US20170087196A1 - Methods and compositions for reducing clostridium difficile infection - Google Patents

Methods and compositions for reducing clostridium difficile infection Download PDF

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US20170087196A1
US20170087196A1 US15/312,610 US201515312610A US2017087196A1 US 20170087196 A1 US20170087196 A1 US 20170087196A1 US 201515312610 A US201515312610 A US 201515312610A US 2017087196 A1 US2017087196 A1 US 2017087196A1
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bile acid
clostridium
antibiotic
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Eric Pamer
Charlie Buffie
Peter McKenney
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Memorial Sloan Kettering Cancer Center
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/54—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one sulfur as the ring hetero atoms, e.g. sulthiame
    • A61K31/542—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one sulfur as the ring hetero atoms, e.g. sulthiame ortho- or peri-condensed with heterocyclic ring systems
    • A61K31/545—Compounds containing 5-thia-1-azabicyclo [4.2.0] octane ring systems, i.e. compounds containing a ring system of the formula:, e.g. cephalosporins, cefaclor, or cephalexine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A61K35/741—Probiotics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66—Microorganisms or materials therefrom
    • A61K35/74—Bacteria
    • A61K35/741—Probiotics
    • A61K35/742—Spore-forming bacteria, e.g. Bacillus coagulans, Bacillus subtilis, clostridium or Lactobacillus sporogenes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43—Enzymes; Proenzymes; Derivatives thereof
    • A61K38/44—Oxidoreductases (1)
    • A61K38/443—Oxidoreductases (1) acting on CH-OH groups as donors, e.g. glucose oxidase, lactate dehydrogenase (1.1)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0006—Oxidoreductases (1.) acting on CH-OH groups as donors (1.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/26—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving oxidoreductase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y101/00—Oxidoreductases acting on the CH-OH group of donors (1.1)
    • C12Y101/01—Oxidoreductases acting on the CH-OH group of donors (1.1) with NAD+ or NADP+ as acceptor (1.1.1)
    • C12Y101/01159—7-Alpha-hydroxysteroid dehydrogenase (1.1.1.159)

Definitions

  • the present invention relates to compositions and methods for decreasing the risk of developing Clostridium difficile infection and for treating Clostridium difficile infection, should it occur.
  • the gastrointestinal tract of mammals is densely colonized by hundreds of microbial species that coexist symbiotically with their hosts.
  • the microbes collectively referred to as the microbiota, contribute to numerous aspects of host health, including nutrient metabolism (Turnbaugh, Nature 457, 480-484 (2009); Koeth, Nat Med (2013)), homeostasis of intestinal tissues (Rakoff Nahoum, Cell 118, 229-241 (2004)), development of innate and adaptive immune responses (Ivanov, Cell 139, 485-498 (2009); Chung, Cell 149, 1578-1593 (2012); Diehl, Nature 494, 116-120 (2013); Duan, Cell Host Microbe 7, 140-150 (2010); Farache, Immunity 38, 581-595 (2013); Olszak, Science 336, 489-493 (2012); Wingender, Gastroenterology 143, 418-428 (2012); Hand, Science 337, 1553-1556 (2012); Hill, Nat Med 18, 538-546 (2012); Lathrop, Nature 4
  • Antibiotic therapies are used for prophylaxis and treatment of a variety of infections with great success in clinical settings, but can eliminate broad swaths of intestinal commensals as collateral damage (Huse, PLoS Genet 4, e1000255 (2008); Dethlefsen, Proc Natl Acad Sci USA 108 Suppl 1, 4554-4561 (2011); Buffie, Infect Immun 80, 62-73 (2012)). Consequently, microbiota-mediated colonization resistance is frequently diminished following antibiotic therapy and may paradoxically enhance susceptibility to a range of life-threatening intestinal pathogens (Brandt, Nature 455, 804-807 (2008); Ubeda, J Clin Invest 120, 4332-4341 (2010); Ferreira, PLoS One 6, e20338 (2011)).
  • Clostridium difficile ( C. difficile ) infection is almost universally associated with preceding antibiotic treatment and results in a spectrum of potentially fatal disease (Rupnik, Nat Rev Microbiol 7, 526-536 (2009)), including diarrhea and pseuodomembranous colitis (Bartlett, N. Engl. J. Med. 298:531-534 (1978), as cited in Chen, Gastroenterology Report 1:153-158 (2013)).
  • the incidence, mortality, and costs associated with C. difficile infection in the United States and Europe are substantial and increasing (Kyne, Clin Infect Dis 34, 346-353 (2002); Zilberberg, Emerg Infect Dis 14, 929-931 (2008)). Treatment of C.
  • compositions of fecal transplants are complex, unstandardized, and incompletely defined, concerns about the transmission of undetected pathogens, regulatory complications, and other microbiome-influenced health outcomes (ex. obesity and inflammatory bowel disease) have limited widespread adoption of FMT (Pamer, Mucosal Immunol. 2014 March; 7(2):210-4).
  • Other attempts to treat C. difficile infection have proposed administering secondary bile acids, or at least one strain of bacteria that is capable of metabolizing primary bile salts to secondary bile salts, for example, Clostridium scindens, Clostridium leptum, and Clostridium hiranonis (also known as TO931). (U.S. Publication No. 2011/028847).
  • Massively parallel DNA sequencing technologies have recently facilitated culture-independent characterization of intestinal microbial communities, including those found in microbiota transplants and antibiotic-treated, C. difficile -infected hosts (Reeves, Gut Microbes 2, 145-158 (2011); Lawley, PLoS Pathog 8, e1002995 (2012); Petrof, Microbiome 1, 3 (2013); Hamilton, Gut Microbes 4, 125-135 (2013)), but the specific bacteria that are critical for protection against C. difficile infection and the mechanisms through which they perform this function have remained largely unknown.
  • the present invention relates to methods and compositions for reducing the risk and severity of C. difficile infection.
  • the present invention provides for a recombinant cell expressing a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, wherein the recombinant cell comprises one or more exogenous nucleic acids encoding the bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, wherein the one or more exogenous nucleic acids are operably linked to a promoter.
  • the bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon can include, for example a baiCD gene encoding a 7 ⁇ -hydroxysteroid dehydrogenase enzyme.
  • the promoter can be an inducible promoter or a constitutively active promoter.
  • the promoter can be a bai operon promoter, or can be another promoter active in the recombinant cell.
  • the recombinant cell can further comprise one or more nucleic acids encoding a bile salt hydrolase enzyme, antibiotic resistance gene and/or antibiotic susceptibility gene.
  • said nucleic acids are comprised in a second recombinant cell that does not include the nucleic acid encoding the bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon.
  • the 7 ⁇ -hydroxysteroid dehydrogenase is a bacterial 7 ⁇ -hydroxysteroid dehydrogenase, wherein the bacteria is selected from the group consisting of Clostridium scindens, Clostridium hiranonis, Clostridium hylemonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-26, Clostridiales VE202-05 and combinations thereof.
  • the bacteria is selected from the group consisting of Clostridium scindens, Clostridium hiranonis, Clostridium hylemonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-26,
  • the present invention provides for a composition
  • a composition comprising an isolated Clostridium scindens bacterium.
  • the bacterium is in a formulation for administration to a subject.
  • the composition further comprising a second bacterium selected from the group consisting of Barnesiella intestihominis, Blautia hansenii, Pseudoflavonifractor capillosus and combinations thereof.
  • the present invention provides for a composition comprising one, two, three, or four bacteria, or spores thereof, selected from the group consisting of an isolated Clostridium scindens bacterium, an isolated Barnesiella intestihominis bacterium, an isolated Blautia hansenii bacterium, and an isolated Pseudoflavonifractor capillosus bacterium.
  • the present invention provides for a method for reducing the risk of C. difficile infection and/or improving resistance to C. difficile infection, as well as for a method for reducing the severity of C. difficile infection and/or decreasing the amount of C. difficile toxin, comprising administering, to a subject in need of such treatment, an effective amount of a recombinant cell expressing a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, or a composition as described herein.
  • the present invention provides for a method for reducing the risk of C. difficile infection and/or improving resistance to C. difficile infection, comprising administering, to a subject in need of such treatment, an effective amount of Clostridium scindens ( C. scindens ) bacteria.
  • bacteria may be administered in the proliferative state or as spores, or a mixture thereof.
  • the present invention provides for a method for reducing the severity of C. difficile infection and/or decreasing the amount of C. difficile toxin, comprising administering, to a subject in need of such treatment, an effective amount of C. scindens bacteria.
  • the present invention provides for a method for reducing the risk of C. difficile infection and/or improving resistance to C. difficile infection, comprising administering, to a subject in need of such treatment, an effective amount of an enzyme that converts a primary bile acid or salt to a secondary bile acid.
  • the present invention provides for a method for reducing the severity of C. difficile infection and/or decreasing the amount of C. difficile toxin, comprising administering, to a subject in need of such treatment, an effective amount of an enzyme that converts a bile salt to a secondary bile acid.
  • the present invention provides for a method for reducing the risk of C. difficile infection and/or improving resistance to C. difficile infection, comprising administering, to a subject in need of such treatment, an effective amount of a secondary bile acid.
  • the present invention provides for a method for reducing the severity of C. difficile infection and/or decreasing the amount of C. difficile toxin, comprising administering, to a subject in need of such treatment, an effective amount of a secondary bile acid.
  • the present disclosure provides for a method for decreasing the severity of one or more symptoms of an intestinal disorder comprising administering, to a subject in need of such treatment, an effective amount of one or more of a recombinant cell as described herein; a composition comprising C.
  • scindens (optionally in combination with one or more other therapeutic bacteria as described herein); and agent selected from the group consisting of an enzyme that converts a bile acid to a secondary bile acid, a secondary bile acid, purified bacteria or spores thereof expressing an enzyme that converts a bile acid to a secondary bile acid, and combinations thereof, wherein the symptoms and/or clinical signs are selected from the group consisting of frequency and/or volume of diarrhea; fever; abdominal cramping, pain, and/or tenderness; elevated level of white blood cells in the blood; loss of serum albumin; weight loss; appearance of pseudomembrane in the intestinal and/or rectal mucosa; and combinations thereof.
  • the present invention also provides for methods of diagnosing or identifying a subject with a C. difficile infection, or at risk for C. difficile infection, comprising determining the level one or more bacterium present in the intestinal microbiota sample that can convert a primary bile acid or salt to a secondary bile acid, wherein the subject is diagnosed or identified as having a C. difficile infection, or at risk for C. difficile infection, when the level or amount of the one or more bacterium present in the intestinal microbiota sample that can convert a primary bile acid or salt to a secondary bile acid is lower than a bacterium reference level.
  • the one or more bacterium is selected from the group consisting of Clostridium scindens, Clostridium hiranonis, Clostridium hylemonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-05, Clostridiales VE202-26, and combinations thereof.
  • the method of diagnosing or identifying a subject with a C. difficile infection, or at risk for C. difficile infection comprises determining the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme present in the intestinal microbiota of a subject, wherein the subject is diagnosed or identified as having a C. difficile infection, or at risk for C. difficile infection, when the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme in the subject's microbiota is lower than a 7 ⁇ -hydroxysteroid dehydrogenase enzyme reference level.
  • the method of diagnosing or identifying a subject with a C. difficile infection, or at risk for C. difficile infection comprises quantifying the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in the fecal sample of a subject, wherein the subject is diagnosed or identified as having a C. difficile infection, or at risk for C. difficile infection, when the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in the fecal sample is lower than a reference bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid level.
  • kits comprising a recombinant cell expressing a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, a Clostridium scindens bacteria (and/or any other therapeutic bacteria described herein), an enzyme that converts a primary bile acid or salt to a secondary bile acid, and/or a secondary bile acid.
  • a recombinant cell expressing a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon
  • a Clostridium scindens bacteria and/or any other therapeutic bacteria described herein
  • an enzyme that converts a primary bile acid or salt to a secondary bile acid, and/or a secondary bile acid.
  • FIG. 1A-G Different antibiotics induce distinct changes to C. difficile infection resistance and intestinal microbiota composition.
  • FIG. 2A-C Stability of bacterial density following antibiotic administration.
  • (a) Strategy for determining C. difficile susceptibility duration post-antibiotic exposure (n 3 separately-housed mouse colonies per antibiotic aim) and relating infection resistance to microbiota structure.
  • FIG. 6 Allo-HSCT patient timelines and C. difficile infection status transitions. Transitions between C. difficile (tcdB-positive) colonization status in patients receiving allogeneic hematopoietic stem cell transplantation, as measured by C. difficile 16S rRNA abundance during the period of hospitalization (light gray bars). Timepoints when C. difficile colonization was determined to be positive (red diamonds) and negative (blue diamonds), and when C. difficile infection was clinically diagnosed (black dots) and metronidazole was administered (dark gray bars), are displayed relative to the time of transplant per patient.
  • FIG. 8 Phylogenetic distribution of resistance-associated intestinal bacteria and isolates selected for adoptive transfer.
  • the maximum likelihood phylogenetic tree (Kimura model, bootstrap of 100 replicates) was constructed using the MEGA 6.06 package from representative sequences of intestinal bacteria associated with resistance to C. difficile infection (blue, +), including cultured representatives subsequently used in adoptive transfer experiments (bold). The tree was rooted using intestinal bacteria associated with susceptibility to infection (red, ++) as an out-group.
  • FIG. 10 Adoptive transfer of four-bacteria consortium or C. scindens reduces intestinal C. difficile cytotoxin load.
  • C. difficile toxin was quantitated in feces 24 hours after infection challenge using a cell-based assay.
  • FIG. 11 Adoptive transfer of four-bacteria consortium or C. scindens protects mice from acute C. difficile -associated weight loss.
  • FIG. 12 Confirmation of in vivo reconstitution of adoptively transferred bacterial isolates. Engraftment of bacterial isolates in the intestinal microbiota of antibiotic-exposed animals was confirmed by analysis of high throughput rRNA sequencing of intestinal content (feces) obtained from mice two days following adoptive transfer of B. intestihominis, P. capillosus, B. hansenii, and/or C. scindens. Numbers under group columns denote the number of mice with detectable engraftment of the given bacterium (out of 10 possible separately-housed animals per group). ****P ⁇ 0.0001, ***P ⁇ 0.001, ns (not significant), Mann-Whitney (two-tailed). Center values (mean), error bars (s.e.m.).
  • FIG. 13A-H C. scindens -mediated C. difficile inhibition is associated with secondary bile acid synthesis and dependent on bile endogenous to intestinal content.
  • FIG. 14 Presence and absence of baiCD among bacterial isolates and intestinal microbiomes of C. difficile -susceptible and resistant animals. PCR-based detection of the 7 ⁇ -HSDH-encoding baiCD gene in bacterial isolates, intestinal microbiomes (feces) of animals prior to antibiotic exposure, and intestinal microbiomes (feces) of animals that, following antibiotic exposure, remained C. difficile -susceptible or recovered resistance to infection spontaneously or following adoptive transfer of bacterial isolates.
  • FIG. 15 Adoptive transfer of four-bacteria consortium or C. scindens restores secondary bile acid biosynthesis gene family abundance.
  • FIG. 16A-H Impacts of bacteria adoptive transfers on intestinal abundance of bile acids.
  • UDCA ursodeoxycholate
  • TCA taurocholic acid
  • CA cholic acid
  • CA chenodeoxycholic acid
  • TCDCA tauro-chenodeoxycholic acid
  • FIG. 17 Nucleic acid sequence of the gene encoding a 7 ⁇ -hydroxysteroid dehydrogenase enzyme from C. scindens.
  • the present invention relates to methods and compositions for reducing the risk and/or severity of C. difficile infection.
  • this section is divided into the following subsections:
  • mammals include, but are not limited to, humans, primates, farm animals, sport animals, rodents and pets.
  • Non-limiting examples of non-human animal subjects include rodents such as mice, rats, hamsters, and guinea pigs; rabbits; dogs; cats; sheep; pigs; goats; cattle; horses; and non-human primates such as apes and monkeys.
  • an “effective amount” of a substance as that term is used herein is that amount sufficient to effect beneficial or desired results, including clinical results, and, as such, an “effective amount” depends upon the context in which it is being applied.
  • an effective amount of a composition described herein is an amount sufficient to treat and/or ameliorate a Clostridium difficile infection, as well as decrease the severity and/or reduce the likelihood of a Clostridium difficile infection.
  • the decrease can be a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98% or 99% decrease in severity of Clostridium difficile infection, or likelihood of becoming infected.
  • An effective amount can be administered in one or more administrations.
  • treatment is an approach for obtaining beneficial or desired results, including clinical results.
  • beneficial or desired clinical results include, but are not limited to, alleviation or amelioration of one or more symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, prevention of disease, delay or slowing of disease progression, and/or amelioration or palliation of the disease state.
  • the decrease can be a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98% or 99% decrease in severity of complications or symptoms.
  • Treatment can also mean prolonging survival as compared to expected survival if not receiving treatment.
  • expression vector is used to denote a nucleic acid molecule that is either linear or circular, into which another nucleic acid sequence fragment of appropriate size can be integrated.
  • nucleic acid fragment(s) can include additional segments that provide for transcription of a gene encoded by the nucleic acid sequence fragment.
  • the additional segments can include and are not limited to: promoters, transcription terminators, enhancers, internal ribosome entry sites, untranslated regions, polyadenylation signals, selectable markers, origins of replication and such, as known in the art.
  • Expression vectors are often derived from plasmids, cosmids, viral vectors and yeast artificial chromosomes; vectors are often recombinant molecules containing nucleic acid sequences from several sources.
  • operably linked when applied to nucleic acid sequences, for example in an expression vector, indicates that the sequences are arranged so that they function cooperatively in order to achieve their intended purposes, i.e., a promoter sequence allows for initiation of transcription that proceeds through a linked coding sequence as far as the termination signal.
  • a “nucleic acid molecule” is a single or double stranded covalently-linked sequence of nucleotides in which the 3′ and 5′ ends on each nucleotide are joined by phosphodiester bonds.
  • the polynucleotide can be made up of deoxyribonucleotide bases or ribonucleotide bases.
  • Polynucleotides include DNA and RNA, and can be manufactured synthetically in vitro or isolated from natural sources.
  • promoter denotes a region within a gene to which transcription factors and/or RNA polymerase can bind so as to control expression of an associated coding sequence. Promoters are commonly, but not always, located in the 5′ non-coding regions of genes, upstream of the translation initiation codon.
  • the promoter region of a gene can include one or more consensus sequences that act as recognizable binding sites for sequence specific nucleic acid binding domains of nucleic acid binding proteins. Nevertheless, such binding sites can also be located in regions outside of the promoter, for example in enhancer regions located in introns or downstream of the coding sequence.
  • a “regulatory gene” is a gene involved in controlling the expression of one or more other genes.
  • the present invention provides for therapeutic compositions which increase resistance to C. difficile infection, and/or reduce the amount of C. difficile toxin, and/or inhibit proliferation and/or growth of C. difficile in a subject.
  • Such therapeutic compositions can comprise, for example, small molecule, polypeptide, or nucleic acid molecules.
  • the composition comprises a recombinant cell expressing an enzyme that converts a bile salt or acid to a secondary bile acid.
  • the recombinant cell comprises one or more exogenous nucleic acids encoding said enzyme, wherein the one or more exogenous nucleic acids are operably linked to a promoter.
  • the promoter can be an inducible promoter or a constitutively active promoter. The promoter can be a bai operon promoter, or can be another promoter active in the recombinant cell.
  • the composition comprises a recombinant cell expressing a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon.
  • the recombinant cell comprises one or more exogenous nucleic acids encoding a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, wherein the one or more exogenous nucleic acids are operably linked to a promoter.
  • a “bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon” refers to a cluster of genes encoding a protein with enzymatic activity to convert primary bile acids to secondary bile acids.
  • the protein can convert a primary bile acid such as cholic acid (CA) and/or chenodeoxycholic acid (CDCA), into secondary bile acids such as deoxycholic acid (DCA) and lithocholic acid (LCA).
  • the protein exhibits dehydroxylation activity.
  • the protein comprises a 7 ⁇ -hydroxysteroid dehydrogenase.
  • Examples of such enzymes are 7 ⁇ -hydroxysteroid dehydrogenase enzymes expressed by Clostridium scindens, Clostridium hiranonis, Clostridium hylemonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-05 and Clostridiales VE202-26, as well as active fragments thereof, and recombinant forms of said enzymes.
  • the 7 ⁇ -hydroxysteroid dehydrogenase is the C. scindens enzyme having the following amino acid sequence:
  • AAB6115I which may be encoded by a nucleic acid as set forth in GenBank Accession No. M58473, and as set forth in FIG. 17 (SEQ ID NO:2).
  • said enzyme may be provided by a host cell, such as a bacterium, engineered to contain a nucleic acid encoding SEQ ID NO:1 or a protein having one, two, or three conservative substitutions therein, operably linked to a constitutively or inducibly active promoter element, as described herein.
  • said enzyme may be provided by a host cell, such as a bacterium, engineered to contain and express a nucleic acid comprising SEQ ID NO:2 or a nucleic acid having a sequence that is at least 90 percent, or at least 95 percent, or at least 99 percent homologous thereto (where homology may be determined using standard software such as BLAST or FASTA).
  • the enzyme may be one of the following, or a combination thereof: an enzyme having the amino acid sequence set forth in GenBank Accession No. EIA17829 (7 ⁇ -hydroxysteroid dehydrogenase from Clostridium perfringens ); and/or an enzyme having the amino acid sequence as set forth in GenBank Accession No. AAA53556 (7 ⁇ -hydroxysteroid dehydrogenase from Clostridium sordellii ).
  • the recombinant cell further comprises one or more exogenous nucleic acids encoding a bile salt hydrolase, antibiotic resistance gene, and/or antibiotic susceptibility gene, wherein the nucleic acids are operably linked to a promoter.
  • the bile salt hydrolase is a bacterial bile salt hydrolase, for example, as encoded by a bshA and/or bshb gene of lactobacillus acidophilus (See, e.g., McAuliffe et al., Appl Environ Microbiol. 2005 August; 71(8):4925-9.).
  • Other bile salt hydrolases are described in Begley et al., Appl Environ Microbial. 2006 March; 72(3):1729-38.).
  • a conjugated bile acid is referred to as a bile salt.
  • the production of a secondary bile acid from a bile salt involves a two-step process: 1) removal of a conjugated taurine or glycine by a bile salt hydrolase (BSH) enzyme and 2) removal of a hydroxyl group from the steroid ring by enzymes comprising an enzyme encoded by the bai-operon.
  • BSH bile salt hydrolase
  • an antibiotic resistance gene by the recombinant cell reduces the inhibition in growth or survival of the recombinant cell caused by exposure to an antibiotic such as, but not limited to, an antibiotic selected from the group consisting of a ⁇ -lactam antibiotic, clindamycin, a cephalosporin, a quinolone antibiotic, levofloxacin, fluoroquinolone, a macrolide antibiotic, trimethoprim, and a sulfonamide antibiotic, as described herein.
  • an antibiotic such as, but not limited to, an antibiotic selected from the group consisting of a ⁇ -lactam antibiotic, clindamycin, a cephalosporin, a quinolone antibiotic, levofloxacin, fluoroquinolone, a macrolide antibiotic, trimethoprim, and a sulfonamide antibiotic, as described herein.
  • an antibiotic susceptibility gene by the recombinant cell increases the inhibition in growth or survival of the recombinant cell caused by exposure to an antibiotic.
  • antibiotics can include, but are not limited to, an antibiotic selected from the group consisting of a ⁇ -lactam antibiotic, clindamycin, a cephalosporin, a quinolone antibiotic, levofloxacin, fluoroquinolone, a macrolide antibiotic, trimethoprim, and a sulfonamide antibiotic, as described herein.
  • the recombinant cell is susceptible to an antibiotic other than the foregoing antibiotics.
  • the enzyme that can convert a primary bile acid to a secondary bile acid can be administered directly to a subject as a therapeutic agent. If enzyme is administered in purified form, it may be administered in a liquid or solid form, optionally may be lyophilized, optionally may comprise a pharmaceutically suitable solvent and/or carrier.
  • compositions disclosed herein include nucleic acid sequences encoding a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, said nucleic acid sequences being part of expression vectors that express the bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon or functional fragments thereof in a suitable host.
  • such nucleic acid sequences have promoters operably linked to the bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon coding region, said promoter being inducible or constitutive, and, optionally, tissue-specific.
  • the promoter comprises a cytomegalovirus (CMV) promoter, or any other promoter known in the art that is effective for expressing a nucleic acid n a eukaryotic cell.
  • CMV cytomegalovirus
  • the promoter comprises a bacterial promoter.
  • nucleic acid into a subject or cell can be either direct, in which case the subject or cell, e.g., bacterial cells of a subject's intestinal microbiota, is directly exposed to the nucleic acid or nucleic acid-carrying vectors, or indirect, in which case, cells, e.g., a host cell, such as isolated bacterial cells of the intestinal microbiota, are first transformed with the nucleic acids in vitro, then transplanted into the subject.
  • a host cell such as isolated bacterial cells of the intestinal microbiota
  • the methods of the present invention involve transferring a gene to a host cell in culture by such methods as electroporation, lipofection, calcium phosphate mediated transfection, or viral infection.
  • the method of transfer includes the transfer of a selectable marker to the host cells. The cells are then placed under selection to isolate those host cells that have taken up and are expressing the transferred gene. Those host cells are then delivered to a patient.
  • the nucleic acid can be introduced into cells, e.g., bacterial host cells, prior to administration in vivo of the resulting recombinant cell by any method known in the art, including but not limited to transfection, electroporation, microinjection, infection with a viral or bacteriophage vector containing the nucleic acid sequences, cell fusion, chromosome-mediated gene transfer, microcell-mediated gene transfer, spheroplast fusion, etc. Numerous techniques are known in the art for the introduction of foreign genes into cells (see, e.g., Loeffler and Behr, Meth. Enzymol. 217:599-618 (1993); Cohen et al., Meth. Enzymol. 217:618-644 (1993); Cline, Pharmac. Ther. 29:69-92m (1985)), and can be used in accordance with the present disclosure, provided that the necessary developmental and physiological functions of the recipient cells are not disrupted.
  • the host cell may be a Clostridium scindens, Lactobacillus, Lactococcus, Bacillus, Bifidobacterium, or attenuated and non-monocytogenes Listeria. In one non-limiting embodiment, a combination of host cells may be used.
  • the resulting recombinant cells can be delivered to a patient by various methods known in the art.
  • the amount of cells envisioned for use depends on the desired effect, patient state, etc., and can be determined by one skilled in the art.
  • nucleic acid sequences encoding a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon are introduced into cells such that they are expressible by the cells or their progeny, and the recombinant cells are then administered in vivo for therapeutic effect.
  • a bacterial progenitor, or stem, or other progenitor cells can be used. Any stem and/or progenitor cells which can be isolated and maintained in vitro can potentially be used (see e.g. PCT Publication WO 94/08598; Porada and Porada, J. Genet Syndr Gene Ther., May 25; S 1. p11:011 (2012); Stemple and Anderson, Cell 71:973-985 (1992); Rheinwald, Meth. Cell Bio. 21A:229 (1980); and Pittelkow and Scott, Mayo Clinic Proc. 61:771 (1986)).
  • the terms “vector” and “expression vector” mean the vehicle by which a DNA or RNA sequence (e.g., a foreign gene) can be introduced into a host cell, so as to transform the host and promote expression (e.g., transcription and translation) of the introduced sequence.
  • Vectors include plasmids, phages, viruses, etc.; they are discussed in greater detail below.
  • a “therapeutic vector” as used herein refers to a vector which is acceptable for administration to an animal, and particularly to a human.
  • Vectors typically include the DNA of a transmissible agent, into which foreign DNA is inserted.
  • a common way to insert one segment of DNA into another segment of DNA involves the use of enzymes called restriction enzymes that cleave DNA at specific sites (specific groups of nucleotides) called restriction sites.
  • restriction enzymes that cleave DNA at specific sites (specific groups of nucleotides) called restriction sites.
  • foreign DNA is inserted at one or more restriction sites of the vector DNA, and then is carried by the vector into a host cell along with the transmissible vector DNA.
  • a segment or sequence of DNA having inserted or added DNA can also be called a “DNA construct.”
  • a common type of vector is a “plasmid”, which generally is a self-contained molecule of double-stranded DNA, usually of bacterial origin, that can readily accept additional (foreign) DNA and which can readily introduced into a suitable host cell.
  • a plasmid vector often contains coding DNA and promoter DNA and has one or more restriction sites suitable for inserting foreign DNA.
  • Coding DNA is a DNA sequence that encodes a particular amino acid sequence for a particular protein or enzyme.
  • Promoter DNA is a DNA sequence which initiates, regulates, or otherwise mediates or controls the expression of the coding DNA.
  • Promoter DNA and coding DNA can be from the same gene or from different genes, and can be from the same or different organisms.
  • a large number of vectors, including plasmid and fungal vectors, have been described for replication and/or expression in a variety of eukaryotic and prokaryotic hosts.
  • Non-limiting examples include pKK plasmids (Clonetech), pUC plasmids, pET plasmids (Novagen, Inc., Madison, Wis.), pRSET plasmids (Invitrogen, San Diego, Calif.), pCDNA3 plasmids (Invitrogen), pREP plasmids (Invitrogen), or pMAL plasmids (New England Biolabs, Beverly, Mass.), and many appropriate host cells, using methods disclosed or cited herein or otherwise known to those skilled in the relevant art.
  • Recombinant cloning vectors will often include one or more replication systems for cloning or expression, one or more markers for selection in the host, e.g., antibiotic resistance, and one or more expression cassettes.
  • Suitable vectors include, for example, bacteriophages, cosmids, plasmids, naked DNA, DNA lipid complexes, and other recombination vehicles typically used in the art which have been described for expression in a variety of eukaryotic and prokaryotic hosts, and can be used for gene therapy as well as for simple protein expression.
  • compositions described herein comprise one or more therapeutic bacteria, or spores thereof, for example, a C. scindens bacterium such as described in Morris et al., “ Clostridium scindens sp. nov., a Human Intestinal Bacterium with Desmolytic Activity on Corticoids,” Int J Syst Bacteriol, October 1985, 35:478-481, and/or Krafft et al., “Purification and characterization of a novel form of 20 alpha-hydroxysteroid dehydrogenase from Clostridium scindens, ” J. Bacterial. June 1989, 171:2925-2932.
  • a C. scindens bacterium is as deposited in, and available from, the American Type Culture Collection, accession number ATCC 35704, Strain Designation VPI 13733.
  • C. scindens 16S ribosomal RNA gene sequence is set forth in GenBank Accession No. AF262238
  • C. scindens genome nucleic acid sequence from a whole genome shotgun sequencing project is set forth in GenBank Accession No. ABFY 02000000.
  • Non-limiting examples of characteristics of C. scindens are expression of the enzymes 20 alpha-hydroxysteroid dehydrogenase, 7-beta dehydrogenase, 7 alpha-dehydroxylase, and steroid desmolase.
  • bacteria may be administered in the proliferative state or as spores, or a mixture thereof.
  • the therapeutic bacteria described herein can be modified, for example, by introducing one or more nucleic acids into the bacteria, thereby producing recombinant bacteria.
  • nucleic acids can comprise, for example, a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, antibiotic resistance gene, antibiotic susceptibility gene, and/or a bile salt hydrolase gene, as described herein.
  • Such recombinant bacteria can be prepared as described herein.
  • C. scindens may be administered in the form of purified bacteria or spores or other progenitors thereof, or alternatively may be administered as a constituent in a mixture of types of bacteria, optionally including one or more probiotic bacterium or yeast. In certain non-limiting embodiments, C.
  • scindens may be administered in combination with one or more of Barnesiella intestihominis (e.g., phylum Bacteroidetes, see, e.g., Buffie and Pamer, Nature Reviews Immunology 13:790-801), and/or Blautia hansenii (e.g., phylum Firmicutes, Family Lachnospiraceae, ATCC 27752), and/or Pseudoilavonifractor capillosus (e.g., phylum Firmicutes), and/or Clostridium hiranonis, and/or Clostridium hylemonae, and/or Clostridium perfringens, and/or Clostridium sordellii, and/or Proteocatella sphenisci, and/or Lachnospiraceae 5_1_157FAA, Clostridiales VE202-05 and/or Clostridiales VE202-26.
  • the present invention provides for pharmaceutical compositions comprising such forms of C. scindens and optionally additional bacteria.
  • the bacteria may be administered in the form of a liquid, a suspension, a dried (e.g. lyophilized) powder, a tablet, a capsule, or a suppository, and may be administered orally or rectally.
  • the bacteria can be administered in a food product, for example, a yogurt food product.
  • a “food product” means a product or composition that is intended for consumption by a human or a non-human animal. Such food products include any food, feed, snack, food supplement, liquid, beverage, treat, toy (chewable and/or consumable toys), meal substitute or meal replacement.
  • the present invention provides for a composition
  • a composition comprising an isolated Clostridium scindens bacterium.
  • the bacterium is in a formulation for administration to a subject.
  • the composition further comprises a second, third or fourth bacterium selected from the group consisting of Barnesiella intestihominis, Blautia hansenii, Pseudoflavonifractor capillosus and combinations thereof.
  • the composition comprises one, two, three, four, five, six, seven, eight, nine, or ten or more bacteria selected from the group consisting of Clostridium scindens, Clostridium hiranonis, Clostridium hylemonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-05, Clostridiales VE202-26, Barnesiella intestihominis, Blautia hansenii, and Pseudoflavonifractor capillosus.
  • Clostridium scindens Clostridium hiranonis
  • Clostridium hylemonae Clostridium perfringens
  • Clostridium sordellii Proteocatella sphenisci
  • the present invention provides for a composition comprising an isolated Clostridium scindens bacterium, an isolated Barnesiella intestihominis bacterium, an isolated Blautia hansenii bacterium, and an isolated Pseudoflavonifractor capillosus bacterium.
  • said bacterium is C. scindens, but alternate or additional bacteria may be comprised in the compositions described herein, for example, bacteria which may be naturally occurring or bacteria engineered to express a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, or peptides expressed therefrom, such as, for example, an enzyme that converts a primary bile acid to a secondary bile acid, for example, 7 ⁇ -hydroxysteroid dehydrogenase.
  • Naturally occurring bacteria other than C. scindens that may be used to provide said enzyme are Clostridium hiranonis and Clostridium hylemonae (Ridlon, J. Lipid Res. 53:66-76 (2012), Ridlon, J Lipid Res 47, 241-259 (2006)).
  • the present disclosure provides for pharmaceutical compositions which include a therapeutic composition, as described herein, such as, for example, a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, and/or a recombinant cell expressing said bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, and/or a therapeutic bacterium, as described herein.
  • a therapeutic composition such as, for example, a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, and/or a recombinant cell expressing said bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, and/or a therapeutic bacterium, as described herein.
  • Such pharmaceutical compositions can further include at least one other agent, such as a stabilizing compound or additional therapeutic agent, and can be administered in any sterile, biocompatible pharmaceutical carrier, including, but not limited to, saline, buffered saline, dextrose
  • the composition can be in a liquid or lyophilized form and includes a diluent (Tris, citrate, acetate or phosphate buffers) having various pH values and ionic strengths, solubilizer such as Tween or Polysorbate, carriers such as human serum albumin or gelatin, preservatives such as thimerosal, parabens, benzylalconium chloride or benzyl alcohol, antioxidants such as ascrobic acid or sodium metabisulfite, and other components such as lysine or glycine. Selection of a particular composition will depend upon a number of factors, including the condition being treated, the route of administration and the pharmacokinetic parameters desired. A more extensive survey of components suitable for pharmaceutical compositions is found in Remington's Pharmaceutical Sciences, 18th ed. A. R. Gennaro, ed. Mack, Easton, Pa. (1980).
  • solubilizer such as Tween or Polysorbate
  • carriers such as human serum albumin or gelatin
  • the methods and compositions of the present disclosure find use in treating Clostridium difficile infection.
  • Bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acids, peptides expressed by a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, recombinant cells expressing a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, therapeutic bacteria, and/or secondary bile acids can be administered to the patient in a pharmaceutically acceptable carrier.
  • the route of administration eventually chosen will depend upon a number of factors and can be ascertained by one skilled in the art.
  • the pharmaceutical compositions of the present disclosure can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for oral or rectal administration.
  • Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral, rectal or nasal ingestion by a patient to be treated.
  • compositions suitable for use in the present disclosure include, in certain embodiments, compositions where the active ingredients are contained in an effective amount to achieve the intended purpose.
  • the amount will vary from one individual to another and will depend upon a number of factors, including the overall physical condition of the patient, e.g., severity of the Clostridium difficile infection.
  • compositions of the present disclosure can be administered for prophylactic and/or therapeutic treatments.
  • pharmaceutical compositions of the present disclosure are administered in an amount sufficient to treat, prevent and/or ameliorate Clostridium difficile infection.
  • dosages for any one patient depends upon many factors, including stage of the disease or condition, the severity of the disease or condition, the patient's size, body surface area, age, the particular compound to be administered, sex, time and route of administration, general health, and interaction with other drugs being concurrently administered.
  • a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid, peptides expressed by a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, recombinant cells expressing a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, therapeutic bacteria, and/or secondary bile acid can be administered to a patient alone, or in combination with one or more other drugs, nucleotide sequences, lifestyle changes, etc. used in the treatment or prevention of Clostridium difficile infection, or symptoms thereof, or in pharmaceutical compositions where it is mixed with excipient(s) or other pharmaceutically acceptable carriers.
  • formulations can be given depending on the dosage and frequency as required and tolerated by the patient.
  • the formulations should provide a sufficient quantity of active agent to effectively treat, prevent or ameliorate the Clostridium difficile infection, or symptoms or complications thereof as described herein.
  • the present invention provides for a method of reducing the risk of C. difficile infection and/or improving resistance to C. difficile infection, and/or reducing the severity of C. difficile infection and/or decreasing the amount of C. difficile toxin, comprising administering, to a subject in need of such treatment, an effective amount of a composition described herein, for example, a recombinant cell and/or a composition comprising one or more therapeutic bacteria, for example, Clostridium scindens optionally in combination with one or more of Barnesiella intestihominis, Blautia hansenii, and Pseudoflavonifractor capillosus.
  • the method of reducing the severity or risk of C. difficile infection comprises reducing the severity or risk of a C. difficile -associated disease, as described herein.
  • Subjects in need of such treatment or compositions include subjects who are either at risk for developing C. difficile infection and/or subjects who have existing C. difficile infection.
  • Subjects at risk for C. difficile infection include individuals who are or have been treated with an antibiotic; individuals who are very young (juvenile) or who are old (geriatric, e.g. humans aged 65 years or older); individuals suffering from an inflammatory bowel disease or condition (including human inflammatory bowel disease IBD and Crohn's Disease); individuals who are hospitalized or in a long-term care facility or who have been, in the past 2, 3, 4, 5, or 6 weeks, hospitalized or in a long-term care facility; individuals with cancer including those undergoing anti-cancer treatment and/or stem cell or bone marrow transplant recipients; individuals who have previously suffered C. difficile infection, and individuals undergoing immunosuppressive therapy or with an otherwise compromised immune system (e.g. subjects infected with an immunodeficiency causing retrovirus such as HIV, FIV, FLV, etc.).
  • an immunodeficiency causing retrovirus such as HIV, FIV, FLV, etc.
  • Non-limiting examples of antibiotics associated with risk of C. difficile infection include ⁇ -lactam antibiotics such as penicillin, ampicillin, and amoxicillin; clindamycin; cephalosporins such as but not limited to cefixime; quinolone antibiotics such as ciprofloxacin, levofloxacin and fluoroquinolone; macrolide antibiotics; trimethoprim; or sulfonamide antibiotics.
  • the antibiotic is not enrofloxacin.
  • C. difficile infection is distinct from the mere presence of the bacterium or C. difficile spores in the host gastrointestinal tract; infection is indicated by the presence of one or more symptom, such as intestinal tenderness, pain, and/or cramping; diarrhea for example watery diarrhea occurring at least 3, at least 5, or at least 8 times per day; blood or pus in stool or diarrhea; fever; loss of appetite; and/or nausea; and/or one or more clinical sign such as an elevated white blood cell count, decreased serum albumin, and/or the appearance of pseudomembrane in the intestinal and/or rectal mucosa.
  • C. difficile infection is distinct from the mere presence of the bacterium or C. difficile spores in the host gastrointestinal tract; infection is indicated by the presence of one or more symptom, such as intestinal tenderness, pain, and/or cramping; diarrhea for example watery diarrhea occurring at least 3, at least 5, or at least 8 times per day; blood or pus in stool or diarrhea; fever; loss of appetite; and/or nausea; and/or one or more clinical sign such as an elevated
  • a “ C. difficile -associated disease” refers to any disease involving unwanted growth, toxin production, or tissue invasion in the bowel by C. difficile.
  • C. difficile -associated diseases are known in the art and include antibiotic-associated diarrhea (i.e., C. difficile pseudomembranous colitis, and C. difficile -associated toxic megacolon.
  • C. difficile colitis generally refers to profuse, watery diarrheal illness associated with the presence of at least one C. difficile toxin.
  • pseudomembranous colitis refers to a severe form of C. difficile colitis further characterized by bloody diarrhea, fever, and bowel wall invasion by C. difficile.
  • the appearance of pseudomembranes on the surface of the colon or rectum, or in the intestinal and/or rectal mucosa, is diagnostic of the condition.
  • the pseudomembranes are composed principally of inflammatory debris and white blood cells.
  • the present invention provides for a method for reducing the risk of C. difficile infection and/or improving resistance to C. difficile infection, comprising administering, to a subject in need of such treatment, an effective amount of a composition or therapeutic bacteria described herein, for example, C. scindens bacteria.
  • an effective amount of a composition or therapeutic bacteria described herein, for example, C. scindens is an amount which increases resistance to C. difficile infection, reduces the amount of C. difficile toxin, and/or inhibits proliferation and/or growth of C. difficile in a subject.
  • an effective amount of C. scindens bacteria is at least 10 5 bacteria, or at least 10 6 bacteria, or at least 10 7 bacteria, or at least 10 8 bacteria, or at least 10 9 bacteria.
  • the present invention provides for a method for reducing the severity of C. difficile infection, and/or decreasing the amount of C. difficile toxin, and/or reducing the risk of C. difficile infection, and/or improving resistance to C. difficile infection, comprising administering, to a subject in need of such treatment, an effective amount of a composition described herein, for example, a recombinant cell or a therapeutic bacteria such as a C. scindens bacteria.
  • Reducing the severity of C. difficile infection refers to an amelioration in the clinical symptoms or signs of infection, for example, but not by way of limitation, one or more of the following: a decrease in the frequency or volume of diarrhea; a decrease in fever; a decrease in abdominal cramping, pain, and/or tenderness; a reduction in white blood cells in the blood; an increase in serum albumin; weight maintenance or gain; and a decrease the appearance of pseudomembrane in the intestinal and/or rectal mucosa.
  • the present invention provides for a method of reducing the severity of C. difficile infection, and/or decreasing the amount of C. difficile toxin, and/or reducing the risk of C. difficile infection, and/or improving resistance to C. difficile infection, comprising administering, to a subject in need of such treatment, an effective amount of an enzyme of C. scindens (see Ridlon, J. Lipid Res. 54:2437-2449 (2013)).
  • the present invention provides for a method for reducing the severity of C. difficile infection, and/or decreasing the amount of C. difficile toxin, and/or reducing the risk of C. difficile infection, and/or improving resistance to C. difficile infection, comprising administering, to a subject in need of such treatment, an effective amount of an enzyme that converts a bile acid to a secondary bile acid.
  • the present invention provides for a method for reducing the severity of C. difficile infection, and/or decreasing the amount of C. difficile toxin, and/or reducing the risk of C. difficile infection, and/or improving resistance to C. difficile infection, comprising administering, to a subject in need of such treatment, an effective amount of a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid, peptides expressed by a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, recombinant cells expressing a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, therapeutic bacteria, and/or secondary bile acid.
  • the compositions of the present invention are administered in purified form.
  • the compositions are contained in and/or produced in the subject by a bacterium or a mixture of bacteria.
  • the present invention provides for a method for reducing the severity of C.difficile infection, and/or decreasing the amount of C. difficile toxin, and/or reducing the risk of C. difficile infection, and/or improving resistance to C. difficile infection, comprising administering, to a subject in need of such treatment, an effective amount of a secondary bile acid.
  • secondary bile acids which may be used include deoxycholic acid, lithocholic acid, or a combination thereof.
  • the present disclosure provides for a method for decreasing the severity of one or more symptoms of an intestinal disorder comprising administering, to a subject in need of such treatment, an effective amount of one or more of a recombinant cell; composition comprising one or more therapeutic bacteria; and an agent selected from the group consisting of an enzyme that converts a bile acid to a secondary bile acid, a secondary bile acid, purified bacteria or spores thereof expressing an enzyme that converts a bile acid to a secondary bile acid, and combinations thereof, as described herein.
  • the symptoms are selected from the group consisting of frequency and/or volume of diarrhea; fever; abdominal cramping, pain, and/or tenderness; elevated level of white blood cells in the blood; loss of serum albumin; weight loss; appearance of pseudomembrane in the intestinal and/or rectal mucosa; and combinations thereof.
  • a subject treated according to the invention may be concurrently or sequentially treated with one or more agent that reduces the risk of and/or ameliorates C. difficile infection, for example, but not limited to, one or more antibiotic for example, but not limited to, vancomycin, metronidazole, and/or fidaxomicin; an immunotherapeutic agent such as an anti-toxin antibody; an herbal remedy such as Puerariae radix, Scutellariae radix, Rhizoma coptidis, garlic, or one or more extract thereof; and/or a probiotic remedy including for example, but not limited to, Lactobaccilus acidophilus, Lactobacillus casei, Bifidobacteriva, Streptococcus thermophiles, and/or Saccharomyces boulardii.
  • the treatment does not further comprise administration of cholestyramine.
  • the present disclosure also provides for methods of diagnosing or identifying a subject with a C. difficile infection, or at risk for C. difficile infection.
  • such methods comprise determining the level of one more bacterium present in an intestinal microbiota sample of a subject that can convert a primary bile acid to a secondary bile acid, for example, C. scindens, wherein the subject is diagnosed or identified as having a C. difficile infection, or at risk for C. difficile infection, when the level or amount of the one or more bacterium in the subject's microbiota is lower than a bacterium reference level.
  • a bacterium reference level is a level of bacterium, for example, C. scindens or any other bacteria that can convert a primary bile acid to a secondary bile acid, present in intestinal microbiota, a level below which is indicative of C.
  • such a reference level can be the level of said bacterium in the microbiota of a subject who does not have a C. difficile infection, or at risk for C. difficile infection.
  • such methods comprise determining the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme present in the intestinal microbiota of a subject, wherein the subject is diagnosed or identified as having a C. difficile infection, or at risk for C. difficile infection, when the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme in the subject's microbiota is lower than a 7 ⁇ -hydroxysteroid dehydrogenase enzyme reference level.
  • a 7 ⁇ -hydroxysteroid dehydrogenase enzyme reference level is an activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme present in intestinal microbiota, a level or activity below which is indicative of C. difficile infection, or risk of C.
  • such a reference level can be the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase in the microbiota of a subject who does not have a C. difficile infection, or at risk for C. difficile infection.
  • such methods comprise quantifying the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in a fecal sample of a subject, wherein the subject is diagnosed or identified as having a C. difficile infection, or at risk for C. difficile infection, when the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in the fecal sample is lower than a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid reference level.
  • a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid reference level is the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in a fecal sample, a level below which is indicative of C. difficile infection, or risk of C. difficile infection, as determined by a medical doctor or person of skill in the art.
  • a reference level can be the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in a fecal sample of a subject who does not have a C. difficile infection, or at risk for C. difficile infection.
  • the level of nucleic acid is quantified using metagenomic sequencing, quantitative PCR, or any other method known in the art for quantifying nucleic acid in a sample.
  • the subject when the level or activity of the one more bacterium present in an intestinal microbiota sample of a subject that can convert a primary bile acid to a secondary bile acid, the 7 ⁇ -hydroxysteroid dehydrogenase enzyme in the subject's microbiota, and/or the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in the fecal sample is above their respective reference levels, the subject is not administered an antibiotic selected from the group consisting of a ⁇ -lactam antibiotic, clindamycin, a cephalosporin, a quinolone antibiotic, levofloxacin, fluoroquinolone, a macrolide antibiotic, trimethoprim, and a sulfonamide antibiotic.
  • an antibiotic selected from the group consisting of a ⁇ -lactam antibiotic, clindamycin, a cephalosporin, a quinolone antibiotic, levofloxacin, fluoroquino
  • compositions and methods for reducing the severity and/or risk of Clostridium difficile infection are provided.
  • the present disclosure provides a recombinant cell expressing a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, wherein the recombinant cell comprises one or more exogenous nucleic acids encoding a bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon, wherein the one or more exogenous nucleic acids are operably linked to a promoter.
  • the recombinant cell further comprises one or more nucleic acids encoding a bile salt hydrolase, antibiotic resistance protein, and/or antibiotic susceptibility protein.
  • the one or more exogenous nucleic acids comprises a baiCD gene encoding a 7 ⁇ -hydroxysteroid dehydrogenase enzyme.
  • the 7 ⁇ -hydroxysteroid dehydrogenase is a bacterial 7 ⁇ -hydroxysteroid dehydrogenase, wherein the bacteria is selected from the group consisting of Clostridium scindens, Clostridium hiranonis, Clostridium hylemonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-26, Clostridiales VE202-05 and combinations thereof.
  • the bacteria is selected from the group consisting of Clostridium scindens, Clostridium hiranonis, Clostridium hylemonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-26,
  • the recombinant cell is a bacterium or spore thereof, for example, a bacterium selected from the group consisting of Clostridium scindens, Lactobacillus, Lactococcus, Bacillus, Bifidobacterium, and attenuated and non-monocytogenes Listeria strains.
  • the bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon is expressed by the recombinant cell in an amount sufficient to transform a primary bile acid to a secondary bile acid by 7 ⁇ / ⁇ -dehydroxylation.
  • the present disclosure provides for a composition
  • a composition comprising an isolated Clostridium scindens bacterium, wherein the bacterium is in a formulation for administration to a subject.
  • the composition further comprises a second bacterium selected from the group consisting of Barnesiella intestihominis, Blautia hansenii, Pseudoflavonifractor capillosus and combinations thereof.
  • the composition comprises one or more, two or more, three or more, or four of the foregoing bacteria.
  • the recombinant cell or compositions described herein are formulated for oral or rectal administration, and can optionally further comprise a probiotic bacterium, probiotic yeast, or a combination thereof.
  • the formulation for oral or rectal administration is a liquid, suspension, dried powder, tablet, capsule or food product.
  • the present disclosure also provides for a method for reducing the risk of Clostridium difficile infection and/or increasing resistance to Clostridium difficile infection in a subject, comprising administering, to a subject in need of such treatment, an effective amount of a recombinant cell and/or composition as described herein.
  • the present disclosure also provides for a method for reducing the severity of Clostridium difficile infection and/or decreasing the amount of Clostridium difficile toxin in a subject, comprising administering, to a subject in need of such treatment, an effective amount of a recombinant cell and/or composition as described herein.
  • the present disclosure also provides for a method for reducing the risk of Clostridium difficile infection and/or increasing resistance to Clostridium difficile infection in a subject, comprising administering, to a subject in need thereof, an effective amount of an agent selected from the group consisting of an enzyme that converts a bile acid to a secondary bile acid, a secondary bile acid, purified bacteria or spores thereof expressing an enzyme that converts a bile acid to a secondary bile acid, and combinations thereof.
  • an agent selected from the group consisting of an enzyme that converts a bile acid to a secondary bile acid, a secondary bile acid, purified bacteria or spores thereof expressing an enzyme that converts a bile acid to a secondary bile acid, and combinations thereof.
  • the present disclosure also provides for a method for reducing the severity of Clostridium difficile infection and/or decreasing the amount of Clostridium difficile toxin in a subject, comprising administering, to a subject in need thereof, an effective amount of an agent selected from the group consisting of an enzyme that converts a bile acid to a secondary bile acid, a secondary bile acid, purified bacteria or spores thereof expressing an enzyme that converts a bile acid to a secondary bile acid, and combinations thereof.
  • an agent selected from the group consisting of an enzyme that converts a bile acid to a secondary bile acid, a secondary bile acid, purified bacteria or spores thereof expressing an enzyme that converts a bile acid to a secondary bile acid, and combinations thereof.
  • the present disclosure also provides for a method for decreasing the severity of a symptom of an intestinal disorder comprising administering, to a subject in need of such treatment, an effective amount of one or more of a recombinant cell or composition described herein, and an agent selected from the group consisting of an enzyme that converts a bile acid to a secondary bile acid, a secondary bile acid, purified bacteria or spores thereof expressing an enzyme that converts a bile acid to a secondary bile acid, and combinations thereof, wherein the symptom is selected from the group consisting of frequency and/or volume of diarrhea; fever; abdominal cramping, pain, and/or tenderness; elevated level of white blood cells in the blood; loss of serum albumin; weight loss; appearance of pseudomembrane in the intestinal and/or rectal mucosa; and combinations thereof.
  • the enzyme that converts a bile salt to a secondary bile acid is a 7 ⁇ -hydroxysteroid dehydrogenase enzyme.
  • the recombinant cell, composition or agent can be administered to the subject in an amount effective to inhibit proliferation of Clostridium difficile in the subject.
  • the recombinant cell, composition or agent is administered to the subject in an amount effective to reduce one or more clinical symptoms of Clostridium difficile infection selected from the group consisting of frequency and/or volume of diarrhea; fever; abdominal cramping, pain, and/or tenderness; elevated level of white blood cells in the blood; loss of serum albumin; weight loss; appearance of pseudomembrane in the intestinal and/or rectal mucosa; and combinations thereof.
  • the composition administered to a subject comprises a purified bacterium or spore thereof selected from the group consisting of Clostridium scindens, Clostridium hiranonis, Clostridium hykmonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-26, Clostridiales VE202-05 and combinations thereof.
  • a purified bacterium or spore thereof selected from the group consisting of Clostridium scindens, Clostridium hiranonis, Clostridium hykmonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-26, Clostridiales
  • the bacterium is a purified Clostridium scindens bacterium.
  • the composition further comprises a second bacterium selected from the group consisting of Barnesiella intestihominis, Blautia hansenii, Pseudoflavonifractor capillosus, and combinations thereof.
  • the composition is a secondary bile acid, for example, a secondary bile acid selected from the group consisting of deoxycholic acid, lithocholic acid, and a combination thereof.
  • the methods described herein further comprise administering to the subject, an antibiotic, an immunotherapeutic agent, an herbal remedy, a probiotic, or combinations thereof.
  • the methods described herein further comprise identifying a subject with a Clostridium difficile infection, or at risk for Clostridium difficile infection, comprising obtaining an intestinal microbiota sample from a subject and determining the level of one or more bacterium present in the intestinal microbiota sample; comparing the level of the one or more bacterium in the sample with a reference bacterium level; and administering the recombinant cell, composition or agent to the subject when the level of one or more bacterium in the sample is lower than the bacterium reference level.
  • the one or more bacterium is selected from the group consisting of Clostridium scindens, Clostridium hiranonis, Clostridium hylemonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-05, Clostridiales VE202-26, and combinations thereof.
  • the method further comprising administering an antibiotic to the subject, wherein, when the level of the one or more bacterium in the sample is equal to or greater than the bacterium reference level, the antibiotic administered to the subject is not an antibiotic selected from the group consisting of a ⁇ -lactam antibiotic, clindamycin, a cephalosporin, a quinolone antibiotic, levofloxacin, fluoroquinolone, a macrolide antibiotic, trimethoprim, and a sulfonamide antibiotic.
  • an antibiotic selected from the group consisting of a ⁇ -lactam antibiotic, clindamycin, a cephalosporin, a quinolone antibiotic, levofloxacin, fluoroquinolone, a macrolide antibiotic, trimethoprim, and a sulfonamide antibiotic.
  • the methods described herein further comprise identifying a subject with a Clostridium difficile infection, or at risk for Clostridium difficile infection, comprising obtaining an intestinal microbiota sample from a subject and determining the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme present in the intestinal microbiota sample; comparing the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme in the sample with a reference 7 ⁇ -hydroxysteroid dehydrogenase enzyme activity or level; and administering the recombinant cell, composition or agent to the subject when the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme in the sample is lower than the reference 7 ⁇ -hydroxysteroid dehydrogenase enzyme activity or level.
  • the present disclosure also provides for a method of diagnosing a subject with a Clostridium difficile infection, or at risk for Clostridium difficile infection, comprising obtaining an intestinal microbiota sample from a subject and determining the level of one or more bacterium present in the intestinal microbiota sample; comparing the level of one or more bacterium in the sample with a reference bacterium level; and diagnosing the subject as having a Clostridium difficile infection, or at risk for Clostridium difficile infection, when the level of the one or more bacterium in the sample is lower than the bacterium reference level.
  • the one or more bacterium is selected from the group consisting of Clostridium scindens, Clostridium hiranonis, Clostridium hylemonae, Clostridium perfringens, Clostridium sordellii, Proteocatella sphenisci, Lachnospiraceae 5_1_57FAA, Clostridiales VE202-05, Clostridiales VE202-26, and combinations thereof.
  • the method further comprising administering an antibiotic to the subject, wherein, when the level of the one or more bacterium in the sample is equal to or greater than the bacterium reference level, the antibiotic administered to the subject is not an antibiotic selected from the group consisting of a ⁇ -lactam antibiotic, clindamycin, a cephalosporin, a quinolone antibiotic, levofloxacin, fluoroquinolone, a macrolide antibiotic, trimethoprim, and a sulfonamide antibiotic.
  • an antibiotic selected from the group consisting of a ⁇ -lactam antibiotic, clindamycin, a cephalosporin, a quinolone antibiotic, levofloxacin, fluoroquinolone, a macrolide antibiotic, trimethoprim, and a sulfonamide antibiotic.
  • the present disclosure provides for a method of diagnosing a subject with a Clostridium difficile infection, or at risk for Clostridium difficile infection, comprising obtaining an intestinal microbiota sample from a subject and determining the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme present in the intestinal microbiota sample; comparing the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme in the sample with a reference 7 ⁇ -hydroxysteroid dehydrogenase enzyme activity or level; and diagnosing the subject as having a Clostridium difficile infection, or at risk for Clostridium difficile infection, when the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme in the sample is lower than the reference 7 ⁇ -hydroxysteroid dehydrogenase enzyme activity or level.
  • the methods described herein further comprise identifying a subject with a Clostridium difficile infection, or at risk for Clostridium difficile infection, comprising obtaining a fecal sample from a subject and quantifying the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in the fecal sample; comparing the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid in the fecal sample with a reference bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid level; and administering the recombinant cell, composition or agent to the subject when the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid in the fecal sample is lower than the reference level.
  • the present disclosure provides for a method of diagnosing a subject with a Clostridium difficile infection, or at risk for Clostridium difficile infection, comprising obtaining a fecal sample from a subject and quantifying the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in the fecal sample; comparing the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in the fecal sample with a reference bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid level; and diagnosing the subject as having a Clostridium difficile infection, or at risk for Clostridium difficile infection, when the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in the fecal sample is lower than the reference level.
  • the methods described herein further comprise administering an antibiotic to the subject, wherein, when the level of one or more bacterium in the sample is equal to or greater than the bacterium reference level; when the activity or level of 7 ⁇ -hydroxysteroid dehydrogenase enzyme in the sample is greater than the reference 7 ⁇ -hydroxysteroid dehydrogenase enzyme activity or level; or when the level of bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon nucleic acid present in the fecal sample is greater than the reference level; wherein the antibiotic administered to the subject is not an antibiotic selected from the group consisting of a ⁇ -lactam antibiotic, clindamycin, a cephalosporin, a quinolone antibiotic, levofloxacin, fluoroquinolone, a macrolide antibiotic, trimethoprim, and a sulfonamide antibiotic.
  • the present disclosure provides for a method of reducing risk of developing Clostridium difficile -associated disease in a subject receiving antibiotic therapy, comprising administering, to a subject in need of such treatment, an effective amount of a recombinant cell or composition described herein.
  • the present disclosure provides for a method of preventing or treating Clostridium difficile -associated disease in a subject comprising administering, to a subject in need of such treatment, an effective amount of a recombinant cell or composition described herein.
  • the Clostridium difficile -associated disease is Clostridium difficile colitis or pseudomembranous colitis.
  • the subject is, has or will receive antibiotic therapy
  • the present disclosure also provides for a kit comprising the recombinant cell, and/or agent, and/or therapeutic composition described herein.
  • FIG. 2 a shows the strategy for determining C. difficile susceptibility during post-antibiotic exposure.
  • Quantitative RT-PCR of total 16S indicated that none of the antibiotic regimens resulted in substantial decreases in bacterial density ( FIG. 2C ).
  • Quantification of C. difficile toxin expression in the supernatant from large intestine content correlated strongly with C. difficile abundance, confirming the infection virulence ( FIG. 1D ).
  • Longitudinal characterization of the intestinal microbiota by 454 pyrosequencing of the bacterial 16S V1-3 region before ( FIGS. 1E-G ) and after C. difficile challenge revealed that the three antibiotics had diverse impacts on the bacterial phylotype composition as well.
  • microbiota alpha diversity correlated poorly with infection resistance during this early period following antibiotic exposure, suggesting that recovery of more precise microbiota features (e.g. individual taxa) resulted in enhanced infection resistance.
  • OTUs operational taxonomic units
  • FIG. 4 operational taxonomic units
  • 11 bacterial OTUs correlated strongly with infection resistance
  • FIG. 3c These OTUs represent a small fraction of the microbiota membership (6%) and were comprised primarily by Clostridium cluster XIVa, including the OTU with the strongest resistance correlation, Clostridium scindens.
  • C. scindens was also one of two OTUs correlated with resistance among animals harboring low-biodiversity microbiota ( FIG. 3 a , red box) that nevertheless remained resistant to C. difficile ( FIG. 3 c ).
  • FIG. 5 a, FIG. 6 , Table 1 we applied this same modeling approach to our murine C. difficile susceptibility timecourse study.
  • mice Following antibiotic administration 43 and a two-day antibiotic washout period, 10 separately-housed mice were administered a suspension containing the 4-bacteria consortium or vehicle (PBS) once daily for two days prior to a C. difficile infection challenge (1,000 spores). Additionally, since C. scindens had the strongest resistance correlation in mice (including animals harboring low-biodiversity intestinal microbiota) ( FIG. 3 c ) and was conserved in the human microbiota as the strongest C. difficile inhibitor ( FIG. 5 b ), we administered a suspension containing only this bacterium in a third arm.
  • PBS 4-bacteria consortium or vehicle
  • Microbiota-derived products can inhibit intestinal pathogens through host-dependent and direct antimicrobial mechanisms, but the bacterial source of most protective products remains undefined.
  • some secondary bile acids can inhibit C. difficile in vitro 44 and are abundant in the intestines of mice and humans 45 , but the precise origin of these compounds and their relative contribution to C. difficile inhibition in vivo remains unclear.
  • C. scindens expresses enzymes crucial for secondary bile acid synthesis 46 that are uncommon among intestinal bacteria 47 , we hypothesized that the C. difficile -protective effects of C. scindens may be associated with and dependent upon this rare biosynthetic capacity.
  • Biochemical quantification of bile acid species indicated that recovery of secondary bile acids correlated with C. difficile resistance following antibiotic exposure ( FIG. 13 a ).
  • PICRUSt 48 to infer the abundance of gene families in bacterial communities from our initial murine intestinal microbiota 16S sequencing ( FIGS. 1, 3 )
  • FIGS. 1, 3 we found that increased abundance of the secondary bile acid biosynthesis gene family was correlated significantly with C. difficile resistance ( FIG. 13 b ).
  • To confirm the predictive metagenomic results we subjected intestinal content samples from a representative subset of the same antibiotic-exposed animals to shotgun metagenomic sequencing and targeted quantification of secondary bile acid biosynthesis gene family members.
  • bile salt hydrolases and genes comprising the bile acid-inducible (bai) 7 ⁇ / ⁇ -dehydroxylation operon possessed by C. scindens.
  • TCA primary bile acids taurocholic acid
  • CA cholic acid
  • DCDCA chenodeoxycholic acid
  • TCDCA tauro-chenodeoxycholic acid
  • Clostridia can present challenges when assigning taxonomy 53-56 , highlighting the importance of integrating functional genomic (e.g. secondary bile acid synthesis genes) and metabolomic (e.g. secondary bile acid species) interrogation with 16S rRNA profiling when screening and validating intestinal microbes of interest, as we have done in this study.
  • functional genomic e.g. secondary bile acid synthesis genes
  • metabolomic e.g. secondary bile acid species
  • C. difficile some strains of C. difficile are not dependent upon bile salts for germination 61 , and germination inhibitors 62 are not effective across all strains either 61 .
  • broadly sequestering the bile pool would theoretically reduce germinants for some C. difficile strains, but would also neutralize secondary bile acids, sometimes disproportionately 63 , effectively disinhibiting vegetative C. difficile growth.
  • C. scindens consumes primary bile salts as substrate (e.g. decreasing C. difficile spore germinants) in the synthesis of secondary bile acids (e.g. increasing vegetative C. difficile inhibitors), remodeling bile species proportions in this fashion may exploit the therapeutic potential of bile modulation better than broad neutralization using sequestrants.
  • Direct manipulation of intestinal bile acids may be effective for treatment and prevention of C. difficile infection, but caution is warranted since some bile species, including secondary bile acids, have been implicated in the promotion of cholesterol gallstone disease and gastrointestinal cancers 64 .
  • Other bile species such as UDCA, may ameliorate or protect against such diseases 50 , and remain at physiological levels in antibiotic-exposed animals reconstituted with C. scindens in our study.
  • potent microbiome-mediated chemistry may be therapeutically optimal when driven by the bacteria of origin; other aspects of C. scindens physiology and ecology may be critical to ensure secondary bile acid is synthesized, targeted, and otherwise regulated to ensure effective pathogen colonization resistance while avoiding pathological imbalances.
  • Knowledge of these mechanisms coupled with an appreciation for the ecological context of those microbes responsible, will facilitate amplification of natural microbiota-mediated pathogen resistance in individuals at risk for C. difficile infection.

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