence of CRC in a subject, the method comprising one or more of the following steps: culturing or having cultured an isolated native bacteria cell from a donating subject to yield a cultured population of the isolated bacteria cell; transforming or having transformed the cultured population with one or more polynucleotides heterologous to the bacteria cell to generate a population of transformed bacteria cells comprising the heterologous polynucleotide(s); and administering or having administered at least a portion of the population of transformed bacteria cells comprising the heterologous polynucleotide(s) to a receiving subject, wherein the receiving subject is the same as the donating subject, and wherein the population of transformed bacteria cells colonizes in or on the receiving subject and expresses a heterologous protein (e.g., the protein that is encoded by the heterologous polynucleotide(s)), thereby reducing the risk of occurrence or delaying the occurrence of CRC in the receiving subject. In some of these methods, the one or more heterologous polynucleotides encode bile salt hydrolase (BSH). For example, the one or more heterologous polynucleotides can encode L. salivarius BSH (LsBSH) or D. newyorkensis–A0A1U7NKD7 BSH (DnBSH1). Allogeneic In some instances of the present methods, allogeneic ENB are administered to a subject. For example, ENB produced by the present methods can be introduced to a subject who is different from the donating subject but is of the same species as the donating subject. A donating subject is a subject from whom the native bacteria cells are isolated. Thus, ENB generated from native bacteria cells isolated from a human Attorney Docket No.15670-0408WO1 subject can be administered to a different human subject. For example, described herein are methods for treating CRC in a subject, the method comprising one or more of the following steps: culturing or having cultured an isolated native bacteria cell from a donating subject to yield a cultured population of the isolated bacteria cell; transforming or having transformed the cultured population with one or more polynucleotides heterologous to the bacteria cell to generate a population of transformed bacteria cells comprising the heterologous polynucleotide(s); and administering or having administered at least a portion of the population of transformed bacteria cells comprising the heterologous polynucleotide(s) to a receiving subject, wherein the receiving subject is different from the donating subject but is of the same species as the donating subject, and wherein the population of transformed bacteria cells colonizes in or on the receiving subject and expresses a heterologous protein (e.g., the protein that is encoded by the heterologous polynucleotide(s)), thereby treating CRC in the receiving subject. Also described herein are methods for reducing the risk of occurrence or delaying the occurrence of CRC in a subject, the method comprising one or more of the following steps: culturing or having cultured an isolated native bacteria cell from a donating subject to yield a cultured population of the isolated bacteria cell; transforming or having transformed the cultured population with one or more polynucleotides heterologous to the bacteria cell to generate a population of transformed bacteria cells comprising the heterologous polynucleotide(s); and administering or having administered at least a portion of the population of transformed bacteria cells comprising the heterologous polynucleotide(s) to a receiving subject, wherein the receiving subject is different from the donating subject but is of the same species as the donating subject, and wherein the population of transformed bacteria cells colonizes in or on the receiving subject and expresses a heterologous protein (e.g., the protein that is encoded by the heterologous polynucleotide(s)), thereby reducing the risk of occurrence or delaying the occurrence of CRC in the receiving subject. In some of these methods, the one or more heterologous polynucleotides encode bile salt hydrolase (BSH). For example, the one or more heterologous polynucleotides can encode L. salivarius BSH (LsBSH) or D. newyorkensis–A0A1U7NKD7 BSH (DnBSH1). Attorney Docket No.15670-0408WO1 Administration ENB of the present disclosure or a population (or at least a part of the population) thereof can be administered to a receiving subject by local and / or systemic administration. System administration of ENB can comprise enteral administration (e.g., orally (PO), rectally (PR, e.g., administration as a suppository), or through a tube such as a nasogastric (NG) tube, nasointestinal (NI) tube, or percutaneous endoscopic gastrostomy (PEG) tube), parenteral administration (e.g., by injections (e.g., intravenous, intramuscular, subcutaneous), infusions, or implantations), pulmonary administration, and / or topical / transdermal administration. Routes of administration for ENB can include, without limitation, oral (per as (P.O.)), rectal (e.g., administration as a suppository), vaginal, nasal or inhalation, topical contact (e.g., to skin or eyes), or intralesional administration to a receiving subject. For example, a population (or at least a part of a population) of ENB can be administered to a receiving subject orally and / or rectally. For oral administration to a receiving subject, the population of ENB can be administered via a gastric tube or in an edible composition. The edible composition can comprise one or more of: pills, tablets, gel capsules, chewable, gummies, yogurt, milk, ice cream, smoothies, vegetable puree, fruit puree, sorbet, oatmeal, and / or beverage. The beverage can be a buffered solution. ENB prepared from native bacteria cells isolated from any of the biological samples of a donating subject can be administered to a receiving subject by any of the routes. ENB prepared from native bacteria cells isolated from a biological sample of a donating subject can be administered to a different tissue or surface from which the biological sample was obtained. For example, ENB prepared from native bacteria cells isolated from a stool sample of a donating subject can be administered to a receiving subject by topical contact. ENB prepared from native bacteria cells isolated from a biological sample of a donating subject can also be administered to the same tissue or surface from which the biological sample was obtained. Also, native bacteria cells can be obtained from a biological sample from the GI tract (e.g., saliva, stool, biopsy or swab of mucosal GI tract, biopsy or swab of mouth, biopsy or swab of anus / rectum, biopsy or swab of cheek / mouth, intestinal tumor tissues, and / or CRC tumor tissues) of a donating subject, and the population of ENB can be administered to a receiving subject orally or rectally. Attorney Docket No.15670-0408WO1 In the present methods, administration of ENB to a receiving subject can include self-administration. Administration of ENB to a receiving subject can also be performed by a health worker (e.g., a medical professional (e.g., a physician, nurse, physician’s assistant)) or a person controlling the medical care of the subject (e.g., controlling and / or permitting the administration of the ENB to the subject). In the present methods, ENB can also be caused to be administered to a reference subject, and this can refer to administration of ENB to the receiving subject by a health worker (e.g., a medical professional (e.g., a physician, nurse, physician’s assistant)) or a person controlling the medical care of the subject (e.g., controlling and / or permitting the administration of the ENB to the subject). Following administration to a receiving subject, ENB of the present disclosure can colonize in or on the receiving subject and expresses a heterologous protein (e.g., the protein that is encoded by the heterologous polynucleotide(s)). Thus, following administration to a receiving subject, the population of transformed bacteria cells can colonize (e.g., can establish themselves and divide (e.g., multiply)) at or in the vicinity of the lumen or tissue of the receiving subject to which they have been administered, such that they remain, at least for 48 hours (i.e., 2 days), 3 days, 4 days, 5 days, 6 days, 7 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 10 weeks, 15 weeks, 20 weeks, 25 weeks, 30 weeks, 35 weeks, 40 weeks, 45 weeks, 50 weeks, 55 weeks, 60 weeks, 75 weeks, 100 weeks, or 125 weeks, or longer, e.g., for the duration of the life of the receiving subject or for a time period that is within a range defined by any two of the aforementioned time periods. For example, following administration to a receiving subject, the population of transformed bacteria cells can colonize (e.g., can establish themselves and divide (e.g., multiply)) at or in the vicinity of the lumen or tissue of the receiving subject to which they have been administered, such that they remain, at least for 6 weeks, or longer. In the present methods, a population (or at least a part of the population) of ENB comprising at least or at least about 106, 107, 108, 109, 1010, 1011, 1012, 1013transformed bacteria cells can be administered to a receiving subject at a time. ENB of the present disclosure or a population (or at least a part of the population) thereof can be administered to a receiving subject one time (e.g., a single administration). Alternatively, ENB of the present disclosure or a population (or at least a part of the population) thereof can be administered to a receiving subject multiple times (e.g., 2 Attorney Docket No.15670-0408WO1 times, 3 times, 4 times, 5 times, 6 times, or more). Multiple administrations of the ENB can be at hourly, daily, weekly, bi-weekly, monthly, or bi-monthly intervals. In some instances of the methods, administration of the ENB does not alter the microbiome of the receiving subject. The methods described herein can further comprise administration of one or more additional therapies. For example, the present methods can further comprise administration of one or more additional cancer therapies and dietary interventions. Additional cancer therapies can comprise one or more of: surgery, radiation therapy, blood stem cell transplant, bone marrow transplant, hypothermia, photodynamic therapy, chemotherapy, immunotherapy, hormone therapy, and / or targeted therapy. For example, additional cancer therapies can comprise additional therapeutic agents (e.g., one or more of chemotherapy, immunotherapy, hormone therapy, and / or targeted therapy). Thus, the present methods can further comprise administration of one or more additional therapeutic agents (e.g., anti-cancer therapeutic agents) to the receiving subjects. The additional therapeutic agents can comprise chemotherapeutic agents (e.g., alkylating agents, antimetabolites, anti-microtubule agents, topoisomerase inhibitors, cytotoxic antibiotics, and / or a combination of 5- fluorouracil, folinic acid, and oxaliplatin); immunotherapeutic agents (e.g., checkpoint inhibitors, T-cell transfer therapy, monoclonal antibodies, cancer vaccines, and / or immune system modulators); radiotherapeutic agents; hormone therapeutic agents; and / or targeted therapeutic agents (e.g., small molecule drugs and / or monoclonal antibodies). The present methods can also comprise co-administration(s) and / or concurrent administration(s). Co-administration or concurrent administration can refer to administration of multiple populations of ENB such that the multiple populations of ENB can simultaneously achieve a physiological effect. Co-administration or concurrent administration can also refer to administration of one or more populations of ENB with one or more additional therapeutic agents, such that the population(s) of ENB and the additional therapeutic agent(s) can simultaneously achieve a physiological effect. For co-administration or concurrent administration, the population(s) of ENB and / or the additional therapeutic agent(s) can be administered together (e.g., as part of a single pharmaceutical composition or simultaneously in separate pharmaceutical compositions). Alternatively, for co-administration or Attorney Docket No.15670-0408WO1 concurrent administration, the population(s) of ENB and / or the additional therapeutic agent(s) can be administered separately, e.g., administration of one can precede the administration of the other. Simultaneous physiological effect need not necessarily require presence of both agents (e.g., presence of multiple populations of ENB; or presence of the population(s) of ENB and the additional therapeutic agent(s)) in the circulation at the same time. However, in some instances, co-administration can result in both agents (e.g., presence of multiple populations of ENB; or presence of the population(s) of ENB and the additional therapeutic agent(s)) being simultaneously present in the body (e.g., in the plasma) of the receiving subject at a significant fraction (e.g., 20% or greater, such as 30%, 40%, 50% or greater (e.g., 50%, 60%, 70%, 80%, or 90% or greater)) of their maximum serum concentration for any given dose. Compositions Also described herein are compositions comprising the ENB of the present disclosure or a population (or at least a part of the population) thereof. For example, the ENB of the present disclosure or a population (or at least a part of the population) thereof can be formulated into compositions (e.g., bacterial compositions) for administration to subjects (e.g., human subjects and other mammalian subjects) in need thereof. The compositions can be combined with additional active and / or inactive materials in order to produce a final product, which can be in single dosage unit or in a multi-dose format. In some embodiments, the compositions comprise one or more populations of ENB, as described herein. In some embodiments, the compositions comprise one or more ENB populations and one or more prebiotics. The composition(s) can include different types of carriers depending on whether it is to be administered in solid or liquid state. The compositions can be administered orally, intravaginally, intrarectally, topically (e.g., including into the eye or conjunctiva), intratumorally, via vesicle instillation (e.g., into the bladder), intralesionally, intranasally, topically, or buccally. The compositions can be administered via food, drink, capsule, gavage, enema, suppository, infusion, continuous infusion, localized perfusion bathing target cells directly, via a catheter, via a lavage, in lipid compositions (e.g., liposomes), as an aerosol, or by other method or any combination of the foregoing as would be known to one of ordinary skill in the Attorney Docket No.15670-0408WO1 art (see, for example, Lloyd V. Allen, Jr., Remington: The Science and Practice of Pharmacy, 22nd Edition, 2012, Pharmaceutical Press, incorporated herein by reference in its entirety). The compositions can comprise at least one prebiotic carbohydrate. A “carbohydrate” refers to a sugar or polymer of sugars. The terms “saccharide”, “polysaccharide”, “carbohydrate”, and “oligosaccharide” can be used interchangeably. Most carbohydrates are aldehydes or ketones with many hydroxyl groups, usually one on each carbon atom of the molecule. Carbohydrates generally have the molecular formula CnH2nOn. A carbohydrate can be a monosaccharide, a disaccharide, trisaccharide, oligosaccharide, or polysaccharide. The most basic carbohydrate is a monosaccharide, such as glucose, sucrose, galactose, mannose, ribose, arabinose, xylose, and fructose. Disaccharides are two joined monosaccharides. Illustrative disaccharides include sucrose, maltose, cellobiose, and lactose. Typically, an oligosaccharide includes between three and six monosaccharide units (e.g., raffinose, or stachyose), and polysaccharides include six or more monosaccharide units. Exemplary polysaccharides include starch, glycogen, and / or cellulose. Carbohydrates can contain modified saccharide units, such as 2'- deoxyribose wherein a hydroxyl group is removed, 2'-fluororibose wherein a hydroxyl group is replaced with a fluorine, or N-acetylglucosamine, a nitrogen-containing form of glucose (e.g., 2'-fluororibose, deoxyribose, and / or hexose). Carbohydrates can exist in many different forms, for example, conformers, cyclic forms, acyclic forms, stereoisomers, tautomers, anomers, and / or isomers. The compositions can comprise at least one lipid. As used herein, a “lipid” includes fats, oils, triglycerides, cholesterol, phospholipids, fatty acids in any form including free fatty acids. Fats, oils and fatty acids can be saturated, unsaturated (cis or trans) or partially unsaturated (cis or trans). In some embodiments, the lipid comprises at least one fatty acid selected from lauric acid (12:0), myristic acid (14:0), palmitic acid (16:0), palmitoleic acid (16: 1), margaric acid (17:0), heptadecenoic acid (17: 1), stearic acid (18:0), oleic acid (18: 1), linoleic acid (18:2), linolenic acid (18:3), octadecatetraenoic acid (18:4), arachidic acid (20:0), eicosenoic acid (20: 1), eicosadienoic acid (20:2), eicosatetraenoic acid (20:4), eicosapentaenoic acid (20:5) (EPA), docosanoic acid (22:0), docosenoic acid (22: 1), docosapentaenoic acid (22:5), docosahexaenoic acid (22:6) (DHA), and / or tetracosanoic acid (24:0). In some Attorney Docket No.15670-0408WO1 embodiments, the composition comprises at least one modified lipid, for example, a lipid that has been modified by cooking. The compositions can comprise at least one supplemental mineral or mineral source. Examples of minerals include, without limitation: chloride, sodium, calcium, iron, chromium, copper, iodine, zinc, magnesium, manganese, molybdenum, phosphorus, potassium, and / or selenium. Suitable forms of any of the foregoing minerals include soluble mineral salts, slightly soluble mineral salts, insoluble mineral salts, chelated minerals, mineral complexes, non-reactive minerals such as carbonyl minerals, and / or reduced minerals, and combinations thereof. The compositions can comprise at least one supplemental vitamin and / or an antioxidant. The at least one vitamin can be fat-soluble or water-soluble vitamins. Suitable vitamins include but are not limited to vitamin C, vitamin A, vitamin E, vitamin B12, vitamin K, riboflavin, niacin, vitamin D, vitamin B6, folic acid, pyridoxine, thiamine, pantothenic acid, and / or biotin. Suitable forms of any of the foregoing are salts of the vitamin, derivatives of the vitamin, compounds having the same or similar activity of the vitamin, and metabolites of the vitamin. The compositions can comprise an excipient. Non-limiting examples of suitable excipients include a buffering agent, a preservative, a stabilizer, a binder, a compaction agent, a lubricant, a dispersion enhancer, a disintegration agent, a flavoring agent, a sweetener, and / or a coloring agent. The compositions can comprise a buffering agent as an excipient. Non- limiting examples of suitable buffering agents include sodium citrate, magnesium carbonate, magnesium bicarbonate, calcium carbonate, and / or calcium bicarbonate. The compositions can comprise a preservative as an excipient. Non-limiting examples of suitable preservatives include antioxidants, such as alpha-tocopherol and ascorbate, and antimicrobials, such as parabens, chlorobutanol, and / or phenol. In cases where a composition contains anerobic bacteria strains, the excipients can be selected to prevent exposure of the bacterial strain to oxygen. The compositions can comprise a binder as an excipient. Non-limiting examples of suitable binders include starches, pregelatinized starches, gelatin, polyvinylpyrolidone, cellulose, methylcellulose, sodium carboxymethylcellulose, ethylcellulose, polyacrylamides, polyvinyloxoazolidone, polyvinylalcohols, C12-C18 Attorney Docket No.15670-0408WO1 fatty acid alcohol, polyethylene glycol, polyols, saccharides, or oligosaccharides, and combinations thereof. The compositions can comprise a lubricant as an excipient. Non-limiting examples of suitable lubricants include magnesium stearate, calcium stearate, zinc stearate, hydrogenated vegetable oils, sterotex, polyoxyethylene monostearate, talc, polyethyleneglycol, sodium benzoate, sodium lauryl sulfate, magnesium lauryl sulfate, and / or light mineral oil. The compositions can comprise a a dispersion enhancer as an excipient. Non- limiting examples of suitable dispersants include starch, alginic acid, polyvinylpyrrolidones, guar gum, kaolin, bentonite, purified wood cellulose, sodium starch glycolate, isoamorphous silicate, and / or microcrystalline cellulose as high HLB emulsifier surfactants. The compositions can comprise a disintegrant as an excipient. The disintegrant can be a non-effervescent disintegrant. Nonlimiting examples of suitable non-effervescent disintegrants include starches such as corn starch, potato starch, pregelatinized and / or modified starches thereof, sweeteners, clays, such as bentonite, micro-crystalline cellulose, alginates, sodium starch glycolate, or gums such as agar, guar, locust bean, karaya, pecitin, and / or tragacanth. The disintegrant can be an effervescent disintegrant. Non-limiting examples of suitable effervescent disintegrants include sodium bicarbonate in combination with citric acid, and / or sodium bicarbonate in combination with tartaric acid. The excipient can comprise a flavoring agent. Flavoring agents can be synthetic flavor oils and / or flavoring aromatics; natural oils; extracts from plants, leaves, flowers, and / or fruits; and combinations thereof. The flavoring agent can be cinnamon oils; oil of wintergreen; peppermint oils; clover oil; hay oil; anise oil; eucalyptus; vanilla; citrus oil such as lemon oil, orange oil, grape and / or grapefruit oil; and / or fruit essences including apple, peach, pear, strawberry, raspberry, cherry, plum, pineapple, and / or apricot. The excipient can comprise a sweetener. Non-limiting examples of suitable sweeteners include glucose (corn syrup), dextrose, invert sugar, fructose, and / or mixtures thereof (when not used as a carrier); saccharin and / or its various salts such as the sodium salt; dipeptide sweeteners such as aspartame; dihydrochalcone compounds, glycyrrhizin; Stevia Rebaudiana (Stevioside); chloro derivatives of Attorney Docket No.15670-0408WO1 sucrose such as sucralose; and / or sugar alcohols such as sorbitol, mannitol, sylitol, and the like. Also contemplated are hydrogenated starch hydrolysates and the synthetic sweetener 3,6-dihydro-6-methy 1-1,2,3-oxathiazin-4-one-2,2-di oxide, particularly the potassium salt (acesulfame-K), and / or sodium and calcium salts thereof. The compositions can comprise a coloring agent. Nonlimiting examples of suitable color agents include food, drug and cosmetic colors (FD&C), drug and cosmetic colors (D&C), and / or external drug and cosmetic colors (Ext. D&C). The coloring agents can be used as dyes or their corresponding lakes. The weight fraction of the excipient or combination of excipients in the formulation can be about or at 99% or less (but not zero), such as about or at 95% or less (but not zero), about or at 90% or less (but not zero), about or at 85% or less (but not zero), about or at 80% or less (but not zero), about or at 75% or less (but not zero), about or at 70% or less (but not zero), about or at 65% or less (but not zero), about or at 60% or less (but not zero), about or at 55% or less (but not zero), about or at 50% or less (but not zero), about or at 45% or less (but not zero), about or at 40% or less (but not zero), about or at 35% or less (but not zero), about or at 30% or less (but not zero), about or at 25% or less (but not zero), about or at 20% or less (but not zero), about or at 15% or less (but not zero), about or at 10% or less (but not zero), about or at 5% or less (but not zero), about or at 2% or less (but not zero), or about or at I% or less (but not zero) of the total weight of the composition. Solid forms of the compositions (e.g., for oral administration to a receiving subject) can include capsules, tablets, caplets, pills, troches, lozenges, powders, and / or granules. A capsule can comprise a core material comprising the composition (e.g., bacterial composition) and a shell wall that encapsulates the core material. The core material can comprise at least one of a solid, a liquid, and / or an emulsion. The shell wall material can comprise at least one of a soft gelatin, a hard gelatin, and / or a polymer. Suitable polymers include, but are not limited to: cellulosic polymers such as hydroxypropyl cellulose, hydroxyethyl cellulose, hydroxypropyl methyl cellulose (HPMC), methyl cellulose, ethyl cellulose, cellulose acetate, cellulose acetate phthalate, cellulose acetate trimellitate, hydroxypropylmethyl cellulose phthalate, hydroxypropylmethyl cellulose succinate and carboxymethylcellulose sodium; acrylic acid polymers and / or copolymers, such as those formed from acrylic acid, methacrylic Attorney Docket No.15670-0408WO1 acid, methyl acrylate, ammonia methylacrylate, ethyl acrylate, methyl methacrylate and / or ethyl methacrylate (e.g., those copolymers sold under the trade name “Eudragit”); vinyl polymers and / or copolymers such as polyvinyl pyrrolidone, polyvinyl acetate, polyvinylacetate phthalate, vinylacetate crotonic acid copolymer, and / or ethylenevinyl acetate copolymers; and / or shellac (purified lac). At least one polymer can function as taste-masking agents. Tablets, pills, and the like can be compressed, multiply compressed, multiply layered, and / or coated. The coating can be single or multiple. The coating material can comprise at least one of a saccharide, a polysaccharide, and / or glycoproteins extracted from at least one of a plant, a fungus, and / or a microbe. Nonlimiting examples include corn starch, wheat starch, potato starch, tapioca starch, cellulose, hemicellulose, dextrans, maltodextrin, cyclodextrins, inulins, pectin, mannans, gum arabic, locust bean gum, mesquite gum, guar gum, gum karaya, gum ghatti, tragacanth gum, funori, carrageenans, agar, alginates, chitosans, or gellan gum. The coating material can comprise a protein. The coating material can comprise at least one of a fat and an oil. The fat and the oil can have a high melting temperature. The fat and the oil can be hydrogenated or partially hydrogenated. The fat and the oil can be derived from a plant. The fat and the oil can comprise at least one of glycerides, free fatty acids, and / or fatty acid esters. The coating material can comprise at least one edible wax. The edible wax can be derived from animals, insects, or plants. Non- limiting examples include beeswax, lanolin, bayberry wax, carnauba wax, and / or rice bran wax. Tablets and pills can additionally be prepared with enteric coatings. Solid forms of the compositions (e.g., for oral administration to a receiving subject) can include powders and / or granules. Powders or granules comprising the compositions disclosed herein can be incorporated into a food product. The food product can be a drink for oral administration. Non-limiting examples of a suitable drink include fruit juice, a fruit drink, an artificially flavored drink, an artificially sweetened drink, a carbonated beverage, a sports drink, a liquid diary product, a shake, an alcoholic beverage, a caffeinated beverage, or infant formula. Other suitable products for oral administration include aqueous and nonaqueous solutions, emulsions, suspensions and / or solutions and / or suspensions reconstituted from non- effervescent granules, containing at least one of suitable solvents, preservatives, Attorney Docket No.15670-0408WO1 emulsifying agents, suspending agents, diluents, sweeteners, coloring agents, and / or flavoring agents. The food product can be a solid foodstuff. Suitable examples of a solid foodstuff include without limitation a food bar, a snack bar, a cookie, a brownie, a muffin, a cracker, ice cream or an ice cream bar, yogurt or a frozen yogurt bar. In some embodiments, the compositions disclosed herein are incorporated into a therapeutic food. The therapeutic food can be a ready-to-use food that optionally contains some or all essential macronutrients and micronutrients. In some embodiments, the compositions disclosed herein are incorporated into a supplementary food that is designed to be blended into an existing meal. The supplemental food or neutraceutical can contain some or all essential macronutrients and micronutrients. In some embodiments, the compositions disclosed herein are blended with or added to an existing food to fortify the food's protein nutrition. Examples include food staples (grain, salt, sugar, cooking oil, or margarine), beverages (coffee, tea, soda, waters, beer, liquor, or sports drinks), snacks, or sweets and other foods. In some embodiments, the compositions disclosed herein are filled into gelatin capsules for oral administration. For example, the capsule can be a 250 mg gelatin capsule containing from 10 (up to 100 mg) of lyophilized powder (e.g., from 108to 1011bacteria cells), 160 mg microcrystalline cellulose, 77.5 mg gelatin, and 2.5 mg magnesium stearate. In some embodiments, from 105to 1012bacteria cells can be used, e.g., 105to 107, 106to 107, or 108to 1010bacteria cells, with attendant adjustments of the excipients if necessary. In some embodiment, an enteric-coated capsule or tablet or with a buffering or protective composition can be used. The compositions, with or without one or more prebiotics can be formulated for oral or gastric administration, typically to a mammalian subject. In some embodiments, the composition is formulated for oral administration as a solid, semi- solid, gel, or liquid form, such as in the form of a pill, tablet, capsule, or lozenge. In some embodiments, such formulations contain or are coated by an enteric coating to protect the bacteria through the stomach and small intestine, although spores are generally resistant to the stomach and small intestines. In some embodiments, the bacterial compositions, with or without one or more prebiotics, can be formulated with a germinant to enhance engraftment, or efficacy. In some embodiments, the Attorney Docket No.15670-0408WO1 bacterial compositions can be co-formulated or co-administered with prebiotic substances, to enhance engraftment or efficacy. In some embodiments, bacterial compositions can be co-formulated or co-administered with prebiotic substances, to enhance engraftment or efficacy. The bacterial compositions, with or without one or more prebiotics, can be formulated to be effective in a given mammalian subject in a single administration or over multiple administrations. For example, a single administration can be substantially effective to reduce or increase a monitored symptom or a biomarker of a targeted disease condition, reduce one or more symptoms of CRC, in a mammalian subject to whom the composition is administered. Substantially effective means that the monitored symptom or biomarker is reduced or increased in the subject by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or greater than 99% following administration of the composition. The composition can be formulated such that a single oral dose contains at least or at least about 1x104colony forming units of the bacteria cells, and a single oral dose can contain about or at least about 1x104, 1x105, 1x106, 1x107, 1x108, 1x109, 1x1010, 1x1011, 1x1012, 1x1013, 1x1014, 1x1015, or greater than 1x1015CFUs of the bacteria cells. For example, the concentration of cells of a given strain, or the aggregate of all strains, can be, e.g., 1x104, 1x105, 1x106, 1x107, 1x108, 1x109, 1x1010, 1x101, 1x1012, 1x1013, 1x1014, 1x1015, or greater than 1x1015viable bacteria cells (e.g., CFUs) per gram of composition or per administered dose. The composition can be formulated to contain at least or at least about 0.5%, 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or greater than 90% bacteria cells on a mass basis. In some formulations, the administered dose does not exceed 200, 300, 400, 500, 600, 700, 800, 900 milligrams or 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, or 1.9 grams in mass. Kits Also described herein are kits comprising one or more containers comprising one or more populations of ENB described herein. Also described herein are kits comprising one or more containers comprising one or more compositions (e.g., compositions comprising one or more populations of ENB) described herein. The containers can comprise multiple unitary portions or doses of the compositions. For Attorney Docket No.15670-0408WO1 example, the containers can comprise multiple unitary portions or doses of compositions comprising populations of ENB that that been transformed to express one or more heterologous polynucleotides. The containers can contain edible compositions, e.g., food product, beverages, or capsules. The containers can contain unitary volumes of buffered solutions or suspensions comprising populations of ENB. The containers can contain unitary doses of lyophilized ENBs, optionally with buffered solution for reconstituting. EXAMPLES The invention is further described in the following examples, which do not limit the scope of the invention described in the claims. Example 1. BSH-Expressing EcAZ Strains Differentially Activate FXR Signaling in the Ileum Through the targeted and untargeted search of bile salt hydrolase (BSH) transcripts, we show there is species-level variability in BSH expression, and some microbes may have higher BSH expression under certain conditions. To go beyond correlation and mechanistically understand the potential physiological effects of these transcripts, we expressed them in an engineered native bacteria chassis. Based on the species-level variation in BSH expression, we selected seven BSHs to be engineered into native bacteria using our previously characterized native Escherichia coli chassis, EcAZ, that expresses its target gene under a constitutively expressed promoter.12,43We chose this chassis due to its ability to stably colonize the gut after just a single gavage into fully conventional mice without the need of antibiotic pretreatment, which can affect the metabolic phenotype.44Engineered native bacteria can be used to introduce new functions into the gut lumen that can lead to luminal metabolome changes without detectable change in 16S composition, making them an ideal method to study specific functions in the gut microbiome.12,43The seven BSHs chosen for engineering were: (1) D. newyorkensis–A0A1U7NKD7 (DnBSH1), (2) D. newyorkensis–A0A1U7NP31 (DnBSH2), (3) L. gasseri BSH (LgBSH), (4) E. plexicaudatum BSH (EpBSH), (5) Lachnospiraceae CAG-95 sp009917455 BSH (LCAG95BSH), (6) Lachnospiraceae 14-2 sp000403315 BSH, and (7) B. uniformis–A0A3E5F5J9. We chose the two D. newyorkensis and one B. Attorney Docket No.15670-0408WO1 uniformis BSH for their diurnal expression differences under FT, the L. gasseri BSH for high enrichment under FA, and the E. plexicaudatum and two Lachnospiraceae BSHs, CAG-35095 sp009917455 and 14-2 sp000403315, for their consistent enrichment under NA conditions. Five out of seven BSHs were successfully engineered into the chassis (Figure 1A). The B. uniformis and Lachnospiraceae 14-2 sp000403315 BSH could not be engineered due to acquired mutations, potentially affecting the E. coli strain’s fitness. To investigate the differences in deconjugation among the five newly engineered native E. coli strains (BSH ENBs) compared to our previously described BSH-expressing ENB, EcAZ-2BSH+which contains a well-described BSH from Lactobacillus salivarius (BSH+),12,13,45each strain was cultured in rich media supplemented with one of ten bile acids (BAs) (glycocholic acid, GCA; glycochenodeoxycholic acid, GCDCA; glycodeoxycholic acid, GDCA; glycolithocholic acid, GLCA; glycoursodeoxycholic acid, GUDCA; taurocholic acid, TCA; taurochenodeoxycholic acid, TCDCA; taurodeoxycholic acid, TDCA; taurolithocholic acid, TLCA; tauroursodeoxycholic acid, TUDCA), and all metabolites were analyzed using untargeted liquid chromatography tandem mass spectrometry (LC-MS / MS)-based metabolomics at 0h and 48h (Figure 1B). There were notable differences in the abundance of known or predicted BAs between 0h and 48h, influenced by the combination of BSH ENB and the supplemented BAs in the culture (Student’s t-test, p < 0.05). We confirmed their annotations by MS / MS and retention time matching to the synthetic standards. We observed variations in substrate specificities among the BSH ENBs in their ability to reduce the levels of the supplemented BAs from baseline, our proxy for deconjugation, within the cultures (Student’s t-test, p < 0.05, Figure 1C). For example, while our new EcAZ-1DnBSH1was able to reduce the levels of most of the BAs (represented by peak areas), including both glycine- and taurine- conjugated forms, EcAZ-2BSH+was only able to reduce the levels of the taurine-conjugated BAs. Based on previously functional studies of BSH structure, the presence of a GTG motif in the BSH selectivity loop region of EcAZ-1DnBSH1and EcAZ-2BSH+suggested they would preferentially deconjugate taurine (Figure 1D).46However, our results indicate that EcAZ-1DnBSH1exhibits greater promiscuity by performing both taurine and glycine deconjugations. Similarly, EcAZ-1LCAG95BSHwas able to perform both taurine and glycine Attorney Docket No.15670-0408WO1 deconjugation, despite having the glycine-preferring SRG motif in the selectivity loop region (Figures 1C-1D). These findings indicate that the BSH ENBs display differential specificity in their ability to deconjugate bile acids and that other factors may potentially influence the deconjugating specificity of BSHs. Bile acids conjugated with amino acids, referred to as bacterial bile acid amidates (BBAAs), were among the BAs significantly different between 0h and 48h timepoints. BSHs can catalyze amidation reactions,36,47prompting our interest in investigating the variation in amidation activity among our BSH ENBs. We validated four of six BBAAs detected using retention time matching between the cultures of the ENBs and synthetic standards (Figure 1E). We did not validate Trp- and Tyr-UDCA because these BBAAs were present in both our empty chassis (EcAZ-1-cat) and the non-inoculated culture (no ENB), indicating they were not amidation products of the BSHs but rather background components in the rich media that our BSHs can potentially modulate in amount. We did, however, normalize our abundance to the “no ENB” negative control to find the abundance difference in BBAAs from 0h to 48h, our proxy for measuring amidation activity. Notably, we observed similar patterns of amidation activity between EcAZ-2BSH+and EcAZ-1DnBSH1 (Figure 1E). For example, isoleucine / leucine-conjugated ursodeoxycholic acid (Ile / Leu- UDCA) increased from 0h to 48h in the EcAZ-2BSH+ and EcAZ-1DnBSH1cultures supplemented with TUDCA and GUDCA (Student’s t-test, EcAZ-2BSH+-TUDCA: p = 0.040, EcAZ-1DnBSH1-TUDCA: p < 0.001, EcAZ-2BSH+-GUDCA: p < 0.001, EcAZ- 1DnBSH1-GUDCA: p = 0.015, Figure 1F). Similarly, alanine-conjugated ursodeoxycholic acid (Ala-UDCA) showed an increase from 0h to 48h in the EcAZ- 2BSH+cultures with TUDCA and GUDCA (Student’s t-test, EcAZ-2BSH+-TUDCA: p = 0.002, EcAZ-2BSH+-GUDCA: p = 0.002), but not in the EcAZ-1DnBSH1cultures (Student’s t-test, EcAZ-1DnBSH1-TUDCA: p = 0.65, EcAZ-1DnBSH1-GUDCA: p = 0.83, Figure 1G). These amidation patterns were also observed in other BA supplemented cultures. Lysine-conjugated cholic acid (Lys-CA) increased in the TCA supplemented culture for both strains (Student’s t-test, EcAZ-2BSH+: p = 0.025, EcAZ-1DnBSH1: p = 0.026, Figure 1H). In the GCDCA culture, lysine-conjugated chenodeoxycholic acid (Lys-CDCA) showed an increase for EcAZ-2BSH+(Student’s t-test, p < 0.001) but not for EcAZ-1DnBSH1(Student’s t-test, p = 0.26, Figure 1I). Considering there is some lag time in the timing of culture sample collections, our findings suggest that EcAZ- Attorney Docket No.15670-0408WO1 1DnBSH1may produce these amidated bile acids more rapidly than EcAZ-2BSH+. Except for Ala-UDCA which also increased in the EcAZ-1LCAG95BSH-TUDCA culture (Student’s t-test, p = 0.046), these BBAAs were uniquely produced by EcAZ-2BSH+and EcAZ-1DnBSH1. Despite having the most closely related BSHs protein sequences from the new BSH ENBs, EcAZ-1DnBSH1and EcAZ-1DnBSH2did not show similarity in deconjugation or amidation activities, highlighting the specificity of BSH activity. Overall, these findings indicate that EcAZ-2BSH+and EcAZ-1DnBSH1share similar deconjugation and amidation activities, which may result in similar phenotypic effects in vivo. Example 2. Engineered E. coli with the D. newyorkensis BSH1 has a more pronounced phenotypic effect than other BSHs The BA quantification revealed that EcAZ-2BSH+and EcAZ-1DnBSH1exhibit similar amidation activity. We also previously showed EcAZ-2BSH+can improve insulin sensitivity and glucose tolerance in fully conventional mice.12To investigate whether EcAZ-1DnBSH1can produce similar phenotypic effects to EcAZ-2BSH+, we introduced these strains, along with EcAZ-1LgBSH(BSH enriched under FA; however did not show amidation) and EcAZ-2 (empty chassis), into 8-week old fully conventional C57BL / 6 male mice fed a normal chow diet and then metabolically characterized them 6 weeks after a single gavage (Figure 2A). Consistent with our previous observations, all the BSH ENBs successfully colonized their hosts (Figure 2B). Although there were no significant differences in colonization among the BSH ENBs (n = 10 mice / group; pairwise Student’s t-test, α < 0.05), qualitative differences were observed in the ability of the fecal-isolated ENBs to deconjugate TDCA. Specifically, EcAZ-1DnBSH1exhibited less deconjugation compared to EcAZ-2BSH+and EcAZ-1LgBSH, which had more DCA precipitates (Figure 2C). In addition, we also observed no significant differences in food intake or mouse weights among the BSH ENBs throughout the experiment (n = 10 mice / group; pairwise Student’s t-test, α < 0.05, Figures 2D-2E). These results were consistent with the initial effects observed with the first BSH ENB, EcAZ-2BSH+.21Consistent with previous findings, engraftment with EcAZ-2BSH+led to a significant decrease in postprandial blood glucose (Student’s t-test, p = 0.011) when compared to the control, EcAZ-2 (Figure 2F). Similarly, EcAZ-1DnBSH1, the ENB Attorney Docket No.15670-0408WO1 expressing the BSH identified from the metatranscriptome of the FT mice, also significantly decreased postprandial blood glucose levels (Student’s t-test, p = 0.041), compared to EcAZ-2 (Figure 2F). However, EcAZ-1LgBSH, the ENB expressing the BSH identified from the metatranscriptome of FA mice, did not result in a decrease in glucose. Hence, the two BSHs that can produce BBAAs, one of which was identified through the metatranscriptome of TRF mice, have a pronounced effect on postprandial glucose in vivo. Interestingly, though we had previously shown that after 12 weeks of engraftment mice colonized with EcAZ-2BSH+had lower postprandial insulin, in this shorter 6 week experiment we did not observe a significant decrease in postprandial insulin levels (Student’s t-test, p = 0.22). However, mice engrafted with EcAZ- 1DnBSH1showed a significant reduction in postprandial insulin compared to EcAZ-2 (Student’s t-test, p = 0.025, Figure 2G). The effects of EcAZ-1LgBSHon postprandial insulin did not approach significance. Consistent with what we showed before, EcAZ- 2BSH+did not affect fasting blood glucose levels (Student’s t-test, p = 0.316). However, both EcAZ-1DnBSH1(Student’s t-test, p = 0.028) and EcAZ-1LgBSH(Student’s t-test, p = 0.0044) did, compared to EcAZ-2. The reductions in postprandial glucose and insulin induced by EcAZ-1DnBSH1suggests that this ENB can improve insulin sensitivity and glucose tolerance to a greater extent than the previously characterized EcAZ-2BSH+. We also determined the effects of the different BSHs on body composition. EcAZ-2BSH+, as well as EcAZ-1LgBSH(ENB expressing the BSH from FA mice), did not have an effect on either fat mass (Figure 2H) or lean mass (Figure 2I). However, EcAZ-1DnBSH1was the only strain that significantly decreased fat mass (Student’s t- test, p = 0.0075, Figure 2H) and increased lean mass (Student’s t-test, p = 0.033, Figure 2I) compared to the control EcAZ-2 in these fully conventional, non-obese mice. Thus, EcAZ-1DnBSH1can influence lipid deposition compared to EcAZ-2BSH+and may potentially offer greater overall benefits to metabolic health. Overall, mice engrafted with the ENB expressing the BSH identified from FT metatranscriptomics recapitulated many of the metabolic phenotypes observed in FT mice, including decreased fasting and postprandial blood glucose, decreased postprandial insulin levels, decreased fat mass, and increased lean mass. Attorney Docket No.15670-0408WO1 We also performed untargeted LC-MS / MS on fecal samples collected during the light (ZT3) and dark (ZT15) phases, 6 weeks post-gavage, and conducted a differential abundance analysis between the BSH ENBs and the empty chassis, separated by phase. We accounted for the phase of collection because, although the BSHs in these ENBs are under a constitutively expressed promoter, microbiome- or host-driven circadian effects could interact with the BSH ENBs to alter the BA pool. This analysis revealed that the ENBs induce changes to the fecal BA pool. Notably, serine-conjugated chenodeoxycholic acid (Ser-CDCA) was the only BBAA that exhibited higher abundance in EcAZ-1DnBSH1compared to the control, EcAZ-2, and this was exclusive to the light phase (Tukey’s LSD from linear mixed-effects model, p = 0.017). These findings suggest that EcAZ-1DnBSH1may confer metabolic benefits, either directly or indirectly, through the modification of BBAAs in the gut lumen. Example 3. Engineered Native E. coli Capable of Modifying Luminal Bile Acids Can Prevent Colorectal Cancer Development in High-Risk Hosts The objective of this study was to evaluate whether sustained delivery of specific microbial bile acid–modifying functions via engineered native E. coli can prevent or suppress colorectal cancer development in a genetic mouse model. Bile acid composition can promote or suppress colorectal cancer depending on context. Activation of the bile acid receptor FXR protects against tumor development in APC- mutant mouse models, whereas suppression of FXR—often through accumulation of TbMCA—accelerates intestinal tumorigenesis. Microbial BSH shapes the luminal bile acid pool and can reduce FXR antagonists like TbMCA, suggesting that targeted BSH delivery could help prevent tumors in high-risk individuals. However, BSH enzymes differ in substrate specificity and function. Some BSHs activate protective signaling, while others worsen colorectal cancer in APC-mutant mice on a high-fat diet. These findings highlight the need to define how distinct bile acid–modifying activities influence colorectal cancer risk and their potential for tumor suppression. Thus, described herein is a study that tested whether sustained delivery of select BSH functions prevents colorectal cancer in a high-risk genetic model (ApcF / F;Cdx2- CreER+ mice). This approach assessed how bile acid deconjugation and amidation (BBAA formation) affect tumor initiation and progression, and identified microbial Attorney Docket No.15670-0408WO1 bile acid–modifying activities that could be harnessed to suppress adenoma-to- carcinoma progression. EcAZLsBSH+Prevents Polyp Formation ApcF / WT;Cdx2-Cre+ / +mice develop adenomas in the distal gut at 13 weeks of age. We gavaged 6-week-old ApcF / WT;Cdx2-Cre+ / +mice one single time with 1010CFU of either EcAZ or EcAZLsBSH+and euthanized them at the age of 13 weeks (Figure 3A). A single dose of EcAZLsBSH+prevented colonic polyp formation (Figures 3B-3C). At the endpoint, both EcAZ and EcAZLsBSH+colonized the whole intestine (Figure 3D). These results suggest that L. salivarius BSH (LsBSH) can protect against polyp development. EcAZLsBSH+Colonize Different Mouse Models of Colorectal Cancer We tested EcAZLsBSH+in a second APC-driven model (i.e., ApcF / F;Cdx2- CreER+ mice, Figure 4A). Mice were gavaged with 1010CFU of EcAZ or EcAZLsBSH+one week prior to tumor induction by intraperitoneal tamoxifen injection. EcAZ and EcAZLsBSH+successfully colonized the mice throughout the experiment, with EcAZLsBSH+maintaining a lower level than EcAZ (Figure 4B). BSH-Expressing Native E. coli Activate FXR Signaling in the Ileum To assess whether engineered BSH activity influences host bile acid signaling, we measured FXR target gene expression in the ileum of mice treated with different BSH-expressing native E. coli (Figure 5). Mice receiving EcAZLsBSH+and EcAZDnBSH+, which produce BBAAs, had significantly higher expression of FXR targets Nr0b2 (Shp), Fgf15, Slc51a, and Slc51b, compared to those treated with EcAZ or EcAZLgBSH+(which do not produce BBAAs). These findings suggest certain BSH enzymes enhance FXR signaling in vivo, potentially suppressing colorectal cancer. Experimental Design Animal Models For the studies described in this Example, 6-week-old ApcF / WT;Cdx2-Cre+ / +(7 mice; 3-4 mice / treatment) and ApcF / F;Cdx2-CreER+ mice (45 mice; 15 mice / treatment) were used. In the ApcF / F;Cdx2-CreER+ model, tamoxifen-induced Attorney Docket No.15670-0408WO1 Cre recombinase deletes Apc specifically in the distal intestine, leading to tumor formation. Mice were monitored weekly for disease signs (e.g., bloody stool, diarrhea) and body weight and euthanized at 15 weeks or earlier if showing distress (e.g., >20% weight loss). Monitoring of Bacterial Colonization and BSH Activity Before tumor induction, ApcF / F;Cdx2-CreER+ mice were gavaged once with either PBS (Vehicle), EcAZ, EcAZLsBSH(45 mice total; 15 mice per condition, half female). Colonization was monitored weekly. Colonization checks assessed the EcAZ fluorescence and BSH function via TDCA plates, visualized by precipitated deoxycholic acid (DCA) around colonies (1). Post-Mortem Tumor Assessment (Main Endpoint Measure) At the end of the experiment (13 weeks post- bacterial gavage), tumor number, size, and weight in the ileum, cecum, and colon was assessed. H&E staining of tissues was done at the UCSD Moores Cancer Center Histology Core to evaluate inflammation and tumor stage. Power Analysis of Tumor Assessment The primary outcome for the present study was tumor burden—including presence / absence, number, and size—in mice treated with EcAZ strains expressing different BSH variants compared to vehicle controls. Preliminary data suggested some engineered strains fully prevent tumor development in a subset of mice, thus binary outcomes (tumor-free vs. tumor-bearing) was first analyzed using a χ2 test. Based on a power analysis (α = 0.05, power = 0.80) comparing 0% tumor-free in controls to 67% in BSH-treated mice, 9 mice per group are sufficient to detect this effect. To account for comparisons across multiple strains, sex differences, and potential dropouts, 7 males and 8 females per group (n = 15) were used. In our published work, female mice responded similarly to EcAZLsBSHtreatment (1), and we expect no sex differences. 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Claims

Attorney Docket No.15670-0408WO1 WHAT IS CLAIMED IS:

1. A method for treating colorectal cancer (CRC) in a subject in need thereof, the method comprising: a) culturing or having cultured an isolated native bacteria cell from a donating subject to yield a cultured population of the isolated bacteria cell; b) transforming or having transformed the cultured population with one or more polynucleotides heterologous to the bacteria cell to generate a population of transformed bacteria cells comprising the heterologous polynucleotide(s), wherein the one or more polynucleotides encode bile salt hydrolase (BSH); and c) administering or having administered at least a portion of the population of transformed bacteria cells comprising the heterologous polynucleotide(s) to a receiving subject, wherein the population of transformed bacteria cells colonizes in or on the receiving subject and expresses BSH, thereby treating CRC in the receiving subject.

2. The method of claim 1, further comprising administering to the subject one or more additional therapeutic agents, optionally wherein the one or more additional therapeutic agents is an immunotherapeutic agent, a chemotherapeutic agent, and / or a radiotherapeutic agent.

3. A method for reducing the risk of occurrence or delaying the occurrence of colorectal cancer (CRC) in a subject, the method comprising: a) culturing or having cultured an isolated native bacteria cell from a donating subject to yield a cultured population of the isolated bacteria cell; b) transforming or having transformed the cultured population with one or more polynucleotides heterologous to the bacteria cell to generate a population of transformed bacteria cells comprising the heterologous polynucleotide(s), wherein the one or more polynucleotides encode bile salt hydrolase (BSH); and c) administering or having administered at least a portion of the population of transformed bacteria cells comprising the heterologous polynucleotide(s) to a receiving subject, wherein the population of transformed bacteria cells colonizes in or on the receiving subject and expresses BSH, thereby reducing the risk of occurrence or delaying the occurrence of CRC in the receiving subject.Attorney Docket No.15670-0408WO1 4. The method of claim 3, wherein the subject is at risk for developing CRC.

5. The method of claim 4, wherein the subject has genetic predisposition for CRC, optionally wherein the subject has familial adenomatous polyposis syndrome or Lynch syndrome.

6. The method of claim 4, wherein the subject has a disease that increases the risk for CRC, optionally wherein the disease is inflammatory bowel disease (IBD).

7. The method of any one of claims 1-6, wherein the receiving subject is same as the donating subject.

8. The method of any one of claims 1-6, wherein the receiving subject is different from the donating subject and is of the same species as the donating subject.

9. The method of any one of claims 1-8, wherein the native bacteria cell is isolated from a biological sample from the donating subject.

10. The method of claim 9, further comprising obtaining the biological sample from the donating subject.

11. The method of claim 9 or 10, wherein the biological sample is selected from the group consisting of a bodily excretion, a biopsy or swab of a surface, and a pathological specimen.

12. The method of any one of claims 9-11, wherein the biological sample comprises a fecal sample, a colon biopsy, and / or a CRC tissue.

13. The method of any one of claims 1-12, wherein the bacteria cell is not from a laboratory adapted bacterial strain.Attorney Docket No.15670-0408WO1 14. The method of any one of claims 1-13, wherein the bacteria cell is derived from a bacteria genus selected from the group consisting of Bacteroides, Clostridium, Streptococcus, Lactococcus, Eubacterium rectale, Escherichia coli, Enterobacter sp., Klebsiella sp., Bifidobacterium, Staphylococcus, Lactobacillus, Veillonella, Haemophilus, Moraxella, Corynebacterium and Propionibacterium.

15. The method of any one of claims 1-14, wherein the bacteria cell is derived from Escherichia coli.

16. The method of any one of claims 1-15, wherein the bacteria cell does not comprise one or more polynucleotides encoding for one or more pathogenic toxins selected from the group consisting of AB toxin, Alpha toxin, Anthrax toxin, Botulinum toxin, Cereulide, Cholesterol-dependent cytolysin, Clostridial Cytotoxin family, Clostridium botulinum C3 toxin, Clostridium difficile toxin A, Clostridium difficile toxin B, Clostridium enterotoxin, Clostridium perfringens alpha toxin, Clostridium perfringens beta toxin, Cry1Ac, Cry6Aa, Cry34Ab1, Delta endotoxin, Diphtheria toxin, Enterotoxins, Enterotoxin type B, Erythrogenic toxin, Exfoliatin, Fragilysin, Haemolysin E, Heat-labile enterotoxin, Heat-stable enterotoxin, Hemolysin, HrpZ Family, Leukocidin, Listeriolysin O, Panton–Valentine leucocidin, intact Pathogenicity island, Phenol-soluble modulin, Pneumolysin, Pore-forming toxin, Pseudomonas exotoxin, Pyocyanin, anti-eukaryotic Rhs toxins, RTX toxin, Shiga toxins, Shiga-like toxin, Staphylococcus aureus alpha toxin, Staphylococcus aureus beta toxin, Staphylococcus aureus delta toxin, Streptolysin, Tetanolysin, Tetanospasmin, Toxic shock syndrome toxin, Tracheal cytotoxin, and Verocytotoxin.

17. The method of any one of claims 1-16, wherein the bacteria cell is antibiotic sensitive or transformed with one or more polynucleotides to be antibiotic sensitive to one or more antibiotic agents used for selection of transformed bacteria cells, optionally wherein the one or more antibiotic agents used for selection of transformed bacteria cells comprises kanamycin, chloramphenicol, carbenicillin, hygromycin, or trimethoprim.Attorney Docket No.15670-0408WO1 18. The method of any one of claims 1-17, wherein the bacteria cell is not antibiotic resistant to one or more clinically used antibiotic agents, optionally wherein the one or more clinically used antibiotic agents comprises antibiotic macrolides, rifamycins, polymyxins, quinolone antibiotics, beta-lactams, aminoglycosides, cephalosporins, monobactams, carbapenems, or tetracyclines.

19. The method of any one of claims 1-18, wherein the one or more polynucleotides encode Lactobacillus salivarius BSH (LsBSH).

20. The method of claim 19, wherein the one or more heterologous polynucleotides encoding LsBSH is engineered into a native E. coli chassis.

21. The method of any one of claims 1-18, wherein the one or more polynucleotides encode Dubosiella newyorkensis–A0A1U7NKD7 BSH (DnBSH1).

22. The method of claim 21, wherein the one or more heterologous polynucleotides encoding DnBSH1 is engineered into a native E. coli chassis.

23. The method of any one of claims 1-22, wherein the one or more heterologous polynucleotides comprise codon bias configured to improve or enhance expression of BSH in the transformed bacteria cells.

24. The method of any one of claims 1-23, wherein the one or more heterologous polynucleotides are integrated into the chromosome of the transformed bacteria cells, optionally wherein the one or more heterologous polynucleotides are integrated into the attB and / or yfgG genes of the bacterial genome.

25. The method of any one of claims 1-23, wherein the one or more heterologous polynucleotides are episomally introduced into the transformed bacteria cells in a plasmid.

26. The method of claim 25, wherein the transformed bacteria cells further comprise a plasmid retention or maintenance system, optionally wherein the plasmidAttorney Docket No.15670-0408WO1 retention or maintenance system comprises a partitioning system or a toxin-antitoxin module or system.

27. The method of any one of claims 1-26, wherein the one or more heterologous polynucleotides are integrated into an expression cassette and are expressed under the control of a Ptrc promoter.

28. The method of any one of claims 1-27, wherein the population of transformed bacteria cells colonizes in or on the receiving subject permanently or long-term, optionally wherein the population of transformed bacteria cells colonizes in or on the receiving subject for at least 48 hours.

29. The method of any one of claims 1-28, further comprising determining and / or measuring the colonization or presence of the administered population of transformed bacteria cells in or on the receiving subject.

30. The method of any one of claims 1-29, wherein the one or more heterologous polynucleotides further encode a fluorescent protein, optionally wherein the fluorescent protein comprises green fluorescent protein, yellow fluorescent protein, red fluorescent protein (mCherry, mEos2, mRuby2, mRuby3, mClover3, mApple, mKate2, mMaple, mCardinal, mNeptune), mTurquoise, or mVenus.

31. The method of any one of claims 1-30, wherein the population of transformed bacteria cells is administered to the receiving subject multiple times.

32. The method of any one of claims 1-31, wherein the population of transformed bacteria cells is administered to the receiving subject at daily, weekly, biweekly, or monthly intervals.

33. The method of any one of claims 1-32, wherein administration of the population of transformed bacteria cells do not substantially alter the microbiome of the receiving subject.Attorney Docket No.15670-0408WO1 34. The method of any one of claims 1-33, wherein expression of BSH by the population of transformed bacteria cells results in deconjugation of one or more bile acids in the receiving subject.

35. The method of any one of claims 1-34, wherein expression of BSH by the population of transformed bacteria cells results in activation of farnesoid X receptor (FXR) signaling in the receiving subject.

36. The method of any one of claims 1-35, wherein the donating subject and / or the receiving subject is a human.

37. A population of bacteria cells transformed with one or more polynucleotides heterologous to the bacteria cells, wherein the one or more polynucleotides encode bile salt hydrolase (BSH), and wherein the bacteria cells are obtained from and adapted to or configured for the microbiome of a mammalian subject, and are not adapted for or configured for culture in a laboratory environment.

38. The population of bacteria cells of claim 37, wherein the one or more polynucleotides encode Lactobacillus salivarius BSH (LsBSH).

39. The population of bacteria cells of claim 37, wherein the one or more polynucleotides encode Dubosiella newyorkensis–A0A1U7NKD7 BSH (DnBSH1).

40. The population of bacteria cells of any one of claims 37-39, wherein the bacteria cell is isolated from a biological sample from a donating mammalian subject.

41. The population of bacteria cells of claim 40, wherein the biological sample is selected from the group consisting of a bodily excretion, a biopsy or swab of a surface, and a pathological specimen.Attorney Docket No.15670-0408WO1 42. The population of bacteria cells of claim 40 or 41, wherein the biological sample comprises a fecal sample, a colon biopsy, and / or a CRC tissue.

43. The population of bacteria cells of any one of claims 37-42, wherein the bacteria cell is not from a laboratory adapted bacterial strain.

44. The population of bacteria cells of any one of claims 37-43, wherein the bacteria cell is derived from a bacteria genus selected from the group consisting of Bacteroides, Clostridium, Streptococcus, Lactococcus, Eubacterium rectale, Escherichia coli, Enterobacter sp., Klebsiella sp., Bifidobacterium, Staphylococcus, Lactobacillus, Veillonella, Haemophilus, Moraxella, Corynebacterium and Propionibacterium.

45. The population of bacteria cells of any one of claims 37-44, wherein the bacteria cell is derived from Escherichia coli.

46. The population of bacteria cells of any one of claims 37-45, wherein the bacteria cell does not comprise one or more polynucleotides encoding for one or more pathogenic toxins selected from the group consisting of AB toxin, Alpha toxin, Anthrax toxin, Botulinum toxin, Cereulide, Cholesterol-dependent cytolysin, Clostridial Cytotoxin family, Clostridium botulinum C3 toxin, Clostridium difficile toxin A, Clostridium difficile toxin B, Clostridium enterotoxin, Clostridium perfringens alpha toxin, Clostridium perfringens beta toxin, Cry1Ac, Cry6Aa, Cry34Ab1, Delta endotoxin, Diphtheria toxin, Enterotoxins, Enterotoxin type B, Erythrogenic toxin, Exfoliatin, Fragilysin, Haemolysin E, Heat-labile enterotoxin, Heat-stable enterotoxin, Hemolysin, HrpZ Family, Leukocidin, Listeriolysin O, Panton–Valentine leucocidin, intact Pathogenicity island, Phenol-soluble modulin, Pneumolysin, Pore-forming toxin, Pseudomonas exotoxin, Pyocyanin, anti-eukaryotic Rhs toxins, RTX toxin, Shiga toxins, Shiga-like toxin, Staphylococcus aureus alpha toxin, Staphylococcus aureus beta toxin, Staphylococcus aureus delta toxin, Streptolysin, Tetanolysin, Tetanospasmin, Toxic shock syndrome toxin, Tracheal cytotoxin, and Verocytotoxin.Attorney Docket No.15670-0408WO1 47. The population of bacteria cells of any one of claims 37-46, wherein the bacteria cell is antibiotic sensitive or transformed with one or more polynucleotides to be antibiotic sensitive to one or more antibiotic agents used for selection of transformed bacteria cells, optionally wherein the one or more antibiotic agents used for selection of transformed bacteria cells comprises kanamycin, chloramphenicol, carbenicillin, hygromycin, or trimethoprim.

48. The population of bacteria cells of any one of claims 37-47, wherein the bacteria cell is not antibiotic resistant to one or more clinically used antibiotic agents, optionally wherein the one or more clinically used antibiotic agents comprises antibiotic macrolides, rifamycins, polymyxins, quinolone antibiotics, beta-lactams, aminoglycosides, cephalosporins, monobactams, carbapenems, or tetracyclines.

49. The population of bacteria cells of any one of claims 37-48, wherein the population of bacteria cells expresses BSH when administered to a receiving mammalian subject.

50. The population of bacteria cells of claim 49, wherein the population of bacteria cells is capable of colonizing or is configured to colonize in or on the receiving mammalian subject permanently or long-term.

51. A composition comprising the population of bacteria cells of any one of claims 37-50.

52. The composition of claim 51, wherein the composition is an edible composition.

53. The composition of claim 52, wherein the edible composition comprises a gel capsule.

54. The composition of claim 52, wherein the edible composition comprises a beverage.Attorney Docket No.15670-0408WO1 55. The composition of claim 52, wherein the edible composition is selected from the group consisting of yogurt, milk, ice cream, vegetable puree, fruit puree, sorbet, and oatmeal.

56. A kit comprising one or more containers comprising the composition of any one of claims 51-55.

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