Methods for treating ulcerative colitis

Abstract

The present disclosure provides methods and treatment regimens for treating ulcerative colitis in a subject in need of treatment. Specifically, the methods described herein include treating a subject in need of treatment with a treatment regimen that involves administering a pharmaceutical composition containing live non-pathogenic fecal bacteria at least three times per week for at least eight weeks. In some embodiments, the subject in need of treatment has a Mayo endoscopic score of 3 or less. In some embodiments, the subject in need of treatment is not taking concomitant corticosteroids during the method, and has not taken corticosteroids immediately before starting the method.

Description

[Technical Field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Patent Application No. 62 / 370,508, filed August 3, 2016, and U.S. Patent Application No. 15 / 360,703, filed November 23, 2016, the entire contents of which are incorporated herein by reference.

[0002] The present disclosure relates to methods and dosing regimens suitable for treating ulcerative colitis in a subject in need thereof. [Background technology]

[0003] Mammals harbor a diverse range of microbial species in their gastrointestinal (GI) tract. Interactions between these microorganisms and between microorganisms and the host, including the host immune system, form the microbiota. A healthy microbiota provides multiple benefits to the host, including resistance to colonization by a wide range of pathogens, biosynthesis and absorption of essential nutrients, and immune stimulation that maintains a healthy intestinal epithelium and well-regulated systemic immunity. An imbalanced microbiota (also known as "dysbiosis" or "disrupted symbiosis") can lead to loss of microbiota function, resulting in increased susceptibility to pathogens, altered metabolic profiles, or the induction of inflammatory signals that lead to local or systemic inflammation or autoimmunity. The gut microbiota plays an important role in the pathogenesis of many diseases, such as enteric pathogenic infections.

[0004] Ulcerative colitis is a chronic disease of the large intestine, also known as the colon, in which the lining of the colon becomes inflamed and develops small open sores, or ulcers, that form pus and mucus. Ulcerative colitis most frequently occurs in people between the ages of 15 and 30, but the disease can afflict people of any age. Ulcerative colitis affects men and women equally, and ulcerative colitis appears to run in some families.

[0005] Ulcerative colitis is a disease characterized by inflammation and microulcers in the surface layer of the large intestine. Inflammation usually occurs in the rectum and lower colon, but it can affect the entire large intestine (pancolitis). Ulcerative colitis very rarely affects the small intestine, the distal part of the large intestine (reflux ileitis).

[0006] Inflammation is usually accompanied by diarrhea, which can cause profuse bleeding. Microulcers form where inflammation destroys the cells lining the intestine, causing these areas to bleed and produce pus and mucus. Ulcerative colitis, especially in mild cases, can be difficult to diagnose because symptoms resemble those of other intestinal diseases, most notably another type of irritable bowel disease (IBD) called Crohn's disease and even irritable bowel syndrome (IBS). Crohn's disease differs from ulcerative colitis because it causes inflammation throughout the thickness of the intestinal wall, resulting in deep ulcers. Crohn's disease usually occurs in the small intestine but can also occur in the large intestine, anus, esophagus, stomach, appendix, and mouth. Crohn's disease causes fistulas, whereas ulcerative colitis does not. Both Crohn's disease and ulcerative colitis can occur simultaneously in the same patient. The combination of inflammation and ulceration can cause abdominal discomfort and frequent colonic emptying. Existing treatments for ulcerative colitis involve strong and long combined drug therapy with significant side effects, or even require surgery to remove part of the colon. Furthermore, a significant proportion of ulcerative colitis patients are resistant to standard drug therapy. Therefore, there is a need for more effective treatments for ulcerative colitis that are easier to administer.

[0007] The transplantation or administration of human colonic microbiota into the intestine of a diseased patient is called fecal microbiota transplantation (FMT), also widely known as fecal bacteriotherapy. FMT is thought to repopulate the intestine with a diverse microbial population that controls major pathogens by creating an ecological environment hostile to the growth and survival of the transplant. FMT represents a therapeutic protocol that allows for the rapid reconstitution of a normal compositional and functional gut microbial community.

[0008] Fecal microbiota transplantation (FMT), also known as "fecal bacteriotherapy," represents one treatment protocol that allows for the most rapid reconstitution of a normal composition and functional gut microbial community. For decades, FMT has typically been offered worldwide by select centers as a last-resort option for patients with recurrent Clostridium difficile infection (CDI). FMT has also been proposed for the treatment of other enteric infections, such as Escherichia coli and vancomycin-resistant Enterococci (VRE). Currently, FMT is administered by several routes, including infusion of human microbiota in the form of homogenized stool, homogenized stool extract, or cultured stool components via colonoscopy, enema, or nasojejunal tube. [Prior art documents] [Patent documents]

[0009] [Patent Document 1] U.S. Provisional Patent Application No. 62 / 370,508 [Patent Document 2] U.S. Patent Application No. 15 / 360,703 Summary of the Invention [Means for solving the problem]

[0010] The present disclosure provides methods and dosing regimens for treating or preventing ulcerative colitis.

[0011] In one aspect, the disclosure provides a method for treating ulcerative colitis in a subject in need thereof, the method comprising treating the patient with a treatment regimen comprising administering a pharmaceutical composition comprising live non-pathogenic fecal bacteria at least three times per week for at least eight weeks.

[0012] In one aspect, the present disclosure provides a method for treating ulcerative colitis (UC) in a subject in need of treatment and exhibiting a Mayo endoscopic score of 3 or less, the method comprising administering to the subject a pharmaceutical composition comprising live non-pathogenic fecal bacteria.

[0013] In some aspects, the disclosure provides a method for treating ulcerative colitis in a subject in need thereof, the method comprising administering to the subject a pharmaceutical composition comprising live non-pathogenic fecal bacteria, wherein the subject is not taking concomitant corticosteroids during the method and has been free of corticosteroid use immediately prior to initiating the method.

[0014] In one aspect, the present disclosure provides a method for selecting a treatment plan for treating ulcerative colitis (UC) in a subject in need of treatment, the method comprising determining levels of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella in the intestine of the subject, and recommending a fecal bacterial treatment if the levels of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella are above a predetermined level.

[0015] In one aspect, the present disclosure provides a method for selecting a treatment regimen for treating ulcerative colitis (UC) in a subject in need thereof, the method comprising determining a level of one or more bacteria selected from the group consisting of Barnesiella, Parabacteroides, Clostridium IV, Ruminococcus, Blautia, Dorea, Ruminococcus 2, and Clostridium XVIII in the intestine of the subject, and recommending a fecal bacterial treatment if the level of one or more bacteria selected from the group consisting of these bacteria is above a predetermined level. [Brief explanation of the drawings]

[0016] [Figure 1] FIG. 1 shows a clinical trial patient CONSORT (Improving the Reporting of Randomized Controlled Trials) flow diagram according to Example 1 of the present disclosure. [Figure 2] 1 shows a diagrammatic representation of a clinical trial design according to Example 4 of the present disclosure. [Figure 3A] 1 shows the number of patients in the FMT and placebo treatment groups achieving the primary outcomes of steroid-free clinical and endoscopic remission or response at 8 weeks post-treatment according to Example 5 of the present disclosure. [Figure 3B] 1 shows the number of patients achieving steroid-free clinical remission and clinical response at 8 weeks after treatment with examples of the present disclosure. [Figure 3C] 1 shows the number of patients achieving steroid-free endoscopic response and complete mucosal healing after treatment with an embodiment of the present disclosure. [Figure 4A] 1 shows an exemplary baseline endoscopic appearance of 25 cm of active rectosigmoid colitis according to Example 5 of the present disclosure. [Figure 4B] 10 shows exemplary endoscopic appearances at the end of 8 weeks of blinded FMT treatment according to Example 5 of the present disclosure. [Figure 4C] 10 shows an exemplary baseline endoscopic appearance of extensive colitis resulting in hepatic deflection according to Example 5 of the present disclosure. [Figure 4D] 10 shows exemplary endoscopic appearances at the completion of open-label FMT at week 8 according to Example 5 of the present disclosure. [Figure 5] This shows how quickly the therapeutic effect of Example 5 of the present disclosure begins to appear. [Figure 6A] FIG. 1 shows the number of operational taxonomic units (OTUs) per fecal sample according to Example 6 of the present disclosure. [Figure 6B] 1 shows phylogenetic diversity within each fecal sample according to Example 6 of the present disclosure. [Figure 6C] 1 shows a principal component analysis of fecal samples at the genus taxonomic level according to Example 6 of the present disclosure. [Figure 6D] 1 shows the number of OTUs in blinded trial patients receiving FMT treatment according to primary outcome, individual donor, and donor population according to Example 6 of the present disclosure. [Figure 7A] Endoscopic images show significant UC inflammation in the rectum before treatment (left 1 and 2); a dramatic reduction in inflammation with stool adhering to the rectal mucosa at 20 weeks (right 1); significant UC inflammation in the sigmoid colon before treatment (left 3 and 4); and a significant reduction in inflammation in the sigmoid colon at 20 weeks (right 2 and 3). Right 2 shows stool adhering to the inflamed sigmoid colon wall. Right 3 shows scattered inflammatory changes. [Figure 7B] Endoscopic images of inflammation and significant mucosal thickening in the transverse colon at 8 weeks after treatment (left images 7, 8, 9, and 10); and improvement in inflammation at 20 weeks (right image 6). In right image 6, inflammation in the transverse colon has improved but is still visible. Blood vessels are not visible. DETAILED DESCRIPTION OF THE INVENTION

[0017] Before describing the compositions and methods, it should be understood that this disclosure is not limited to the particular processes, compositions, or methods described, as these may vary. It should also be understood that the terminology used in the description is for the purpose of describing particular versions or embodiments only, and is not intended to limit the scope of the present invention, which is limited solely by the appended claims. For example, features described with respect to one embodiment may be incorporated into other embodiments, and features described with respect to a particular embodiment may be omitted from that embodiment. Thus, it is contemplated that some embodiments of the present disclosure may exclude or omit any feature or combination of features described herein. Furthermore, numerous modifications and additions to the various embodiments suggested herein will become apparent to those skilled in the art upon consideration of the present disclosure without departing from the scope of the present disclosure. In other instances, well-known structures, interfaces, and processes have not been shown in detail so as not to unnecessarily obscure the present invention. It is intended that no portion of this specification should be construed as resulting in a denial of any portion of the full scope of the present invention. Therefore, the following description is intended to illustrate some particular aspects of the present disclosure, but is not intended to exhaustively identify all permutations, combinations, and variations of these aspects.

[0018] Unless otherwise defined herein, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art. The terminology used in describing the present disclosure herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the disclosure.

[0019] All publications, patent applications, patents, and other references cited herein are incorporated by reference in their entirety.

[0020] Unless otherwise clearly indicated from the context, it is specifically intended that the various features of the present disclosure described herein can be used in any combination. Furthermore, the present disclosure also contemplates that some embodiments of the present disclosure may exclude or omit any feature or combination of features described herein.

[0021] The methods disclosed herein may include one or more steps or processes that achieve the described method. Method steps and / or processes may be interchanged with one another without departing from the scope of the present invention. In other words, unless a specific order of steps or processes is required for the proper operation of an embodiment, the order and / or use of specific steps and / or processes may be changed without departing from the scope of the present invention.

[0022] As used in the description of this disclosure and the appended claims, the singular forms "a," "an," and "the" are intended to include the plural forms as well, unless the context clearly indicates otherwise.

[0023] As used herein, "and / or" refers to and includes any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted as alternatives ("or").

[0024] As used herein, the terms "about" and "approximately," when referring to measurable values ​​such as percentage, density, volume, etc., are meant to include 20%, 10%, 5%, 1%, 0.5%, or 0.1% of the specified amount.

[0025] As used herein, phrases such as "between X and Y" and "between about X and Y" should be interpreted to include X and Y. As used herein, phrases such as "between about X and Y" mean "between about X and about Y," and phrases such as "from about X to Y" mean "from about X to about Y."

[0026] As used herein, the term "substantially free," when referring to the presence of a substance in a composition, is meant to include the substance making up less than 1%, less than 0.5%, less than 0.1%, or even less than 0.01% of the total substance by volume or mass.

[0027] As used herein, the term "treating" refers to (i) completely or partially inhibiting a disease, disorder, or condition, e.g., preventing its onset; (ii) completely or partially alleviating a disease, disorder, or condition, e.g., causing regression of the disease, disorder, and / or condition; or (iii) completely or partially preventing a disease, disorder, or condition from developing in a patient who is susceptible to, but has not yet been diagnosed with, the disease, disorder, and / or condition. Similarly, "treatment" refers to both therapeutic therapy and prophylactic or preventative measures.

[0028] As used herein, "therapeutically effective amount" or "pharmaceutically active dose" refers to an amount of a composition that is effective to treat a specified disease, disorder, or condition.

[0029] As used herein, "microbiota" and "flora" refer to the community of microorganisms, including eukaryotes, archaea, bacteria, and viruses (including bacterial viruses (i.e., phages)), living in or on a subject's body, both persistently and transiently. Non-selective fecal microbiota refers to a community or mixture of fecal microorganisms derived from a fecal sample of a donor without selection, and is substantially similar to the microbial components and microbial community structure found in such a fecal sample.

[0030] As used herein, "remission," "cure," or "resolution rate" refers to the proportion of patients who are cured or experience remission or complete resolution of symptoms in response to a given treatment. As used herein, "clinical remission sustaining rate" refers to the proportion of patients who maintain clinical remission after a specific treatment period among all patients who achieve remission at the completion of treatment. Quantitatively, remission, cure, or resolution is achieved when a patient's UCDAI score is 2 or less, as assessed after 8 weeks of treatment. Remission, cure, or resolution can be further confirmed by endoscopic healing and mucosal healing.

[0031] As used herein, "steroid-free" refers to the complete or substantial absence of steroid use.

[0032] As used herein, "primary outcome rate" refers to the proportion of patients who achieve the primary outcome after a particular treatment or treatment regimen among all patients receiving that treatment or treatment regimen.

[0033] As used herein, "response rate" refers to the proportion of patients who achieve a cure with a given treatment. Quantitatively, a patient is on the cure path with a treatment if their UCDAI (Ulcerative Colitis Disease Activity Index) score decreases by at least 2 from baseline by week 8.

[0034] As used herein, "Mayo Clinic score" or "Mayo score" refers to an index system for assessing the severity of ulcerative colitis disease symptoms. See Table 1 and the article by Schoeder et al. in N Engl J Med 1987;317:1625-9. The Mayo Clinical Score ranges from 0 to 12, with subscores of 0 to 3, with higher scores indicating more severe disease. In some embodiments, subscores can be assessed for stool frequency, rectal bleeding, mucosal appearance on endoscopy, and physician global assessment (PGA). [Table 1]

[0035] As used herein, "ulcerative colitis endoscopic index of severity" or "UCEIS" refers to an index for assessing endoscopic disease activity. The index evaluates three criteria, including vascular pattern, bleeding, erosion, and ulcers (Table 2). See Travis et al., "Development of an Instrument to Assess the Endoscopic Severity of Ulcerative Colitis: The Ulcerative Colitis Endoscopic Severity Index (UCEIS)." Higher scores represent increasing disease severity. [Table 2]

[0036] As used herein, the term "ulcerative colitis disease activity index" or "UCDAI" refers to an index system for assessing the severity or response of symptoms in patients with ulcerative colitis. The index assesses four variables, including stool frequency, bleeding severity, colonic mucosal appearance, and a physician's overall assessment of disease activity (Table 3). See the article "5-aminosalicylic acid enemas in the treatment of distal ulcerative colitis, rectosigmoiditis, and proctitis" by Sutherland et al., Gastroenterology. 1987;92:1894-8. Each variable is scored on a scale of 0 to 3, resulting in a total index score ranging from 0 to 12, with remission ranging from 0 to 2, mild disease ranging from 3 to 6, moderate disease ranging from 7 to 10, and severe ulcerative colitis >10. [Table 3]

[0037] As used herein, "eukaryotic" refers to cells that contain a nucleus and membrane-bound organelles.

[0038] As used herein, "bacteria," "bacterium," and "archaea" refer to unicellular prokaryotic organisms that lack a membrane-bound nucleus and lack organelles.

[0039] As used herein, "fecal bacteria" refers to bacteria that can be present in fecal material.

[0040] As used herein, "viable" means having the ability to grow.

[0041] As used herein, "isolated" or "purified" refers to (1) bacteria or other entities or substances that have been separated from at least some of the components that were associated with them when they were originally produced (whether in nature or in a laboratory setting) and / or (2) bacteria or other entities or substances that have been produced, prepared, purified, and / or manufactured by the hand of man. Isolated or purified bacteria can be separated from at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more of the other components that were originally associated with the bacteria.

[0042] As used herein, the terms "pathogen" and "pathogenic" referring to a bacterium or any other organism or entity include any such organism or entity that can cause or affect a disease, disorder, or symptom in a host organism that contains the organism or entity.

[0043] As used herein, a "spore" or population of "spores" generally comprises bacteria (or other single-celled organisms) that are viable and more resistant to environmental influences such as heat and disinfectants than the vegetative form of the same bacterium, and typically capable of germination and proliferation. "Spore-formers" or bacteria "capable of forming spores" are bacteria that contain the genes and other necessary capabilities to produce spores under suitable environmental conditions.

[0044] As used herein, a "combination" of two or more bacteria includes the physical coexistence of the two bacteria either in the same material or product, or in a physically associated product, as well as the temporal co-administration or co-localization of the two bacteria.

[0045] As used herein, "subject" refers to any animal subject, including humans, laboratory animals (e.g., primates, rats, mice), farm animals (e.g., cattle, sheep, goats, pigs, turkeys, chickens), and household pets (e.g., dogs, cats, rodents, etc.). A subject or patient can be healthy, or may be suffering from an infection with a gastrointestinal pathogen, or at risk of developing or transmitting an infection with a gastrointestinal pathogen to others.

[0046] As used herein, "Shannon Diversity Index" refers to a diversity index that describes the abundance and evenness of species present in a given community using a mathematical formula:

number

[0047] As used herein, "operational taxonomic unit" or "OTU" refers to a group of closely related microbial species determined based on 16S or 18S rRNA marker genes.

[0048] As used herein, "antibiotic" refers to a substance used to treat and / or prevent bacterial infections by killing bacteria, inhibiting the growth of bacteria, or reducing the viability of bacteria.

[0049] As used herein, an "intermittent dosing schedule" means that a therapeutic composition is administered for a predetermined period of time, followed by a predetermined period (a treatment period) during which treatment with such therapeutic composition is withheld (a rest period). An intermittent dosing regimen can be expressed as a treatment period of several days or weeks / a rest period of several days or weeks. For example, a 4 / 1 intermittent dosing schedule refers to an intermittent dosing schedule with a treatment period of 4 weeks / 4 days and a rest period of 1 week / 1 day.

[0050] As used herein, a "continuous dosing schedule" refers to a dosing schedule in which a therapeutic composition is administered during a treatment period without a rest period. Throughout the treatment period of a continuous dosing schedule, the therapeutic composition can be administered, for example, every day, every other day, or every third day. On days when a therapeutic composition is administered, the therapeutic composition can be administered in a single dose or multiple doses throughout the day.

[0051] As used herein, "dosing frequency" refers to how often a given dose of a therapeutic composition is administered within a given period of time. Dosing frequency can be expressed as the number of doses per given period of time, e.g., once per day, once per week, or once every two weeks.

[0052] As used herein, "dosing interval" refers to the length of time that elapses between multiple doses being administered to a subject.

[0053] There are different types of ulcerative colitis. As used herein, "ulcerative proctitis" refers to a disease state in which intestinal inflammation is limited to the rectum. Because ulcerative proctitis is limited in extent (usually less than 6 inches (15.24 cm) of the rectum), it tends to be a milder form of ulcerative colitis. Ulcerative proctitis occurs with very rare complications, resulting in a better outlook than the more widespread disease. For approximately 30% of all patients with ulcerative colitis, the disease begins as ulcerative proctitis.

[0054] As used herein, "proctosigmoiditis" refers to a form of colitis that affects the rectum and sigmoid colon, the lower part of the colon located just above the rectum. Symptoms include bloody diarrhea, cramps, and a persistent feeling of incomplete evacuation, known as tenesmus. Moderate pain in the lower left side of the abdomen may occur with active disease.

[0055] As used herein, "left-sided colitis" refers to a continuous inflammation that begins in the rectum and extends to the curve of the colon called the splenic flexure near the spleen. Symptoms include loss of appetite, weight loss, diarrhea, severe pain on the left side of the abdomen, and bleeding.

[0056] As used herein, "pan-ulcerative (total) colitis" affects the entire colon. Symptoms include diarrhea, severe abdominal pain, cramps, and extreme weight loss. Potentially severe complications include heavy bleeding and acute dilation of the colon (toxic megacolon), which can lead to perforation of the intestinal wall. Severe complications may require surgery.

[0057] Several theories have been proposed for the cause of ulcerative colitis. Some evidence suggests that the body's immune system responds to environmental, dietary, or infectious pathogens in genetically susceptible individuals, causing inflammation of the intestinal wall. The latest suspected causative agent, identified by Japanese researchers as Fusobacterium varium, may cause infection of the lining. Ulcerative colitis is not caused by emotional distress or sensitivity to specific foods, although these factors may contribute to the onset of symptoms in some individuals. Ulcerative colitis is likely an infectious disease, not an abnormal reaction.

[0058] The most common symptoms of ulcerative colitis are bloody diarrhea and abdominal pain. Patients may also experience fever, rectal bleeding, fatigue, anemia, loss of appetite, weight loss, and loss of body fluids and nutrients, leading to nutritional deficiencies. These symptoms occur in intermittent attacks with periods of time until the symptoms subside (remission). These disease-free periods can last for months or even years. Attacks usually begin with an increased urge to defecate, mild lower abdominal cramps, and blood and mucus in the stool.

[0059] Ulcerative colitis can lead to long-term problems such as arthritis, eye inflammation, liver disease (fatty liver, hepatitis, cirrhosis, and primary sclerosing cholangitis), osteoporosis, skin rashes, anemia, and kidney stones. These complications can occur when the immune system causes inflammation in other parts of the body. These problems may go away when the colitis is effectively treated.

[0060] Treatment for ulcerative colitis varies depending on the severity of the disease. Most people are treated with medications. Some people who have symptoms caused by certain foods can suppress these symptoms by avoiding foods that upset their intestines, such as highly seasoned foods or dairy products. Because each person may experience ulcerative colitis differently, treatment is tailored to each individual.

[0061] Many patients with mild or moderate disease are initially treated with 5-ASA agents, which include a combination of the drug 5-aminosalicylic acid and sulfasalazine, which help suppress inflammation. Sulfasalazine is the most widely used of these drugs. Sulfasalazine can be used as long as needed and can be given with other medications. Patients who do not respond to sulfasalazine may respond to newer 5-ASA agents. Possible side effects of 5-ASA preparations include nausea, vomiting, heartburn, diarrhea, and headache.

[0062] Those with severe disease and those who do not respond to 5-ASA medications can be treated by adding corticosteroids. Prednisone, budesonide, and hydrocortisone are corticosteroids used to reduce inflammation. These corticosteroids can be administered orally, intravenously, via enema, or as a suppository, depending on the site of inflammation. Because corticosteroids can cause side effects such as weight gain, acne, facial hair loss, high blood pressure, diabetes, mood swings, and an increased risk of infection, doctors closely monitor patients taking these medications.

[0063] Immunosuppressants such as azathioprine, 6-mercaptopurine (6-MP), and methotrexate are often used, often resulting in significant improvement at low doses with few side effects. Other drugs may be administered to relax the patient or to relieve pain, diarrhea, or infection. Occasionally, symptoms become severe enough that the person must be hospitalized. For example, a person may experience severe bleeding that leads to dehydration or severe diarrhea. In such cases, doctors attempt to stop the diarrhea and bleeding, the exudation of fluids, and the exudation of mineral salts. The patient may require a special diet, intravenous medications, or even surgery.

[0064] In severe cases, patients may require surgery to remove the diseased colon. If drug treatment fails, or if the side effects of corticosteroids or other drugs threaten the patient's health, a doctor may recommend removing the colon.

[0065] In one embodiment, the present disclosure provides a method for reducing calprotectin levels in a subject in need of treatment, the method comprising treating the patient with a treatment regimen comprising administering a pharmaceutical composition comprising live, non-pathogenic fecal bacteria at least three times per week for at least eight weeks. In another embodiment, any of the methods or treatment regimens provided herein can be further used to reduce calprotectin and inflammation levels in a subject in need of treatment. In certain embodiments, the present disclosure provides a method for reducing calprotectin levels in a subject in need of treatment by at least 10% compared to pre-treatment calprotectin levels. In another embodiment, calprotectin levels are reduced by at least 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%. In another embodiment, calprotectin levels are reduced by 2-10%, 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-85%, 85-90%, 90-95%, and 95-99% compared to pre-treatment calprotectin levels. In yet another embodiment, calprotectin levels are reduced to less than 100 μg / g, less than 90 μg / g, less than 80 μg / g, less than 70 μg / g, less than 60 μg / g, less than 65 μg / g, less than 55 μg / g, less than 50 μg / g, less than 45 μg / g, less than 40 μg / g, or less than 35 μg / g. In another embodiment, calprotectin levels are reduced in a subject in need of treatment after a treatment regimen lasting at least 8 weeks. In another embodiment, the level of calprotectin is reduced in a subject in need of treatment 8 weeks after completion of the treatment regimen. In yet another embodiment, the level of calprotectin is reduced in a subject in need of treatment 1 to 12 weeks, 2 to 12 weeks, 3 to 12 weeks, 4 to 12 weeks, 5 to 12 weeks, 6 to 12 weeks, 7 to 12 weeks, 8 to 12 weeks, 9 to 12 weeks, 10 to 12 weeks, 1 to 2 weeks, 2 to 3 weeks, 3 to 4 weeks, 4 to 5 weeks, 5 to 6 weeks, 6 to 7 weeks, 7 to 8 weeks, 8 to 9 weeks, 9 to 10 weeks, or 10 to 11 weeks after completion of the treatment regimen.In yet another embodiment, the level of calprotectin is reduced in a subject in need of treatment 12 to 30 weeks, 12 to 28 weeks, 12 to 20 weeks, 14 to 20 weeks, 14 to 26 weeks, 12 to 18 weeks, 12 to 16 weeks, 20 to 30 weeks, 25 to 30 weeks, and 21 to 27 weeks after completion of the treatment regimen. In another embodiment, the level of calprotectin is reduced in a subject in need of treatment 1 week or more, 2 weeks or more, 3 weeks or more, 4 weeks or more, 5 weeks or more, 6 weeks or more, 7 weeks or more, 8 weeks or more, 9 weeks or more, 10 weeks or more, 11 weeks or more, 12 weeks or more, 13 weeks or more, 14 weeks or more, 15 weeks or more, 16 weeks or more, 18 weeks or more, 20 weeks or more, 22 weeks or more, 24 weeks or more, 26 weeks or more, 28 weeks or more, 30 weeks or more, 40 weeks or more, 50 weeks or more after completion of the treatment regimen.

[0066] In one aspect, the present disclosure provides a method for treating ulcerative colitis in a subject in need thereof, the method comprising treating the patient with a therapeutic regimen of administering a pharmaceutical composition comprising live, non-pathogenic fecal bacteria at least three times per week for at least eight weeks. In another aspect, any of the methods or therapeutic regimens provided herein can further be used to treat one or more indications selected from the group consisting of collagenous colitis, lymphocytic colitis, Crohn's colitis, diverticulitis, and pouchitis.

[0067] In one embodiment, the present disclosure provides a method for treating ulcerative colitis in a subject in need of treatment and exhibiting a Mayo endoscopic score of 3 or less, the method comprising administering to the subject a pharmaceutical composition comprising live non-pathogenic fecal bacteria. In one embodiment, the administration is carried out according to a treatment regimen lasting at least 8 weeks. In one embodiment, the administration is carried out according to a treatment regimen lasting at least 8 weeks and at least 3 times per week. In one embodiment, the administration is carried out according to a treatment regimen lasting at least 8 weeks and at least 3 times per week.

[0068] In some embodiments, the present disclosure provides a method for treating ulcerative colitis in a subject in need thereof, the method comprising administering to the subject a pharmaceutical composition comprising live non-pathogenic fecal bacteria, wherein the subject is not taking concomitant corticosteroids during the method and has not taken corticosteroids immediately prior to initiating the method. In one embodiment, the administration is according to a treatment regimen lasting at least 9 weeks. In some embodiments, the administration is according to a treatment regimen lasting at least 8 weeks and at least 3 times per week.

[0069] In certain embodiments, a subject of the present disclosure exhibits a pre-treatment Mayo score of at least 4, such as a Mayo score of 4, 5, 6, 7, 8, 9, or 10. In one embodiment, a subject of the present disclosure exhibits a pre-treatment Mayo score of 4-10, such as a 4-9, 5-10, 5-8, or 6-8.

[0070] In certain embodiments, a subject of the present disclosure exhibits a pre-treatment UCEIS score of at least 4, such as a UCEIS score of 4, 5, 6, 7, 8, 9, or 10. In one embodiment, a subject of the present disclosure exhibits a pre-treatment UCEIS score of 4-10, such as 4-9, 5-10, 5-8, or 6-8.

[0071] In one embodiment, a subject of the present disclosure can achieve a primary outcome at the end of a treatment regimen, where the primary outcome is defined as steroid-free clinical remission and endoscopic remission or response at the end of the treatment regimen, where steroid-free clinical remission is defined as a total Mayo score of 2 or less and a subscore of 1 or less, and endoscopic remission or response is defined as a reduction in endoscopic score of at least 1 point from baseline. In another embodiment, a subject of the present disclosure can achieve a primary outcome at the end of a treatment regimen, where the primary outcome is defined as steroid-free clinical remission, where the total Mayo score is 2 or less and a subscore of 1 or less. In yet another embodiment, a subject of the present disclosure can achieve a primary outcome at the end of a treatment regimen, where the primary outcome is defined as steroid-free endoscopic remission or response, where the primary outcome is a reduction in endoscopic score of at least 1 point from baseline.

[0072] In one embodiment, the subject of the present disclosure has been free of steroid use within at least one week before starting the method provided herein.In another embodiment, the subject of the present disclosure has been free of steroid use within at least 2, 3, 4, or 5 weeks before starting the method provided herein.In yet another embodiment, the subject of the present disclosure has been free of steroid use within at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 days before starting the method provided herein.In one embodiment, the steroid can be prednisone, budesonide, or hydrocortisone.In one embodiment, the subject of the present disclosure has been free of corticosteroid use within at least one week before starting the method provided herein.In one embodiment, the subject of the present disclosure has been free of corticosteroid use within at least one week before starting the method provided herein.

[0073] In some embodiments, the methods of the present disclosure further comprise determining the subject's baseline gut bacterial diversity. In some embodiments, the subject's baseline gut bacterial diversity is assessed by analyzing the Shannon diversity of the subject's fecal sample before the treatment step. In one embodiment, the subject's baseline fecal Shannon diversity is between 0.5 and 2.2, e.g., between 0.5 and 2.0, between 1.0 and 2.2, or between 1.0 and 1.5, based on bacterial species levels. In some embodiments, the subject's fecal Shannon diversity is increased by at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, 99.5%, 99.8%, or 99.9% compared to pre-treatment. In one embodiment, the subject's fecal Shannon diversity is increased by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 20, or 30-fold compared to pre-treatment. In one embodiment, the subject's post-treatment fecal Shannon diversity is between 1.5 and 6.0 based on the bacterial species level, e.g., between 1.5 and 5.0, between 1.5 and 4.5, between 1.5 and 4.0, between 1.5 and 3.5, between 1.5 and 3.0, between 1.5 and 2.5, between 1.5 and 2.0, between 2.0 and 4.5, between 2.5 and 4.0, between 3.0 and 3.5, between 2.0 and 6.0, between 2.5 and 6.0, between 3.0 and 6.0, between 3.5 and 6.0, between 4.0 and 6.0, between 4.5 and 6.0, between 5.0 and 6.0, and between 5.5 and 6.0.

[0074] In certain embodiments, the disclosed methods further include determining the level of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella in the gut of the subject. In some embodiments, the disclosed methods further include determining the level of one or more bacteria selected from the group consisting of Barnesiella, Parabacteroides, Clostridium IV, Ruminococcus, Blautia, Dorea, Ruminococcus 2, and Clostridium XVIII in the gut of the subject.

[0075] In certain embodiments, the present disclosure provides treatment regimens capable of achieving a primary outcome rate at least two-fold higher than the primary outcome rate from placebo, where the primary outcome is defined as steroid-free clinical and endoscopic remission or response at the end of the treatment regimen, where clinical remission is defined as a total Mayo score of 2 or less and all subscores of 1 or less, and endoscopic remission or response is defined as a reduction of at least one point from baseline in the Mayo endoscopic score. In one embodiment, the present disclosure provides treatment regimens capable of achieving a primary outcome rate higher than the primary outcome rate from placebo, where the primary outcome is defined as steroid-free clinical and endoscopic remission or response at the end of the treatment regimen, where clinical remission is defined as a total Mayo score of 2 or less and all subscores of 1 or less, and endoscopic remission or response is defined as a reduction of at least one point from baseline in the Mayo endoscopic score.

[0076] In one embodiment, a treatment regimen according to the present disclosure can achieve a primary outcome rate of at least 25%, e.g., at least 20%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or at least 99.9%. In certain embodiments, a treatment regimen can achieve a primary outcome rate of 20% to 40%, e.g., 20% to 35%, 25% to 40%, 25% to 35%, 25% to 30%, or 30% to 35%.

[0077] In one embodiment, a treatment regimen according to the present disclosure can achieve a clinical remission maintenance rate of at least 40% 8 weeks after completion of the treatment regimen. In certain embodiments, a treatment regimen can achieve a clinical remission maintenance rate of at least 45%, e.g., at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or at least 99.9%, 8 weeks after completion of the treatment regimen. In certain embodiments, a treatment regimen can achieve a clinical remission maintenance rate of 35% to 60%, e.g., 35% to 55%, 40% to 60%, 40% to 55%, 40% to 50%, 45% to 55%, or 45% to 50%, 8 weeks after completion of the treatment regimen.

[0078] In one embodiment, a treatment regimen according to the present disclosure can achieve a steroid-free clinical remission rate that is at least 2-fold higher than the steroid-free clinical remission rate from placebo, where clinical remission is defined as a total Mayo score for rectal bleeding and bowel frequency of 1 or less. In some embodiments, a treatment regimen according to the present disclosure can achieve a steroid-free clinical remission rate that is higher than the steroid-free clinical remission rate from placebo, where clinical remission is defined as a total Mayo score for rectal bleeding and bowel frequency of 1 or less. In some embodiments, a treatment regimen can achieve a steroid-free clinical remission rate of at least 40%, for example, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or at least 99.9%. In one embodiment, the treatment regimen can achieve a steroid-free clinical remission rate of 35% to 55%, e.g., 40% to 55%, 35% to 50%, 40% to 50%, 40% to 45%, or 45% to 50%.

[0079] In certain embodiments, a treatment regimen according to the present disclosure can achieve a steroid-free clinical response rate that is at least 2-fold higher than the steroid-free clinical response rate from placebo, where clinical response is defined as a total Mayo score reduction of 3 or greater, or a 50% or greater reduction from baseline in the combined score for rectal bleeding and bowel frequency. In one embodiment, a treatment regimen according to the present disclosure can achieve a steroid-free clinical response rate that is higher than the steroid-free clinical response rate from placebo, where clinical response is defined as a total Mayo score reduction of 3 or greater, or a 50% or greater reduction from baseline in the combined score for rectal bleeding and bowel frequency. In one embodiment, a treatment regimen can achieve a steroid-free clinical response rate of at least 50%, e.g., at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or at least 99.9%. In certain embodiments, treatment regimens according to the present disclosure can achieve steroid-free clinical response rates of 45% to 65%, e.g., 45% to 60%, 50% to 65%, 50% to 60%, 50% to 55%, or 55% to 60%.

[0080] In one embodiment, a treatment regimen according to the present disclosure can achieve an endoscopic response rate that is at least 2-fold higher than the endoscopic response rate from placebo, where endoscopic response is defined as a reduction in the total UCEIS score of 3 or greater or 50% or greater from baseline. In one embodiment, a treatment regimen according to the present disclosure can achieve an endoscopic response rate that is higher than the endoscopic response rate from placebo, where endoscopic response is defined as a reduction in the total UCEIS score of 3 or greater or 50% or greater from baseline. In certain embodiments, a treatment regimen can achieve an endoscopic improvement rate of at least 30%, e.g., at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or at least 99.9%. In one embodiment, the treatment regimen can achieve an endoscopic response rate of 30% to 45%, for example, 30% to 40%, 35% to 45%, or 35% to 40%.

[0081] In one aspect, the present disclosure provides a method for treating ulcerative colitis in a subject in need thereof, the method comprising administering to the subject a pharmacologically active dose of a therapeutic composition comprising live non-pathogenic fecal bacteria. In another aspect, the present disclosure enables the use of a composition comprising live non-pathogenic fecal bacteria to manufacture a medicament for treating ulcerative colitis.

[0082] In some embodiments, the methods of the present disclosure treat a condition of ulcerative colitis selected from the group consisting of ulcerative proctitis, proctosigmoiditis, left-sided colitis, and panulcerative colitis. In certain embodiments, a pharmaceutical composition according to the present disclosure comprises a fecal microbial preparation. In one embodiment, the pharmaceutical composition comprises an isolated or purified community of live, non-pathogenic fecal bacteria. In certain embodiments, the pharmaceutical composition comprises a non-selective fecal microbiota. In one embodiment, the pharmaceutical composition comprises a non-selective, substantially complete fecal microbiota. In certain embodiments, the pharmaceutical composition comprises a full-spectrum identified fecal microbiota. In one embodiment, the method further comprises administering a 5-aminosalicylate agent, a corticosteroid, an immunosuppressant, or a combination of these substances. In another embodiment, the method further comprises administering 5-aminosalicylic acid or a derivative of 5-aminosalicylic acid, sulfasalazine or a derivative of sulfasalazine, or a combination of these substances.

[0083] In one aspect, the present disclosure provides a method for treating ulcerative colitis in a subject in need of treatment, the method comprising determining the level of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella in the intestine of the subject, and recommending fecal bacteriotherapy if the level of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella is above a predetermined level. In one embodiment, the level of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella is about 8% above a predetermined level, e.g., about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 100%, about 150%, or about 200% above a predetermined level. In one embodiment, the present disclosure provides a method for selecting a treatment regimen for treating ulcerative colitis in a subject in need thereof, the method comprising determining the level of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella in the subject's intestine and recommending fecal bacteriotherapy if the level of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella is within a predetermined range. In one embodiment, the predetermined range is about 8% to about 50% above the predetermined level, e.g., about 8% to about 40%, about 10% to about 50%, about 15% to about 40%, about 20% to about 35%, or about 25% to about 30% above the predetermined level. In some embodiments, the predetermined range is about 50% to about 200% above the predetermined level, e.g., about 50% to about 150%, about 50% to about 100%, about 100% to 150%, about 80% to about 120%, about 90% to about 110%, or about 98% to about 100% above the predetermined level. In some embodiments, the level of one or more bacteria is determined by analyzing the subject's feces.

[0084] In one aspect, the present disclosure provides a method for selecting a treatment regimen for treating ulcerative colitis in a subject in need thereof, the method comprising: determining a level of one or more bacteria selected from the group consisting of Barnesiella, Parabacteroides, Clostridium IV, Ruminococcus, Blautia, Dorea, Ruminococcus 2, and Clostridium XVIII in the intestine of the subject; and recommending fecal bacteriotherapy if the level of the selected one or more bacteria is above a predetermined level. In certain embodiments, the level of the selected one or more bacteria is about 8% above the predetermined level, e.g., about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 100%, about 150%, or about 200% above the predetermined level. In one aspect, the present disclosure provides a method for selecting a treatment regimen for treating ulcerative colitis in a subject in need thereof, the method comprising: determining a level of one or more bacteria selected from the group consisting of Barnesiella, Parabacteroides, Clostridium IV, Ruminococcus, Blautia, Dorea, Ruminococcus 2, and Clostridium XVIII in the intestine of the subject; and recommending fecal bacteriotherapy if the level of the selected one or more bacteria is within a predetermined range. In one embodiment, the predetermined range is about 8% to about 50% above the predetermined level, e.g., about 8% to about 40%, about 10% to 50%, about 15% to about 40%, about 20% to about 35%, or about 25% to about 30% above the predetermined level.In some embodiments, the predetermined range is about 50% to about 200% above the predetermined level, e.g., about 50% to about 150%, about 50% to about 100%, about 100% to 150%, about 80% to about 120%, about 90% to about 110%, or about 98% to about 100% above the predetermined level. In some embodiments, the level of one or more bacteria is determined by analyzing the subject's feces.

[0085] In one embodiment, the predetermined level is established by the corresponding levels of one or more selected bacteria in a healthy subject. In some embodiments, the predetermined level is established by the corresponding levels of one or more selected bacteria in a healthy subject belonging to the same demographic category as the subject. In one embodiment, the predetermined level is established by the abundance of the total Clostridium or Bacteriodetes bacterial community in the same subject.

[0086] In one aspect, the present disclosure provides a method of eliminating or reducing one or more ulcerative colitis symptoms selected from the group consisting of diarrhea, cramps, tenesmus, weight loss, bleeding, loss of appetite, abdominal pain, fever, fatigue, anemia, inflammation, and microulcers.

[0087] In one aspect, the present disclosure provides a method for treating ulcerative colitis in a subject in need of treatment, the method comprising administering to the subject a pharmacologically active dose of a therapeutic composition comprising live non-pathogenic bacteria. In one aspect, the present disclosure provides a method for treating ulcerative colitis in a subject in need of treatment, the method comprising administering to the subject a pharmacologically active dose of a therapeutic composition comprising live non-pathogenic fecal bacteria daily. In one aspect, the therapeutic composition is administered to an ulcerative colitis patient in need of treatment at least once daily for at least two consecutive days. In one aspect, the therapeutic composition is administered at least once daily for at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 consecutive days. In another embodiment, the therapeutic composition is administered at least once daily for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive weeks. In one embodiment, the therapeutic composition is administered at least once daily for up to 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 consecutive days or for up to 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 consecutive weeks. In another embodiment, the therapeutic composition is administered at least once daily for up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive weeks, or for up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive months. In yet another embodiment, the therapeutic composition is administered chronically for the entire lifespan of the subject, or indefinitely, at least once daily for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive months, or for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive years.

[0088] In one embodiment, the therapeutic composition is administered to a patient with ulcerative colitis in need of treatment at least twice daily for at least two consecutive days. In one embodiment, the therapeutic composition is administered at least twice daily for at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 consecutive days. In another embodiment, the therapeutic composition is administered at least twice daily for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive weeks. In one embodiment, the therapeutic composition is administered at least twice daily for up to 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 consecutive days, or for up to 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 consecutive weeks. In another embodiment, the therapeutic composition is administered at least twice daily for up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive weeks, or for up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive months. In yet another embodiment, the therapeutic composition is administered chronically for the entire lifespan of the subject, or indefinitely, at least twice daily for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive months, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive years.

[0089] In one embodiment, the therapeutic composition is administered to a patient with ulcerative colitis in need of treatment at least three times daily for at least two consecutive days. In one embodiment, the therapeutic composition is administered at least three times daily for at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 consecutive days. In another embodiment, the therapeutic composition is administered at least three times daily for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive weeks. In one embodiment, the therapeutic composition is administered at least three times daily for up to 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 consecutive days, or for up to 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 consecutive weeks. In another embodiment, the therapeutic composition is administered at least three times daily for up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive weeks, or for up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive months. In yet another embodiment, the therapeutic composition is administered chronically for the entire life of the subject, or indefinitely, at least three times daily for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive months, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 consecutive years.

[0090] In one aspect, the disclosure provides a method for treating ulcerative colitis in a subject in need thereof, the method comprising orally administering to the subject a pharmacologically active dose of a therapeutic composition comprising a non-pathogenic live synthetic bacterial mixture or a non-pathogenic live purified or extracted fecal microbiota, wherein the dose is administered on a dosing schedule of at least once or twice daily for at least three consecutive days or three weeks. In another aspect, the dose is administered at least once, twice, or three times daily for a period of 1-12 weeks, 2-12 weeks, 3-12 weeks, 4-12 weeks, 5-12 weeks, 6-12 weeks, 7-12 weeks, 8-12 weeks, 9-12 weeks, 10-12 weeks, 1-2 weeks, 2-3 weeks, 3-4 weeks, 4-5 weeks, 5-6 weeks, 6-7 weeks, 7-8 weeks, 8-9 weeks, 9-10 weeks, or 10-11 weeks.

[0091] In one embodiment, the present disclosure provides a method for treating ulcerative colitis in a subject in need thereof, the method comprising a first dosing schedule and a second dosing schedule following the first dosing schedule. In one embodiment, the first dosing schedule comprises a treatment or induction dose. In one embodiment, the first dosing schedule comprises a continuous dosing schedule. In another embodiment, the second dosing schedule comprises a maintenance dose equal to or less than the pharmacologically active dose of the first dosing schedule. In another embodiment, the second dosing schedule continues for at least about 2, 4, 6, 8, 10, 12, 18, 24, 36, 48, 72, or 96 months. In one embodiment, the second dosing schedule continues for the entire lifespan of the treated subject or indefinitely. In one embodiment, the second dosing schedule is a continuous dosing schedule. In another embodiment, the second dosing schedule is an intermittent dosing schedule. In yet another embodiment, the second dosing schedule is an intermittent dosing schedule comprising a treatment period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 days, followed by a rest period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 days. In another embodiment, the second dosing schedule comprises administering a second dose (e.g., a maintenance dose) every other day, every third day, or every third, fourth, fifth, sixth, seventh, or eighth day. In another embodiment, the maintenance dose is administered over an extended period of time, with or without titration (or otherwise altering the dose or dosing schedule). In one embodiment, the interval between the first and second dosing schedules is at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 weeks. In another embodiment, the second dosing schedule (e.g., maintenance dosing) comprises doses that are about 2, 5, 10, 50, 100, 200, 400, 800, 1000, 5000, or more times lower than the doses used in the first dosing schedule (e.g., initial treatment doses). In another embodiment, the second dosing schedule (e.g., maintenance dosing schedule) has a dosing frequency that is the same as or less than the first dosing schedule (e.g., initial treatment dosing schedule).In another embodiment, the second dosing schedule (eg, the maintenance dosing schedule) has a longer interval between doses than the first dosing schedule (eg, the initial treatment dosing schedule).

[0092] In one embodiment, the first or second administration schedule used in a method can be once a week, twice a week, or three times a week. The term "once a week" means that the dose is administered once a week, preferably on the same day each week. "Twice a week" means that the dose is administered twice a week, preferably on the same two days each week. "Thrice a week" means that the dose is administered three times a week, preferably on the same three days each week.

[0093] In one embodiment, the subject to be treated is a subject who already suffers from ulcerative colitis. Administration of the disclosed therapeutic composition to a clinically asymptomatic human subject who is genetically predisposed or susceptible to ulcerative colitis is also useful for preventing the onset of clinical symptoms of ulcerative colitis. A human subject who is genetically predisposed or susceptible to ulcerative colitis can be a human subject who has a close family member or relative who exhibits or suffers from ulcerative colitis. In another embodiment, the subject to be treated is a subject who needs to be prevented from ulcerative colitis. In another embodiment, the subject to be treated is predisposed or susceptible to ulcerative colitis. In another embodiment, the subject to be treated is a subject who has been diagnosed with ulcerative colitis. In one embodiment, the subject to be treated is a patient in need of treatment.

[0094] In one embodiment, the subject to be treated is a human patient. In one embodiment, the patient is a male patient. In one embodiment, the patient is a female patient. In one embodiment, the patient is a premature infant. In one embodiment, the patient is a full-term infant. In one embodiment, the patient is a newborn. In one embodiment, the patient is an infant. In one embodiment, the patient is a toddler. In one embodiment, the patient is a young child. In one embodiment, the patient is a child. In one embodiment, the patient is an adolescent. In one embodiment, the patient is a pediatric patient. In one embodiment, the patient is a geriatric patient. In one embodiment, the human patient is a minor patient about 18, 15, 12, 10, 8, 6, 4, 3, 2, or 1 year old or younger. In another embodiment, the human patient is an adult patient. In another embodiment, the human patient is a geriatric patient. In yet another embodiment, the human patient is greater than about 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or 95 years of age. In another embodiment, the patient is about 1-5 years, 2-10 years, 3-18 years, 21-50 years, 21-40 years, 21-30 years, 50-90 years, 60-90 years, 70-90 years, 60-80 years, or 65-75 years of age. In one embodiment, the patient is a young elderly patient (65-74 years old). In one embodiment, the patient is a moderately elderly patient (75-84 years old). In one embodiment, the patient is a very elderly patient (>85 years old).

[0095] In one embodiment, a method comprises administering the therapeutic composition orally, via enema, or via rectal suppository. In one embodiment, the therapeutic composition administered herein is formulated as an enteric-coated (and / or acid-resistant) capsule or microcapsule, or is formulated as part of, or administered together with, a food, food additive, dairy-based product, soy-based product, or a food derivative thereof, jelly, or yogurt. In another embodiment, the therapeutic composition administered herein is formulated as an acid-resistant enteric capsule. The therapeutic composition can be provided as a powder for sale in combination with a food or beverage. The food or beverage can be a dairy-based product or a soy-based product. In another embodiment, a food or dietary supplement comprises enteric-coated and / or acid-resistant microcapsules containing the therapeutic composition.

[0096] In one embodiment, the therapeutic composition comprises a liquid culture. In another embodiment, the therapeutic composition is lyophilized, crushed, or powdered. The therapeutic composition can then be injected, for example, dissolved in saline as an enema. Alternatively, the powder can be encapsulated as an enteric-coated and / or acid-resistant capsule for oral administration. These capsules can be in the form of enteric-coated and / or acid-resistant microcapsules. Preferably, the powder can be provided in a palatable form for reconstituting a beverage or as a food additive. In yet another embodiment, the food is yogurt. In one embodiment, the powder can be reconstituted and injected using nasoduodenal infusion.

[0097] In another embodiment, the therapeutic composition administered herein is in liquid, frozen, freeze-dried, spray-dried, lyophilized, or powder form. In yet another embodiment, the therapeutic composition administered herein is formulated as a delayed-release dosage form or a sustained-release enteric-coated dosage form. In another embodiment, the therapeutic composition administered herein comprises an excipient, saline, a buffer, a buffering agent, or a fluid-glucose-cellobiose agar (RGCA) medium. In another embodiment, the therapeutic composition administered herein comprises a cryoprotectant. In one embodiment, the cryoprotectant comprises polyethylene glycol, skim milk, erythritol, arabitol, sorbitol, glucose, fructose, alanine, glycine, proline, sucrose, lactose, ribose, trehalose, dimethyl sulfoxide (DMSO), glycerol, or a combination of these substances.

[0098] In one embodiment, the therapeutic composition administered herein further comprises an acid suppressant, an antacid, an H2 antagonist, a proton pump inhibitor, or a combination of these substances. In one embodiment, the therapeutic composition administered herein is substantially free of non-living matter. In another embodiment, the therapeutic composition administered herein is substantially free of acellular matter selected from the group consisting of residual fibers, DNA, antiviral coating material, and non-viable matter.

[0099] In one embodiment, the therapeutic composition also comprises or is supplemented with a prebiotic nutrient selected from the group consisting of polyols, fructooligosaccharides (FOS), oligofructose, inulin, galactooligosaccharides (GOS), xylooligosaccharides (XOS), polydextrose, monosaccharides, tagatose, and / or mannooligosaccharides.

[0100] In one embodiment, a method further comprises pretreating the subject with an antibiotic composition prior to administering the therapeutic bacteria or microbiota composition. In one embodiment, the antibiotic composition administered herein comprises an antibiotic selected from the group consisting of rifabutin, clarithromycin, clofazimine, vancomycin, rifampicin, nitroimidazole, chloramphenicol, and combinations of these substances. In another aspect, the antibiotic composition administered herein comprises an antibiotic selected from the group consisting of rifaximin, rifamycin derivatives, rifampicin, rifabutin, rifapentine, rifalazil, bicozamycin, aminoglycosides, gentamicin, neomycin, streptomycin, paromomycin, beldamcin, mutamycin, sisomicin, netilmicin, retimycin, kanamycin, aztreonam, aztreonam macrolide, clarithromycin, dirithromycin, roxithromycin, telithromycin, azithromycin, bismuth salicylate, vancomycin, streptomycin, fidaxomicin, amikacin, arbekacin, neomycin, netilmicin, paromomycin, rhodostreptomycin, tobramycin, apramycin, and combinations of these substances. In yet another aspect, a method further comprises pretreating the subject with an anti-inflammatory drug prior to administration of the therapeutic bacteria or microbiota composition.

[0101] In one embodiment, a method achieves an ulcerative colitis remission, cure, response, or resolution rate of at least about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99%. In one embodiment, a treatment method achieves a reduction in the Ulcerative Colitis Disease Activity Index (UCDAI) of greater than 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 after 8 weeks of treatment. In another embodiment, the treatment method achieves a reduction in the Ulcerative Colitis Disease Activity Index (UCDAI) of greater than 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 after 8 weeks of treatment in at least 10%, 20%, 30%, 50%, 60%, 70%, 80%, or 90% of the patients in the patient population. In one embodiment, the treatment method achieves at least a 10%, 20%, 30%, 50%, 60%, 70%, 80%, or 90% reduction in the Ulcerative Colitis Disease Activity Index (UCDAI) after 8 weeks of treatment compared to baseline (e.g., immediately before treatment). In one embodiment, the treatment method achieves at least a 10%, 20%, 30%, 50%, 60%, 70%, 80%, or 90% reduction in the Ulcerative Colitis Disease Activity Index (UCDAI) after 8 weeks of treatment compared to baseline (e.g., immediately before treatment) in at least 10%, 20%, 30%, 50%, 60%, 70%, 80%, or 90% of patients.

[0102] In yet another embodiment, patients are assessed using the Disease Activity Index (DAI) or Mayo scoring system, as described in the article by Schroeder et al., N Eng J Med. 1987;317:1625-1629, in which mild to moderately active ulcerative colitis is treated with enteric-coated oral 5-aminosalicylic acid therapy. In one embodiment, the treatment method achieves at least a 10%, 20%, 30%, 50%, 60%, 70%, 80%, or 90% reduction in the Mayo score after 8 weeks of treatment compared to baseline (e.g., immediately before treatment). In one embodiment, the treatment method achieves at least a 10%, 20%, 30%, 50%, 60%, 70%, 80%, or 90% reduction in Mayo score after 8 weeks of treatment compared to baseline (e.g., immediately before treatment) in at least 10%, 20%, 30%, 50%, 60%, 70%, 80%, or 90% of patients.

[0103] In one embodiment, the pharmacologically active dose or therapeutically effective dose is at least about 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , or 10 13 In another embodiment, the pharmacologically active dose or therapeutically effective dose comprises up to about 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , or 10 13 In yet another embodiment, the pharmacologically active dose or therapeutically effective dose comprises 10 8 cfu~10 14 cfu, 10 9 cfu~10 13 cfu, 10 10 cfu~10 12 cfu, 10 9 cfu~10 14 cfu, 109 cfu~10 12 cfu, 10 9 cfu~10 11 cfu, 10 9 cfu~10 10 cfu, 10 10 cfu~10 14 cfu, 10 10 cfu~10 13 cfu, 10 11 cfu~10 14 cfu, 10 11 cfu~10 13 cfu, 10 12 cfu~10 14 cfu, and 10 13 cfu~10 14 cfu.

[0104] In one embodiment, the pharmacologically active dose or therapeutically effective dose is at least about 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , or 10 13 In another embodiment, the pharmacologically active dose or therapeutically effective dose is at most about 10 cells or spores. 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , or 10 13 In yet another embodiment, the pharmacologically active dose or therapeutically effective dose comprises 10 total cells or spores. 8 ~10 14 , 10 9 ~10 13 , 10 10 ~10 12 , 10 9 ~10 14 , 10 9 ~10 12 , 10 9 ~10 11 , 109 ~10 10 , 10 10 ~10 14 , 10 10 ~10 13 , 10 11 ~10 14 , 10 11 ~10 13 , 10 12 ~10 14 and 10 13 ~10 14 In some embodiments, the pharmacologically active or therapeutically effective dose is in terms of viable cells.

[0105] In one embodiment, the therapeutic compositions administered herein comprise fecal bacteria. In one embodiment, the therapeutic compositions administered herein comprise fecal bacteria, such as Clostridium, Bacillus, Collinsella, Bacteroides, Eubacterium, Fusobacterium, Propionibacterium, Lactobacillus, Ruminococcus, Escherichia coli, and the like. The present invention includes one or more, two or more, three or more, four or more, or five or more isolated, purified, or cultured microorganisms selected from the group consisting of Bacillus subtilis, Bacillus anthracis, Bifidobacterium spp., Bacillus subtilis ...

[0106] In one embodiment, the therapeutic compositions administered herein are selected from the group consisting of Bacteroides fragilis ssp. vulgatus, Collinsella aerofaciens, Bacteroides fragilis ssp. thetaiotaomicron, Peptostreptococcus productus II, Parabacteroides distasonis, Fusobacterium prausnitzii, Coprococcus eutactus, Collinsella aerofaciens III, and the like. III, Peptostreptococcus productus I, Ruminococcus bromii, Bifidobacterium adolescentis, Gemmiger formicilis, Bifidobacterium longum, Eubacterium siraeum, Ruminococcus torques, Eubacterium rectale, Eubacterium eligens, Bacteroides eggerthii, Clostridium leptum leptum), Bacteroides fragilis subspecies A (Bacteroides fragilis ssp.A), Eubacterium biforme, Bifidobacterium infantis, Eubacterium rectale III-F, Coprococcus comes, Pseudoflavonifractor capillosus, Ruminococcus albus, Dorea formicigenerans, Eubacterium hallii, Eubacterium ventriosum I, Fusobacterium russi, Ruminococcus obeum obeum, Eubacterium rectale, Clostridium ramosum, Lactobacillus leichmannii, Ruminococcus callidus, Butyrivibrio crossotus, Acidaminococcus fermentans, Eubacterium ventriosum, Bacteroides fragilis ssp.Fragilis, Bacteroides AR, Coprococcus catus, Aerostipes hadrus, Eubacterium cylindroides, Eubacterium ruminantium, Eubacterium CH-1, Staphylococcus epidermidis, Peptostreptococcus BL, Eubacterium limosum, Tissirella praeacuta, Bacteroides L, Fusobacterium mortiferum I mortiferum I, Fusobacterium naviforme, Clostridium innocuum, Clostridium ramosum, Propionibacterium acnes, Ruminococcus flavefaciens, Ruminococcus AT, Peptococcus AU-1, Bacteroides fragilis ssp.ovatus, subspecies d, and subspecies f; Bacteroides L-1 and L-5; Fusobacterium nucleatum, Fusobacterium mortiferum, Escherichia coli, Gemella morbillorum, Finegoldia magnus, Peptococcus G and AU-2; Streptococcus intermedius, Ruminococcus lactaris, Ruminococcus CO Gemmiger X, Coprococcus BH and BC BH,-CC; Eubacterium tenue, Eubacterium ramulus, Bacteroides clostridiiformis ssp. clostridiiformis, Bacteroides coagulans, Prevotella oralis, Prevotella ruminicola, Odoribacter splanchnicus, Desuifomonas pigra, Lactobacillus G, Succinivibrio A A), and combinations thereof, comprising at least one, at least two, at least three, at least four, at least five, at least six, or at least seven fecal microorganisms selected from the group consisting of:

[0107] In one embodiment, the therapeutic compositions administered herein do not contain viable Bacteroides, Fusobacterium, Propionibacterium, Lactobacillus, Ruminococcus, Escherichia coli, Gemmiger, Desulfomonas, Peptostreptococcus, Bifidobacterium, Monilia, or any combination of these substances. In another aspect, the therapeutic compositions administered herein contain viable Bacteroides fragilis ssp. vulgatus, Collinsella aerofaciens, Bacteroides fragilis ssp. thetaiotaomicron, and Bacteroides fragilis ssp.thetaiotaomicron, Peptostreptococcus productus II, Parabacteroides distasonis, Fusobacterium prausnitzii, Coprococcus eutactus, Collinsella aerofaciens III, Peptostreptococcus productus I, Ruminococcus bromii, Bifidobacterium adolescentis, Eubacterium siraeum, Bifidobacterium longum longum, Eubacterium siraeum, Ruminococcus torques, Eubacterium rectale, Eubacterium eligens, Bacteroides eggerthii, Clostridium leptum, Bacteroides fragilis ssp.A), Eubacterium biforme, Bifidobacterium infantis, Eubacterium rectale III-F, Coprococcus comes, Pseudoflavonifractor capillosus, Ruminococcus albus, Dorea formicigenerans, Eubacterium hallii, Eubacterium ventriosum I, Fusobacterium russi, Ruminococcus obeum obeum, Eubacterium rectale, Clostridium ramosum, Lactobacillus leichmannii, Ruminococcus callidus, Butyrivibrio crossotus, Acidaminococcus fermentans, Eubacterium ventriosum, Bacteroides fragilis ssp.fragilis, Bacteroides AR, Coprococcus catus, Aerostipes hadrus, Eubacterium cylindroides, Eubacterium ruminantium, Eubacterium CH-1, Staphylococcus epidermidis, Peptostreptococcus BL, Eubacterium limosum, Tissirella praeacuta, Bacteroides L L), Fusobacterium mortiferum I, Fusobacterium naviforme, Clostridium innocuum, Clostridium ramosum, Propionibacterium acnes, Ruminococcus flavefaciens, Ruminococcus AT, Peptococcus AU-1, Bacteroides fragilis ssp. ovatus, subsp. d, subsp. ff); Bacteroides Ll, ​​L-5; Fusobacterium nucleatum, Fusobacterium mortiferum, Escherichia coli, Gemella morbillorum, Finegoldia magnus, Peptococcus G, -AU-2; Streptococcus intermedius, Ruminococcus lactaris, Ruminococcus CO Gemmiger X, Coprococcus BH, -CC BH,-CC; does not contain Eubacterium tenue, Eubacterium ramulus, Bacteroides clostridiiformis ssp. clostridiiformis, Bacteroides coagulans, Prevotella oralis, Prevotella ruminicola, Odoribacter splanchnicus, Desuifomonas pigra, Lactobacillus G, Succinivibrio A, or combinations of these substances.

[0108] In one embodiment, the therapeutic composition administered herein comprises a fecal microbiota. In another embodiment, the preparation of a fecal microbiota used herein comprises a treatment selected from the group consisting of ethanol treatment, detergent treatment, heat treatment, irradiation, and ultrasonic treatment. In another embodiment, the preparation of a fecal microbiota used herein does not comprise a treatment selected from the group consisting of ethanol treatment, detergent treatment, heat treatment, irradiation, and ultrasonic treatment. In one embodiment, the preparation of a fecal microbiota used herein comprises a separation step selected from the group consisting of density gradient method, filtration treatment (e.g., sieving, nylon mesh), and chromatography. In another embodiment, the preparation of a fecal microbiota used herein does not comprise a separation step selected from the group consisting of density gradient method, filtration treatment (e.g., sieving, nylon mesh), and chromatography. In another embodiment, the fecal microbiota used herein comprises the whole fecal microbiota of a donor. In another embodiment, the therapeutic composition administered herein comprises a fecal microbiota that is substantially free of eukaryotic cells derived from the donor of the fecal microbiota.

[0109] In another embodiment, the therapeutic compositions administered herein comprise a fecal microbiota that has been further supplemented, inoculated, or augmented with fecal microorganisms. In one embodiment, the fecal microbiota is supplemented with non-pathogenic (or attenuated pathogenic) bacteria of Clostridium, Collinsella, Dorea, Ruminococcus, Coprococcus, Prevotella, Veillonella, Bacteroides, Bacillus, or combinations of these substances. In another embodiment, the therapeutic compositions administered herein comprise a fecal microbiota further supplemented, inoculated, or supplemented with species of Veillonellaceae, Firmicutes, Gammaproteobacteria, Bacteroidetes, or a combination of these substances. In another embodiment, the therapeutic compositions administered herein comprise a fecal microbiota further supplemented with fecal bacterial spores. In one embodiment, the fecal bacterial spores are Clostridium spores, Bacillus spores, or both Clostridium spores and Bacillus spores.

[0110] In one aspect, the therapeutic composition comprises fecal microbiota from a subject selected from the group consisting of a human, a cow, a dairy calf, a ruminant, a sheep, a goat, or a deer. In another aspect, the therapeutic composition can be administered to a subject selected from the group consisting of a human, a cow, a dairy calf, a ruminant, a sheep, a goat, or a deer. In one aspect, the therapeutic composition is substantially odorless or nearly odorless.

[0111] In certain aspects, a therapeutic composition provided or administered herein comprises a fecal microbiota having a Shannon diversity index of 0.3 or greater, 0.4 or greater, 0.5 or greater, 0.6 or greater, 0.7 or greater, 0.8 or greater, 0.9 or greater, 1.0 or greater, 1.1 or greater, 1.2 or greater, 1.3 or greater, 1.4 or greater, 1.5 or greater, 1.6 or greater, 1.7 or greater, 1.8 or greater, 1.9 or greater, 2.0 or greater, 2.1 or greater, 2.2 or greater, 2.3 or greater, 2.4 or greater, 2.5 or greater, 3.0 or greater, 3.1 or greater, 3.2 or greater, 3.3 or greater, 3.4 or greater, 3.5 or greater, 3.6 or greater, 3.7 or greater, 3.8 or greater, 3.9 or greater, 4.0 or greater, 4.1 or greater, 4.2 or greater, 4.3 or greater, 4.4 or greater, 4.5 or greater, or 5.0 or greater. In another embodiment, a therapeutic composition comprises a fecal microbiota having a Shannon diversity index of 0.1 to 3.0, 0.1 to 2.5, 0.1 to 2.4, 0.1 to 2.3, 0.1 to 2.2, 0.1 to 2.1, 0.1 to 2.0, 0.4 to 2.5, 0.4 to 3.0, 0.5 to 5.0, 0.7 to 5.0, 0.9 to 5.0, 1.1 to 5.0, 1.3 to 5.0, 1.5 to 5.0, 1.7 to 5.0, 1.9 to 5.0, 2.1 to 5.0, 2.3 to 5.0, 2.5 to 5.0, 2.7 to 5.0, 2.9 to 5.0, 3.1 to 5.0, 3.3 to 5.0, 3.5 to 5.0, 3.7 to 5.0, 31.9 to 5.0, or 4.1 to 5.0. In one embodiment, the Shannon diversity index is calculated at the phylum level. In another embodiment, the Shannon diversity index is calculated at the family level. In one embodiment, the Shannon diversity index is calculated at the genus level. In another embodiment, the Shannon diversity index is calculated at the species level. In yet another embodiment, the therapeutic composition comprises a microbiota preparation with a proportion of content similar to that of normal healthy human fecal microbiota.

[0112] In yet another embodiment, a therapeutic composition comprises fecal bacteria from at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 different families. In yet another embodiment, a therapeutic composition comprises fecal bacteria from multiple donors. In certain embodiments, a therapeutic composition provided or administered herein comprises a fecal microbiota that contains no more than 0.05%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, or 10% non-living / heavy biological matter by weight. In another aspect, the therapeutic compositions provided or administered herein comprise fecal microbiota that contains no more than 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% non-living / heavy biological matter by weight. In another embodiment, the therapeutic compositions provided or administered herein consist of or consist essentially of particles, including particles of non-living material and / or particles of biological material, from a fecal sample that pass through a sieve, column, or similar filtration device having a sieve size, exclusion size, or particle filtration size of 2.0 mm, 1.0 mm, 0.5 mm, 0.25 mm, 0.212 mm, 0.180 mm, 0.150 mm, 0.125 mm, 0.106 mm, 0.090 mm, 0.075 mm, 0.063 mm, 0.053 mm, 0.045 mm, 0.038 mm, 0.032 mm, 0.025 mm, 0.020 mm, 0.01 mm, or 0.2 mm. "Non-living material" does not include excipients, e.g., pharmaceutically inactive substances such as cryoprotectants, that are added to the fecal material being processed. "Biological material" refers to living matter in fecal material, including microorganisms, including prokaryotic cells such as bacteria and archaea (e.g., living prokaryotic cells and spores that can form spores into living prokaryotic cells), protozoa and fungi, and eukaryotic cells such as viruses. In one embodiment, "biological material" refers to living matter present in the colon of a normal, healthy human, such as microorganisms, eukaryotic cells, and viruses.In certain aspects, the therapeutic compositions provided or administered herein comprise an extract of human feces, wherein the composition is substantially odorless. In certain aspects, the therapeutic compositions provided or administered herein comprise fecal material or a fecal microbiota preparation in a lyophilized, crude, semi-purified, or purified formulation.

[0113] In some embodiments, the fecal microbiota in the therapeutic composition comprises a highly refined or purified fecal microbiota, e.g., a fecal microbiota that is substantially free of material other than fecal microbiota material. In some embodiments, the fecal microbiota can be further processed, e.g., microfiltered before, after, or both before and after sieving. In other embodiments, the metabolic products of the highly purified fecal microbiota are ultrafiltered to remove large molecules but retain the therapeutic microbiota, e.g., bacteria.

[0114] In another aspect, the fecal microbiota in a therapeutic composition used herein comprises substantially isolated or purified fecal microbiota or the whole (or substantially all) microbiota, or consists essentially of fecal microbiota or the whole microbiota, where the whole microbiota is (or comprises) an isolate of fecal microbiota, and the isolate is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% of material other than fecal microbiota material. The bacterial flora may be isolated or purified, or may have less than about 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, or 1.0% or more non-fecal flora material, or may be substantially isolated, purified, or may be substantially all of the bacterial flora as described in WO 2012 / 122478 A1 by Sadowsky et al. or WO 2012 / 016287 A2 by Borody et al.

[0115] In some embodiments, the fecal microbiota in the therapeutic composition comprises substantially all or unselected fecal microbiota from the donor, reconstituted fecal material, or synthetic fecal material. In other embodiments, the fecal microbiota in the therapeutic composition does not comprise antibiotic-resistant communities. In other embodiments, the therapeutic composition comprises fecal microbiota and is substantially free of extraneous material (e.g., non-living material including acellular material such as residual fiber, DNA, RNA, viral coat material, non-viable material, and living material such as eukaryotic cells derived from the donor of the fecal material).

[0116] In some embodiments, the fecal microbiota in the therapeutic composition used herein is derived from disease-screened fresh homogenous feces or equivalently freeze-dried and reconstituted feces. In some embodiments, the fresh homogenous feces does not contain antibiotic-resistant communities. In other embodiments, the fecal microbiota in the therapeutic composition is derived from a synthetic fecal composition. In some embodiments, the synthetic fecal composition contains, preferably in proportion, a preparation of live microbiota resembling normal healthy human fecal microbiota, but free of antibiotic-resistant communities. Suitable microorganisms may be selected from the following: Bacteroides, Eubacterium, Fusobacterium, Propionibacterium, Lactobacillus, Ruminococcus, Escherichia coli, Gemmiger, Clostridium, Desulfomonas, Peptostreptococcus, Bifidobacterium, Collinsella, Coprococcus, Dorea, and Ruminococcus.

[0117] In some embodiments, the therapeutic composition is combined with other adjuvants, such as antacids, to inhibit bacterial inactivation in the stomach. (e.g., Mylanta, Mucaine, Gastrogel). In other embodiments, acid secretion in the stomach can be pharmacologic suppressed using H2-antagonists or proton pump inhibitors. An example of an H2-antagonist is ranitidine. An example of a proton pump inhibitor is omeprazole. In one embodiment, the acid suppressant is administered prior to or simultaneously with administration of the therapeutic composition.

[0118] In certain embodiments, the therapeutic composition is in the form of: an enema composition that can be reconstituted with a suitable diluent; an enteric-coated capsule; an enteric-coated microcapsule; an acid-resistant tablet; an acid-resistant capsule; an acid-resistant microcapsule; a powder to be reconstituted with a diluent suitable for intranasal or colonoscopic administration; a powder to be reconstituted with a diluent, flavoring agent, and gastric acid suppressant suitable for oral ingestion; a powder to be reconstituted with a food or beverage; or a food or dietary supplement comprising the enteric-coated and / or acid-resistant microcapsules of the composition, powder, jelly, or liquid.

[0119] In some embodiments, the treatment method results in a cure, reduction, or reduction in the rate of symptoms of ulcerative colitis. The change in the microbiota is preferably as "near-complete" as possible, with the microbiota being replaced by live microorganisms that will necessarily crowd out any remaining original microbiota. Typically, the change in the intestinal microbiota involves the introduction of a set of defined microbiota into the gastrointestinal system; therefore, in a preferred form, the treatment method involves substantially or completely replacing the pathogenic intestinal microbiota in patients in need of such treatment.

[0120] In another embodiment, the therapeutic composition can be administered together with a pharmaceutically acceptable carrier. As used herein, "pharmaceutically acceptable carrier" refers to a non-toxic solvent, dispersant, excipient, adjuvant, or other material that is mixed with live bacteria to form a pharmaceutical composition, e.g., a dosage form that can be administered to a patient. A pharmaceutically acceptable carrier can be a liquid (e.g., saline), gel, or solid diluent, adjuvant, excipient, or acid-resistant encapsulating component. Suitable diluents and excipients include pharmaceutical grade saline, dextrose, glycerol, mannitol, lactose, starch, magnesium stearate, sodium saccharin, cellulose, magnesium carbonate, etc., and combinations thereof. In another embodiment, the therapeutic composition may contain auxiliary substances such as wetting or emulsifying agents, stabilizers, or pH buffering agents. In certain embodiments, a therapeutic composition contains about 1%-5%, 5%-10%, 10%-15%, 15%-20%, 20%-25%, 25-30%, 30-35%, 40-45%, 50%-55%, 1%-95%, 2%-95%, 5%-95%, 10%-95%, 15%-95%, 20%-95%, 25%-95%, 30%-95%, 35%-95%, 40%-95%, 45%-95%, 50%-95%, 55%-95%, 60%-95%, 65%-95%, 70%-95%, 45%-95%, 80%-95%, or 85%-95% of the active ingredient. In certain embodiments, the therapeutic composition contains about 2%-70%, 5%-60%, 10%-50%, 15%-40%, 20%-30%, 25%-60%, 30%-60%, or 35%-60% active ingredient.

[0121] In some embodiments, the therapeutic composition can be formulated into tablets, drenches, boluses, capsules, or premixes. Formulation of these active ingredients into such dosage forms can be achieved by methods well known in the pharmaceutical formulation field. See, for example, U.S. Patent No. 4,394,377. Capsules can be easily manufactured by filling gelatin capsules with active ingredients in any desired dosage form. If necessary, these materials can be diluted with inert powder diluents such as sugar, starch, powdered milk, purified crystalline cellulose, etc., to increase the volume for convenient filling into capsules.

[0122] In some embodiments, tablets containing therapeutic compositions can be prepared using conventional pharmaceutical processes. In addition to the active ingredient, tablets can contain a base, disintegrant, absorbent, binder, and lubricant. Typical bases include lactose, sugar, sodium chloride, starch, and mannitol. Starch, like alginic acid, is also an excellent disintegrant. Surfactants such as sodium lauryl sulfate and dioctyl sodium sulfosuccinate may also be used. Commonly used absorbents include starch and lactose. Magnesium carbonate is also useful for oily substances. Binders that can be used include gelatin, gum, starch, dextrin, polyvinylpyrrolidone, and various cellulose derivatives. Commonly used lubricants include magnesium stearate, talc, paraffin wax, various metal soaps, and polyethylene glycol.

[0123] In some embodiments, when preparing solid compositions such as tablets, the active ingredient is mixed with a pharmaceutical carrier, e.g., conventional tableting ingredients such as corn starch, lactose, sucrose, sorbitol, talc, stearic acid, magnesium stearate, dicalcium phosphate, or gums, or other pharmaceutical diluents, e.g., water, to form a solid preformulation composition containing a homogeneous mixture of the compositions of the present invention. When these preformulation compositions are described as homogeneous, it is meant that the active ingredient is dispersed evenly throughout the composition, allowing the composition to be readily subdivided into equally effective unit dosage forms such as tablets, pills, and capsules. This solid preformulation composition is then mixed with a desired amount (e.g., at least about 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , or 10 13 cfu)。 The therapeutic compositions used herein can be flavored.

[0124] In some embodiments, the therapeutic composition can be in the form of a tablet or pill. In one embodiment, the tablet or pill can be coated or otherwise compounded to form a dosage form that provides the advantage of prolonged action. For example, the tablet or pill can include an inner dosage component and an outer dosage component, with the outer dosage component overlying the inner dosage component. The two components can be separated by an enteric layer, which serves to resist disintegration in the stomach and allow the inner component to pass intact into the duodenum or to delay release of the inner component. A wide variety of materials can be used for such enteric layers or coatings, including polymeric acids and mixtures of polymeric acids with materials such as shellac, cetyl alcohol, and cellulose acetate.

[0125] In some embodiments, the therapeutic composition can be a drench. In one embodiment, the drench is prepared by selecting a therapeutic composition in the form of a suspension in saline. A water-soluble component can be combined with a water-insoluble component by combining one component of the suspension with the other component in an aqueous solution. Any water-insoluble active ingredient can be prepared as a suspension or in several physiologically acceptable solvents, such as polyethylene glycol. A suspension of any water-insoluble active ingredient can be prepared in oils, such as peanut oil, corn oil, sesame oil, etc., in glycols, such as propylene glycol or polyethylene glycol, or in water, depending on the solubility of the particular active ingredient. A suitable physiologically acceptable adjuvant is required to keep the active ingredient in suspension. The adjuvant can include thickeners, such as carboxymethylcellulose, polyvinylpyrrolidone, gelatin, and alginates, and can be selected from among thickeners. Surfactants generally act to suspend active ingredients, especially fat-soluble propionate-enhancing compounds.The most useful ones for making suspensions in liquid non-solvents are alkylphenol polyethylene oxide adducts, naphthalene sulfonates, alkylbenzene sulfonates, and polyoxyethylene sorbitan esters.In addition, many substances that affect the hydrophilicity, density, and surface tension of liquids can make suspensions easier to make in individual cases.For example, silicone antifoams, glycols, sorbitol, and sugars can be useful suspending agents.

[0126] In certain embodiments, the therapeutic composition is selected from the group consisting of Clostridium absonum, Clostridium argentinense, Clostridium baratii, Clostridium botulinum, Clostridium cadaveris, Clostridium carnis, Clostridium celatum, Clostridium chauvoei, Clostridium clostridioforme, Clostridium cochlearium, Clostridium fallax, and Clostridium felsineum. felsineum, Clostridium ghonii, Clostridium glycolicum, Clostridium haemolyticum, Clostridium hastiforme, Clostridium histolyticum, Clostridium indolis, Clostridium irregulare, Clostridium limosum, Clostridium malenominatum, Clostridium novyi, Clostridium oroticum, Clostridium paraputrificum paraputrificum, Clostridium perfringensperfringens, Clostridium piliforme, Clostridium putrefaciens, Clostridium putrificum, Clostridium sardiniense, Clostridium sartagoforme, Clostridium scindens, Clostridium septicum, Clostridium sordellii, Clostridium sphenoides, Clostridium spiroforme, Clostridium sporogenes, Clostridium subterminale The composition comprises non-pathogenic spores of one or more, two or more, three or more, or four or more Clostridium species selected from the group consisting of Clostridium subterminale, Clostridium symbiosum, Clostridium tertium, Clostridium tetani, Clostridium welchii, and Clostridium villosum.

[0127] In one embodiment, a therapeutic composition comprises a purified, isolated, or cultured viable non-pathogenic Clostridium and a plurality of purified, isolated, or cultured viable non-pathogenic microorganisms from one or more genera selected from the group consisting of Collinsella, Coprococcus, Dorea, Eubacterium, and Ruminococcus. In another embodiment, a therapeutic composition comprises a plurality of purified, isolated, or cultured viable non-pathogenic microorganisms from one or more genera selected from the group consisting of Clostridium, Collinsella, Coprococcus, Dorea, Eubacterium, and Ruminococcus.

[0128] In one embodiment, the therapeutic composition comprises two or more genera selected from the group consisting of Collinsella, Coprococcus, Dorea, Eubacterium, and Ruminococcus. In another embodiment, the therapeutic composition comprises two or more genera selected from the group consisting of Coprococcus, Dorea, Eubacterium, and Ruminococcus. In yet another embodiment, a therapeutic composition comprises one or more, two or more, three or more, four or more, or five or more species selected from the group consisting of Coprococcus catus, Coprococcus comes, Dorea longicatena, Eubacterium eligens, Eubacterium hadrum, Eubacterium hallii, Eubacterium rectale, and Ruminococcus torques.

[0129] In one embodiment, the therapeutic composition comprises at least about 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , or 10 13 In another embodiment, the therapeutic composition comprises up to about 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , 10 13 , or 10 14 Contains cfu.

[0130] In another embodiment, the therapeutic composition comprises at least about 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , or 10 13 In another embodiment, the therapeutic composition comprises up to about 10 cells. 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , 10 13 , or 10 14 Contains cells.

[0131] From the foregoing, it will be appreciated that the present invention can be embodied in a variety of ways, including but not limited to the following embodiments.

[0132] 1. A method for treating ulcerative colitis (UC) in a subject in need thereof, comprising treating the subject with a therapeutic regimen of administering a pharmaceutical composition comprising live, non-pathogenic fecal bacteria at least three times per week for at least eight weeks.

[0133] 2. A method for treating a condition in a subject in need thereof, comprising treating the subject with a therapeutic regimen of administering a pharmaceutical composition comprising live non-pathogenic fecal bacteria at least three times per week for at least eight weeks, wherein the condition is selected from the group consisting of collagenous colitis, lymphocytic colitis, Crohn's colitis, diverticulitis, and pouchitis.

[0134] 3. The method of embodiment 1 or 2, wherein the treatment regimen is capable of achieving a primary outcome rate that is at least 2-fold higher than the primary outcome rate from placebo, the primary outcome being defined as steroid-free clinical and endoscopic remission or response at the end of the treatment regimen, wherein clinical remission is defined as a total Mayo score of 2 or less and all subscores of 1 or less, and endoscopic remission or response is defined as a reduction of at least 1 point from baseline in the Mayo endoscopic score.

[0135] 4. The method of embodiment 3, wherein the treatment regimen is capable of achieving a primary outcome rate of at least 25%.

[0136] 5. The method of embodiment 3, wherein the treatment plan can achieve a primary outcome rate of 20% to 40%.

[0137] 6. The method of embodiment 3, wherein the treatment regimen is capable of achieving at least a 40% sustained clinical remission rate 8 weeks after completion of the treatment regimen.

[0138] 7. The method of embodiment 3, wherein the treatment regimen is capable of achieving a clinical remission maintenance rate of 35% to 60% 8 weeks after completion of the treatment regimen.

[0139] 8. The method of embodiment 1 or 2, wherein the treatment regimen is capable of achieving a steroid-free clinical remission rate that is at least 2-fold greater than the steroid-free clinical remission rate from placebo, with clinical remission defined as a combined Mayo score of 1 or less for rectal bleeding and stool frequency.

[0140] 9. The method of embodiment 8, wherein the treatment regimen is capable of achieving a steroid-free clinical remission rate of at least 40%.

[0141] 10. The method of embodiment 8, wherein the treatment regimen is capable of achieving a steroid-free clinical remission rate of 35% to 55%.

[0142] 11. The method of embodiment 1 or 2, wherein the treatment regimen is capable of achieving a steroid-free clinical response rate that is at least 2-fold greater than the steroid-free clinical response rate from placebo, with a reduction in total Mayo score of 3 or greater, or clinical response being defined as a 50% or greater reduction from baseline in the combined scores for rectal bleeding and stool frequency.

[0143] 12. The method of embodiment 11, wherein the treatment regimen is capable of achieving a steroid-free clinical response rate of at least 50%.

[0144] 13. The method of embodiment 11, wherein the treatment regimen is capable of achieving a steroid-free clinical response rate of 45% to 65%.

[0145] 14. The method of embodiment 1 or 2, wherein the treatment regimen is capable of achieving an endoscopic response rate that is at least 2-fold higher than the endoscopic response rate from placebo, with endoscopic response defined as a reduction in total UCEIS score of 3 or greater, or a reduction from baseline of 50% or greater.

[0146] 15. The method of embodiment 14, wherein the treatment regimen is capable of achieving an endoscopic response rate of at least 30%.

[0147] 16. The method of embodiment 14, wherein the treatment regimen is capable of achieving an endoscopic response rate of 30% to 45%.

[0148] 17. The method of embodiment 1 or 2, wherein the method further comprises determining the subject's baseline gut bacterial diversity.

[0149] 18. The method of embodiment 17, wherein the subject's baseline gut bacterial diversity is assessed by analyzing the Shannon diversity of a fecal sample of the subject prior to the treatment step.

[0150] 19. The method of embodiment 18, wherein the Shannon diversity of the subject's feces is 0.5 to 2.2 depending on the bacterial species level.

[0151] 20. The method of embodiment 1 or 2, wherein the method further comprises determining the level of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella in the subject's intestine.

[0152] 21. The method of embodiment 1 or 2, wherein the method further comprises determining the level of one or more bacteria selected from the group consisting of Barnesiella, Parabacteroides, Clostridium IV, Ruminococcus, Blautia, Dorea, Ruminococcus2, and Clostridium XVIII in the subject's intestine.

[0153] 22. The method of embodiment 1 or 2, wherein the pharmaceutical composition comprises a fecal microbial preparation.

[0154] 23. The method of embodiment 1 or 2, wherein the subject exhibits a Mayo score of at least 4 prior to the treatment step.

[0155] 24. The method of embodiment 1 or 2, wherein the subject exhibits a Mayo score of 4 to 10 before the treatment step.

[0156] 25. A method for treating ulcerative colitis (UC) in a subject in need of treatment and having a Mayo endoscopic score of 3 or less, comprising administering to the subject a pharmaceutical composition comprising live non-pathogenic fecal bacteria.

[0157] 26. The method of embodiment 25, wherein the administration is carried out according to a treatment regimen lasting for at least 8 weeks.

[0158] 27. The method of embodiment 25, wherein administration is according to a treatment regimen of at least 8 weeks and at least 3 times per week.

[0159] 28. The method of embodiment 27, wherein the subject achieves the primary outcome at the end of the treatment regimen, the primary outcome being defined as steroid-free clinical remission and endoscopic remission or response at the end of the treatment regimen, where steroid-free clinical remission is defined as a total Mayo score of 2 or less and all subscores of 1 or less, and endoscopic remission or response is defined as a reduction of at least 1 point from baseline in the endoscopic score.

[0160] 29. The method of embodiment 25, wherein the administering step is performed according to a treatment regimen of daily for at least 8 weeks.

[0161] 30. A method for treating ulcerative colitis (UC) in a subject in need thereof, the method comprising administering to the subject a pharmaceutical composition comprising live non-pathogenic fecal bacteria, wherein the subject is not taking concomitant corticosteroids during the method and is corticosteroid-free immediately prior to initiating the method.

[0162] 31. The method of embodiment 30, wherein the subject is free of steroid use within at least one week prior to starting the method.

[0163] 32. The method of embodiment 30, wherein the subject is free of corticosteroid use within at least 1 week prior to starting the method.

[0164] 33. The method of embodiment 30, wherein the subject is free of corticosteroid use prior to starting the method.

[0165] 34. The method of embodiment 30, wherein the administration is carried out according to a treatment regimen lasting for at least 8 weeks.

[0166] 35. The method of embodiment 30, wherein administration is carried out according to a treatment regimen of at least 8 weeks and at least 3 times per week.

[0167] 36. The method of embodiment 35, wherein the subject achieves the primary outcome at the end of the treatment regimen, the primary outcome being defined as steroid-free clinical remission and endoscopic remission or response at the end of the treatment regimen, where steroid-free clinical remission is defined as a total Mayo score of 2 or less and all subscores of 1 or less, and endoscopic remission or response is defined as a reduction of at least 1 point from baseline in the endoscopic score.

[0168] 37. A method for selecting a treatment plan for treating ulcerative colitis (UC) in a subject in need thereof, the method comprising: determining the levels of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella in the subject's intestine; and recommending fecal bacteriotherapy if the levels of Fusobacterium, Sutterella, or both Fusobacterium and Sutterella are below a predetermined level.

[0169] 38. A method for selecting a treatment regimen for treating ulcerative colitis (UC) in a subject in need thereof, the method comprising: determining the level of one or more bacteria selected from the group consisting of Barnesiella, Parabacteroides, Clostridium IV, Ruminococcus, Blautia, Dorea, Ruminococcus 2, and Clostridium XVIII in the intestine of the subject; and recommending fecal bacteriotherapy if the level of one or more bacteria selected from the group consisting of the above bacteria is above a predetermined level.

[0170] 39. The method of embodiment 37 or 38, wherein the level of one or more bacteria is determined by analyzing the subject's feces. [Example]

[0171] Example 1. Patient selection criteria. Patients, both male and female, aged 18 to 75 years, with clinically and endoscopically active ulcerative colitis were included, with a total Mayo score of 4 to 10, incorporating stool frequency, rectal bleeding, endoscopic mucosal appearance, and Physician Global Assessment (PGA). The endoscopic score must be ≥1 and the PGA score must be ≤2. Furthermore, such ulcerative colitis must have lasted for more than 3 months. Any degree of ulcerative colitis, except for isolated proctitis less than 5 cm, was treated. See Table 4 for complete inclusion criteria. [Table 4]

[0172] Patients receiving oral 5-aminosalicylate, thiopurine, and methotrexate therapy must be on stable doses. Isisolon is permitted at enrollment if oral prednisolone is available and available at the appropriate dose. Patients receiving mandatory oral prednisolone may be tapered to a maximum of 2.5 mg per week and must be steroid-free by week 8.

[0173] Patients are excluded if they have received rectal treatment within the past two weeks, antibiotics or probiotics within the past four weeks, or biologic therapy within the past 12 weeks. Patients with a medical history of toxic megacolon and any other severe gastrointestinal condition, including but not limited to irritable bowel syndrome, diverticulitis, and tumors, are also excluded. Patients are excluded if they have been diagnosed with Crohn's disease or indeterminate colitis. Patients with perianal disease, such as fistulas and preexisting fissures, are excluded. Patients with severe anemia, leukopenia, or granulocytopenia are excluded. Patients who have undergone appendectomy within three months prior to treatment are also excluded. Patients with significant food sensitivities are excluded. See Table 5 for all exclusion criteria. [Table 5-1] [Table 5-2]

[0174] Based on the above criteria, 85 patients are being recruited into this trial. Selected patients will be randomized, with 81 starting treatment (Figure 1). The two groups are well matched except for disease severity, with a significant number of patients with the mildest endoscopic disease (Mayo 1) randomized to receive placebo treatment. Table 6 summarizes the baseline characteristics of the recruited patients. [Table 6]

[0175] Example 2. Selection of fecal donors. Fecal donors are included, including men and women aged 18-65 years with no history or current symptoms of gastrointestinal disease, including, but not limited to, inflammatory bowel disease and irritable bowel syndrome. Donors must be free of any major active medical comorbidities. Donors must be free of a minimum of regular medications that may interfere with stool activity within the three months prior to donation, including medications that do not include antimicrobials, probiotics, or proton pump inhibitors. See Table 7 for all donor inclusion criteria. [Table 7]

[0176] To exclude unhealthy donors, potential donor stool is evaluated using one or more of the following tests: Clostridium difficile toxin PCR, fecal microscopy / culture / sensitivity with routine bacterial culture for enteric pathogens, fecal Giardia antigen, fecal Cryptosporidium antigen, fecal eggs / cysts / parasites (including Blastocystis hominis and Dientamoeba fragilis), and norovirus EIA. Potential donor blood is also tested for one or more of the following: complete blood count (CBC), electrolytes, urea, and creatinine (EUC); liver function tests (LFTs); erythrocyte sedimentation rate (ESR); C-reactive protein (CRP); human immunodeficiency virus (HIV) types 1 and 2; hepatitis A virus IgM; hepatitis B virus surface antigen; hepatitis B virus core antibody (IgM+IgG); hepatitis B virus surface antibody; hepatitis C virus antibody; rapid plasma reagin and / or fluorescent treponemal antibody absorption; and human T-cell lymphotropic virus (HTLV) types 1 and 2. [Table 8-1] [Table 8-2]

[0177] Based on the above criteria and testing, 14 donors will be selected.

[0178] Example 3. Preparation and storage of FMT and placebo. FMT infusions consist of mixed feces from 3–7 donors to enhance microbial heterogeneity. Each patient receives all FMT infusions from the same donor population to ensure consistency and reproducibility of the infused fecal microbiota.

[0179] The placebo infusion contains isotonic saline. The odorants, brown food disodium 4,4'-2,4-dihydroxy-5-hydroxymethyl-1,3-phenylene-bisazodi-1-naphthalenesulfonate (to mimic fecal odor and color, respectively), and glycerol cryoprotectant (10% concentration) are added to 150 ml of the placebo infusion and FMT infusion, which are then stored at -80°C.

[0180] Three to seven of the selected donors will contribute to each of the 21 FMT batches in the trial. The use of multiple donors for all infusions is a unique feature of this trial.

[0181] Example 4. Clinical trial design.

[0182] At three clinical centers, patients will be randomized 1:1 to FMT:placebo in a double-blind fashion using permuted blocks of four stratified by study site and concomitant corticosteroid use.

[0183] After completing the bowel preparation, a colonoscopy is performed on the terminal ileum and the first infusion is administered. Patients then administer five enemas per week for eight weeks. After eight weeks, mucosal inflammation is assessed by sigmoidoscopy.

[0184] After the initial 8-week trial period, placebo-treated patients will undergo 8 weeks of open-label FMT (fecal microbiota transplant) enemas, five times per week, without the initial colonoscopy instillation. Sigmoidoscopy will be repeated after open-label FMT (fecal microbiota transplant).

[0185] Figure 2 shows a schematic representation of this trial design.

[0186] Example 5. Clinical Trial Evaluation and Endpoints. Patients will be reviewed every 2 weeks during the blinded and open-label study, with a final review at week 8 after FMT. Blood and stool tests will be performed every 4 weeks during study treatment. Blood tests will include CBC, EUC, LFTs, ESR, and CRP. Stool tests will measure fecal calprotectin.

[0187] Assessment of the worst inflammation site at each endoscopy using the Mayo endoscopic subscore and UCEIS score will be performed using blinded review of all endoscopic images and central consensus scoring by five IBD-specializing gastroenterologists.

[0188] The primary composite outcome rate was steroid-free clinical remission with endoscopic remission or response at week 8, defined as a total Mayo score of 2 or less, all subscores of 1 or less, and a reduction from baseline in the endoscopic score of 1 or more points.

[0189] Eleven of 41 FMT-treated patients (27%) and three of 40 placebo-treated patients (8%) achieved the primary outcome (P = 0.02, OR 4.5 (95% CI 1.2-17.7)) (Figure 3A, Figures 4A-4D).

[0190] Figure 3A shows the number of patients in the FMT and placebo treatment groups who achieved the primary outcome of steroid-free clinical remission and endoscopic remission or response at week 8 (total Mayo score ≤2, all subscores ≤1, and reduction from baseline in endoscopic subscores of ≥1). The total Mayo score can range from 0 to 12, and subscores can range from 0 to 3, with higher scores indicating more severe disease.

[0191] Figures 4A and 4B show the effect of FMT therapy in a 37-year-old female patient with a 4-year history of left-sided ulcerative colitis and acute colitis (six episodes of diarrhea per day with bleeding) despite optimal oral topical 5-ASA therapy. Figure 4A shows an exemplary baseline endoscopic appearance of 25 cm of active rectosigmoid colitis, showing an endoscopic Mayo subscore of 2 and a total Mayo score of 8. Figure 4B shows an exemplary endoscopic appearance in the same patient at the end of 8 weeks of blinded FMT therapy, showing an endoscopic Mayo subscore of 0 and a total Mayo score of 0. This patient maintained clinical remission at the final study follow-up 8 weeks after completion of blinded FMT therapy.

[0192] Figures 4C and 4D show the effect of FMT therapy in a 28-year-old female patient with a 7-year history of extensive ulcerative colitis. This patient had previously failed treatment with mesalamine, probiotics, and adalimumab. Therefore, the patient continued to take azathioprine and allopurinol and was steroid-dependent with oral budesonide 9 mg / day. At study entry, the patient had diarrhea eight times per day, accompanied by bleeding and abdominal pain. Figure 4C shows an exemplary baseline endoscopic appearance of extensive colitis resulting in hepatic deflection, with an endoscopic Mayo subscore of 3 and a total Mayo score of 10. This patient received placebo treatment during the primary trial but was unable to taper corticosteroids, thus failing treatment and not achieving the primary outcome. Figure 4D shows the endoscopic appearance of the same patient at the completion of 8 weeks of open-label FMT, showing an endoscopic Mayo subscore of 0 and a total Mayo score of 0. Eight weeks after open-label FMT, the patient is completely off corticosteroids and in clinical and endoscopic remission.

[0193] Secondary outcomes included steroid-free clinical remission (a combined score of ≤1 corresponding to the Mayo subscore of rectal bleeding plus bowel frequency), clinical response (a reduction of ≥3 points from baseline in the combined Mayo subscore of rectal bleeding plus bowel frequency and / or a reduction of ≥50%), endoscopic response (a Mayo endoscopic subscore of ≤1 with a reduction of ≥1 point from baseline), complete mucosal healing (Mayo endoscopic subscore of 0), and IBDQ. 10 and quality of life with safety.

[0194] A blinded central reading of all endoscopic images was performed using both Mayo and UCEIS scoring. When assessing steroid-free endoscopic outcomes using a ≥3-point and / or ≥50% reduction in UCEIS score from baseline, the difference between FMT-treated and placebo-treated patients at week 8 was 37% vs. 10%, p<0.01, odds ratio (OR) 5.2, 95% CI 1.5-17.5. When using a UCEIS score of ≤1, the difference between FMT-treated and placebo-treated patients at week 8 was 17% vs. 8%, p=0.19, odds ratio (OR) 2.5, 95% CI 0.6-10.6.

[0195] Significant differences were observed in the total Mayo score and reduction in total Mayo score at week 8 between the FMT and placebo treatment groups (Table 9). IBDQ FMT data were available from only 31 patients. All missing data were assigned the worst value in the entire cohort. All continuous variables are reported as median and interquartile range. [Table 9]

[0196] Figure 3B shows the number of patients achieving steroid-free clinical remission (a total score of ≤1 corresponding to the rectal bleeding and bowel frequency Mayo subscore) and clinical response (a reduction of ≥3 points from baseline in the total score corresponding to the rectal bleeding and bowel frequency Mayo subscore and / or a reduction of ≥50%) at week 8. The odds of achieving steroid-free clinical remission (44% vs. 20%, P = 0.02, OR 3.1, 95% CI 1.2–8.4) and steroid-free clinical response (54% vs. 23%, P < 0.01, OR 4.0, 95% CI 1.5–10.4) at week 8 were significantly greater in FMT patients than in placebo-treated patients.

[0197] Figure 3C shows the number of patients achieving a steroid-free endoscopic response (Mayo endoscopic subscore ≤1 with a reduction of ≥1 point from baseline) and complete mucosal healing (Mayo endoscopic subscore 0). At week 8, the rate of steroid-free endoscopic response (32% vs. 10%, P = 0.02, OR 4.2, 95% CI 1.2-14.2) was significantly greater in FMT-treated patients. Complete mucosal healing (Mayo 0:12% vs. 8%, P = 0.48, OR 1.7, 95% CI 0.4-7.7) was greater in the FMT-treated group than in the placebo-treated group, but this difference was not significant. Outcomes were similar for UCEIS scoring (Figure 5). Figure 5 shows the rapidity with which treatment effect began to appear. At the end of week 4, clinical response was significantly greater in FMT patients [17 of 41 (41%)] than in placebo-treated patients [5 of 40 (13%)] (p<0.01, OR (odds ratio) 5.0, 95% CI 1.6-15.3]. Clinical remission did not differ significantly between treatment groups [12 of 41 (29%) vs. 5 of 40 (13%), respectively (p=0.06, OR (odds ratio) 2.9, 95% CI 0.91-9.2)].

[0198] IBDQ scores and inflammatory markers did not differ significantly between groups (Table 9).

[0199] Thirty-seven initially placebo-treated patients proceeded to open-label FMT. After open-label FMT, 10 (27%) met the primary endpoint, 17 (46%) achieved clinical remission, and 8 (22%) achieved complete mucosal healing.

[0200] No relationship between outcome and degree of anatomical disease was observed (P=0.23). The severity of endoscopic inflammation was associated with treatment outcome (P=0.01), with no patients with a Mayo endoscopic score of 3 at study entry achieving the primary outcome. Corticosteroid use was also associated with treatment outcome (P=0.02), with no patients participating in corticosteroid studies achieving the primary endpoint at the end of blinded treatment. One patient taking corticosteroids at the time of entry into open-label FMT met the primary endpoint at completion.

[0201] Sixty-three patients participated in the final 8-week trial follow-up after completing double-blind or open-label FMT; 28 of these patients achieved clinical remission and 20 required escalation of their UC treatment.

[0202] Nine patients receiving blinded FMT and 11 receiving placebo (P = 0.56) withdrew or failed the protocol before week 8. Reasons for withdrawal or protocol failure in blinded treatment included disease worsening with steroid withdrawal (3 FMT, 6 placebo), persistent disease or disease worsening without steroid withdrawal (5 FMT, 3 placebo), and noncompliance (1 FMT, 2 placebo).

[0203] Eleven patients starting open-label FMT either withdrew or failed the protocol: five had disease that worsened with steroid withdrawal, two had disease that persisted or worsened without steroid withdrawal, and four were noncompliant.

[0204] During blinded treatment, 32 FMT patients (78%) and 33 placebo-treated patients (83%) experienced at least one adverse event, with no significant difference in the number or type of adverse events (Table 10). The most common adverse events were self-limiting gastrointestinal illness (abdominal pain, bloating, and flatulence). Six serious adverse events (SAEs) occurred during study treatment: two blinded FMT patients, one placebo patient, and three open-label FMT patients. One patient with refractory colitis during blinded FMT withdrew at week 2 due to clinical and endoscopic (Mayo 2-3, UCEIS 5-7) deterioration and underwent colectomy. One patient with moderate-to-severe colitis remained unwell at week 3 of blinded active treatment, withdrew, and was hospitalized and receiving intravenous corticosteroid treatment. One patient with moderate to severe colitis withdrew from placebo treatment during the third week and required hospitalization. The first three placebo-treated patients failed to improve with open-label FMT and were hospitalized for treatment escalation. [Table 10-1] [Table 10-2]

[0205] Six serious adverse events were observed during study treatment: two on blinded FMT, one on placebo, and three on open-label FMT. One patient with refractory UC on blinded FMT withdrew due to clinical and endoscopic deterioration and underwent colectomy. The first three placebo-treated patients failed to improve with open-label FMT and required hospitalization for intravenous corticosteroid or anti-TNF therapy.

[0206] Intensive administration of multiple-donor FMT for ulcerative colitis (UC) appears to be safe in the short term. The most serious adverse events occur in either corticosteroid-dependent or refractory patients who are unable to tolerate steroid withdrawal or in patients with moderate to severe colitis. Patients undergoing colectomy while undergoing FMT demonstrate that UC patients have a small segment of the body that is susceptible to disease that worsens with this treatment.

[0207] Individual donors or donor cohorts were not significantly associated with the primary outcome, although this particular trial was not motivated to evaluate this. Benefit from one donor was more likely, with 37% of patients achieving the primary outcome using this donor and 18% achieving the primary outcome without this donor (P=0.054). Donor cohorts were not associated with the primary endpoint or serious adverse events.

[0208] Based on available data and anecdotal experience, the expected FMT remission rate is 60%, the placebo rate is 15%, and the dropout rate is 30%. 40 patients per group are required to have an 80% probability of demonstrating a difference with a two-sided alpha level of 0.05 in an intention-to-treat analysis.

[0209] All analyses are intention-to-treat (ITT) and include all patients who received at least one study dose. Patients who escalated treatment, violated the study protocol, failed to discontinue corticosteroids by week 8, or terminated the study for any reason were considered treatment failures. Incomplete missing data were assigned the worst value among the cohort included in the statistical analysis.

[0210] Descriptive statistics are calculated for all variables. Normally distributed continuous data are expressed as mean and standard deviation and analyzed using unpaired t-tests. Non-normally distributed data are expressed as median and interquartile range and analyzed using Wilcoxon rank sum tests. Categorical data are assessed by chi-square and Fisher's exact tests. Results are expressed as odds ratios with 95% confidence intervals. A p-value of less than 0.05 is considered significant.

[0211] Statistical analyses are performed using SPSS version 23.0 software (Chicago, IL).

[0212] Example 6. Gastrointestinal microbiota analysis. Microbiological analysis is performed on patient, individual donor, and FMT population fecal samples. Samples are stored at -80°C. Fecal bacterial DNA is extracted. 16S rRNA gene fragments are amplified using F27 and 519R primers and then subjected to high-throughput sequencing on an Illumina MiSeq platform (2x300bp chemistry) to ensure microbiota diversity and abundance. Raw sequences are analyzed using MOTHUR (Schloss et al., Appl. Environ. Microbiol. 2009;75:7537-41). Statistical tests are performed on counts and relative abundances.

[0213] Diversity (α- and phylogenetic) analyses and statistical analyses including principal component analysis (PCA), CLUSTER with SIMPROF test, permutation MANOVA (PERMANOVA), and PERMDISP were performed on the reads using MOTHUR and Primer-E (Clarke. J. of Ecology 1993;18(1):117-43). Linear discriminant analysis effect size (LEfSe) analyses (Segata et al., Genome Biol. 2011;12:R60) were performed using the Galaxy web application (Goecks et al., Genome Biol. 2010;11:R86).

[0214] Fecal samples were collected from 70 patients. Fecal samples from 314 patients and 113 donors (55 individual donors and 58 group samples) were analyzed. The number of purification sequences performed per sample was 26,976 ± 540, and the rarefaction curves suggest that sampling was saturated.

[0215] The number of operational taxonomic units (OTUs) and phylogenetic diversity are significantly increased in donor populations compared to individual donors (Figures 6A and 6B). The number of OTUs and phylogenetic diversity of donor samples (populations and individuals) are significantly increased compared to baseline patient samples (Figures 6A and 6B). ***In Figures 6A and 6B, P<0.0001 indicates a relationship.

[0216] The number of OTUs and phylogenetic diversity increased significantly (p<0.0001) relative to baseline in all FMT-treated patients at weeks 4 and 8, and persisted for 8 weeks post-FMT (p<0.0001) (Figures 6A and 6B). Similar patterns were observed for species richness and Shannon diversity.

[0217] Significant differences and reduced variance in microbial profiles are observed from the OTU to the class level after FMT. PCA (principal component analysis) confirms the change in microbial profile in patients undergoing FMT (Figure 6C). The patient profile shifts from a predominant Bacteroides to a Prevotella (Figure 6C). The shift in the microbial profile of patients undergoing FMT toward the donor is most pronounced at the OTU level.

[0218] Patient baseline samples were compared with those from weeks 4, 8, and 8 after FMT to identify taxa altered by FMT, and compared with donor samples to identify OTUs associated with the donor population and those associated with the patient. 295 microbial taxa across all taxonomic levels were identified in patients receiving FMT, with 78 of the 295 showing strong association (LDA score >3). Regardless of clinical outcome, there was a decrease in patient Bacteroides (e.g., OTU8, 15, 69) and a significant increase in donor Prevotella (e.g., OTU2) and donor Bacteroides (e.g., OTU12, 26, 56) in patients receiving FMT. This pattern became more apparent when OTUs were selected at higher resolution.

[0219] Blinded FMT-treated patients who achieved the primary outcome tended to have higher baseline alpha diversity than patients who did not (P = 0.1, Figure 6D). Blinded FMT treatment was associated with significantly increased diversity in all patients. However, patients who achieved the primary outcome had greater diversity during FMT and 8 weeks after FMT, achieving levels lower than the donor population but higher than individual donors (Figure 6D). The increase in alpha diversity is specific to FMT. The three patients who achieved the placebo primary outcome showed no change in diversity.

[0220] To identify microbial taxa associated with the primary outcome of FMT, LEfSe analysis was performed for patients undergoing blinded FMT and stratified for patients undergoing open-label FMT. 87 taxa were significantly associated with the primary outcome in blinded patients and 46 taxa were significantly associated with the primary outcome in open-label FMT patients. A range of microbial taxa are associated with remission in blinded FMT patients (e.g., Barnesiella, Parabacteroides, Clostridium IV, and Ruminococcus) and open-label FMT patients (e.g., Blautia, Dorea, Ruminococcus 2, and Clostridium XVIII). Both Fusobacterium and Sutterella are consistently associated with lack of remission in both blinded and open-label FMT patients. In the case of Fusobacterium, this includes either lack of eradication of disease in patients who do not achieve remission, engraftment in patients who do not achieve remission, or eradication of disease in patients who do achieve remission.

[0221] Example 7. Treatment of treatment-naive ulcerative colitis patients with oral fecal microbial therapy. A 44-year-old treatment-naive male patient (Patient DM) presented with a 1-year history of diarrhea, bloody and mucous stools, cramps / abdominal pain, and weight loss. The patient experienced severe pain during bowel movements, incontinence while driving, loss of appetite, nausea, inability to eat spicy foods and fish, brain fog, and a 16-pound (7,257-gram) weight loss. The patient also experienced severe flatulence with a stool consistency of 7 (Bristol), severe abdominal discomfort, and 10 to 12 bowel movements per day accompanied by severe urinary tract infection. The patient was diagnosed with severe pancolitis. A treatment regimen was administered, including acid-resistant / delayed-release double-encapsulated oral capsules containing lyophilized, unselected fecal microbiota derived from donors. Briefly, donor feces was collected and homogenized with a cryoprotectant, and the resulting slurry was freeze-dried to yield approximately 1.6 x 10 fecal pellets.11 The LFSM treatment will be administered in DRcaps® capsules containing live cells / capsules. Patients will be treated with a total of 404 capsules over a 13-week run-in period. During this period, symptom questionnaires will be collected and stool samples will be cultured for pathogens to assess the effectiveness of LFSM treatment.

[0222] The patient's UC symptoms improved (see Table 11). By week 8 of treatment, blood and mucus were barely visible in the stool, and by week 10, they were gone. The patient's incontinence ceased, bowel movements decreased to 2-3 times per day, and stool consistency reached 4 (Bristol). With continued treatment, calprotectin levels decreased from 600 μg / g at week 22 to 344 μg / g at week 26. This confirmed the ongoing reduction in inflammation, as demonstrated by endoscopy in Figure 7. The patient reported no side effects related to treatment tolerance. This case demonstrates the successful treatment of ulcerative colitis (UC) with oral fecal microbial therapy. In addition to the improvement in quality of life (QoL) resulting from the improvement in the patient's UC symptoms, it also resulted in a significant increase in energy levels, allowing daily exercise due to the reduction in incontinence, and confidence in returning to work. The patient continues maintenance therapy with four capsules per day. Oral fecal microbial therapy is effective in treating treatment-naive UC patients with pancolitis and improves overall quality of life. [Table 11]

[0223] Example 8. Treatment of patients with ulcerative colitis with oral fecal microbial therapy. A 31-year-old patient (Patient TD) is treated with fecal microbiota therapy. The treatment regimen includes acid-resistant, delayed-release, dual-encapsulated oral capsules containing lyophilized, donor-derived, unselected fecal microbiota. The patient's symptoms include four bowel movements per day with a stool consistency of 2, moderate bloating, moderate abdominal discomfort, mild urgency, a sensation of pins and needles in the legs, and fatigue. The patient undergoes a six-week treatment protocol consisting of one colonoscopy per week with fecal microbiota therapy solution and one to two rectal enemas per week during the induction period. The patient takes four capsules per day for four weeks during the maintenance period. The patient's symptoms of bloating subside, and the symptoms of abdominal discomfort and urgency disappear. The patient experiences one bowel movement per day with a stool consistency of 3. The patient also experiences mild flatulence and general fatigue. At two weeks after capsule treatment, the patient has a calprotectin measurement of 243 μg / g. At three weeks after the first calprotectin test and four weeks after taking the first capsules, the patient's calprotectin level decreases to 88 μg / g.

[0224] All subject matter contained in the foregoing description should be construed as illustrative, and not limiting, as various changes can be made to the structures and methods described and illustrated herein without departing from the scope of the present disclosure. The breadth and scope of the present disclosure should not be limited by any of the above-described exemplary embodiments, but should be defined only in accordance with the following appended claims and their equivalents. All patent and non-patent literature cited herein is hereby incorporated by reference in its entirety.

Claims

1. A pharmaceutical composition comprising a preparation of live non-pathogenic fecal bacteria for treating ulcerative colitis (UC) in a subject in need thereof, wherein the preparation of live non-pathogenic fecal bacteria comprises (i) a non-selective mixture of non-pathogenic fecal bacteria extracted from the feces of multiple human donors with no history or current symptoms of gastrointestinal disease, supplemented with (ii) a non-pathogenic bacterial isolate, wherein the pharmaceutical composition is orally administered to the subject at least twice per week for a treatment regimen of at least one week.

2. 10. The pharmaceutical composition of claim 1, wherein the treatment regimen comprises administering the pharmaceutical composition at least five times per week for at least four weeks.

3. Preparations of live non-pathogenic fecal bacteria include Clostridium, Bacillus, Collinsella, Bacteroides, Eubacterium, Fusobacterium, Propionibacterium, Lactobacillus, Ruminococcus, Escherichia coli, and the like.

10. The pharmaceutical composition of claim 1, comprising one or more isolates selected from the group consisting of E. coli, Gemmiger, Desulfomonas, Peptostreptococcus, Bifidobacterium, Coprococcus, Dorea, and Monilia.

4. 2. The pharmaceutical composition of claim 1, wherein the preparation of live non-pathogenic fecal bacteria comprises Odoribacter splanchnicus.

5. Preparations of live non-pathogenic fecal bacteria include Clostridium, Bacillus, Collinsella, Bacteroides, Eubacterium, Fusobacterium, Propionibacterium, Lactobacillus, Ruminococcus, Escherichia coli, and the like.

10. The pharmaceutical composition of claim 1, comprising one or more cultured bacterial isolates selected from the group consisting of E. coli, Gemmiger, Desulfomonas, Peptostreptococcus, Bifidobacterium, Coprococcus, Dorea, and Monilia.

6. 2. The pharmaceutical composition of claim 1, wherein the non-selective mixture of non-pathogenic fecal bacteria substantially resembles the microbial components and microbial community structure found in the feces of multiple human donors.

7. 2. The pharmaceutical composition of claim 1, wherein the level of one or more bacteria selected from the group consisting of Fusobacterium, Sutterella, Barnesiella, Parabacteroides, Clostridium IV, Ruminococcus, Blautia, Dorea, Ruminococcus 2, and Clostridium XVIII in the subject's intestine is determined, and then the pharmaceutical composition is orally administered to the subject.

8. 1. A pharmaceutical composition for treating ulcerative colitis (UC) in a subject in need thereof, comprising a preparation of live non-pathogenic fecal bacteria, the preparation of live non-pathogenic fecal bacteria comprises a non-selective mixture of non-pathogenic fecal bacteria extracted from the feces of multiple human donors with no history or current symptoms of gastrointestinal disease, supplemented with cultured non-pathogenic bacterial isolates; the pharmaceutical composition is orally administered to the subject for a treatment regimen of at least one week at least twice per week; the subject is not taking concomitant corticosteroids during the regimen; The subject has been free of steroid use within at least one week prior to starting the regimen. Pharmaceutical compositions.

9. 10. The pharmaceutical composition of claim 8, wherein the treatment regimen comprises administering the pharmaceutical composition at least five times per week for at least four weeks.

10. Preparations of live non-pathogenic fecal bacteria include Clostridium, Bacillus, Collinsella, Bacteroides, Eubacterium, Fusobacterium, Propionibacterium, Lactobacillus, Ruminococcus, Escherichia coli, and the like.

9. The pharmaceutical composition of claim 8, comprising one or more bacterial isolates selected from the group consisting of E. coli, Gemmiger, Desulfomonas, Peptostreptococcus, Bifidobacterium, Coprococcus, Dorea, and Monilia.

11. 9. The pharmaceutical composition of claim 8, wherein the preparation of live non-pathogenic fecal bacteria comprises Odoribacter splanchnicus.

12. Preparations of live non-pathogenic fecal bacteria include Clostridium, Bacillus, Collinsella, Bacteroides, Eubacterium, Fusobacterium, Propionibacterium, Lactobacillus, Ruminococcus, Escherichia coli, and the like.

9. The pharmaceutical composition of claim 8, comprising one or more cultured bacterial isolates selected from the group consisting of E. coli, Gemmiger, Desulfomonas, Peptostreptococcus, Bifidobacterium, Coprococcus, Dorea, and Monilia.

13. 9. The pharmaceutical composition of claim 8, wherein the non-selective mixture of non-pathogenic fecal bacteria substantially resembles the microbial components and microbial community structure found in the feces of multiple human donors.

14. 9. The pharmaceutical composition of claim 8, wherein the pharmaceutical composition is orally administered to the subject after determining the level of one or more bacteria selected from the group consisting of Fusobacterium, Sutterella, Barnesiella, Parabacteroides, Clostridium IV, Ruminococcus, Blautia, Dorea, Ruminococcus 2, and Clostridium XVIII in the subject's intestine.

15. 9. The pharmaceutical composition of claim 8, wherein the live non-pathogenic fecal bacteria include Clostridium, Ruminococcus, Blautia, and Dorea.

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