Small molecules from the human microbiota

Microbial bioactive molecules Human cells are outnumbered by the microbial cells of our commensals by an order of magnitude. All of these organisms are metabolically active and secrete multiple bioactive molecules. Genomics has unveiled a remarkable array of biosynthetic gene clusters in the human microbiota, which encode diverse metabolites. Donia et al. review how molecules ranging from lantibiotics and microcins to indoxyl sulfate and immunemodulatory oligosaccharides and lipids could affect the health and physiology of the whole organism, depending on the composition of an individual's microbial community. Science, this issue p. 10.1126/science.1254766 BACKGROUND Two developments in distinct fields are converging to create interest in discovering small molecules from the human microbiome. First, the use of genomics to guide natural product discovery has led to the unexpected discovery of numerous biosynthetic gene clusters in genomes of the human microbiota. Second, the microbiome research community is moving from a focus on “who’s there?” to “what are they doing?” with an accompanying emphasis on understanding microbiota-host interactions at the level of molecular mechanism. This merger has sparked a concerted hunt for the mediators of microbe-host and microbe-microbe interactions, including microbiota-derived small molecules. ADVANCES Numerous small molecules are known that are produced by the human microbiota. The microbiota-derived ribosomally synthesized, posttranslationally modified peptides (RiPPs) include widely distributed lantibiotics and microcins; these molecules have narrow-spectrum activity and are presumptive mediators of interactions among closely related species. Another notable RiPP is Escherichia coli heat-stable enterotoxin, a guanylate cyclase 2C agonist from which the recently approved gastrointestinal motility drug linaclotide was derived. Fewer amino acid metabolites are synthesized by the microbiota, but they are produced at very high levels that vary widely among individuals (e.g., indoxyl sulfate at 10 to 200 mg/day). Gut bacterial species convert common dietary amino acids into distinct end products, such as tryptophan to indoxyl sulfate, indole propionic acid, and tryptamine—indicating that humans with the same diet but different gut colonists can have widely varying gut metabolic profiles. Microbially produced oligosaccharides differ from other natural products because they are cell-associated (i.e., nondiffusible) and because many more biosynthetic loci exist for them than for other small molecule classes. Well-characterized examples, such as Bacteroides polysaccharide A, show that oligosaccharides may not simply play a structural role or mediate adhesion; rather, they can be involved in highly specific ligand-receptor interactions that result in immune modulation. Similarly, the (glyco)lipids α-galactosylceramide and mycolic acid can play roles in immune signaling. The most prominent microbiota-derived terpenoids are microbial conversion products of the cholic acid and chenodeoxycholic acid in host bile. These secondary bile acids can reach high concentration (mM) in the gut and vary widely in composition among individuals. Several canonical virulence factors from pathogens are derived from nonribosomal peptides (NRPs) and polyketides (PKs), but less is known about NRPs and PKs from the commensal microbiota. A recent computational effort has identified ~14,000 biosynthetic gene clusters in sequenced genomes from the human microbiota, 3118 of which were present in one or more of the 752 metagenomic sequence samples from the NIH Human Microbiome Project. Nearly all of the gene clusters that were present in >10% of the samples from the body site of origin are uncharacterized, highlighting the potential for identifying the molecules they encode and studying their biological activities. OUTLOOK There are two central challenges facing the field. The first is to distinguish, from among thousands of microbiota-derived molecules, which ones drive a key phenotype at physiologically relevant concentrations. Second, which experimental systems are appropriate for testing the activity of an individual molecule from a complex milieu? Meeting these challenges will require developing new computational and experimental technologies, including a capacity to identify biosynthetic genes and predict the structure and target of their biological activity, and systems in which germ-free mice are colonized by mock communities that differ only by the presence or absence of a biosynthetic gene cluster. Small-molecule–mediated microbe-host and microbe-microbe interactions. Commensal organisms of the human microbiota produce many diverse small molecules with an equally diverse array of targets that can exacerbate or modulate immune responses and other physiological functions in the host. Several act as antibacterials to remove competing organisms, but many other products have unknown targets and effects on commensals and the host. Developments in the use of genomics to guide natural product discovery and a recent emphasis on understanding the molecular mechanisms of microbiota-host interactions have converged on the discovery of small molecules from the human microbiome. Here, we review what is known about small molecules produced by the human microbiota. Numerous molecules representing each of the major metabolite classes have been found that have a variety of biological activities, including immune modulation and antibiosis. We discuss technologies that will affect how microbiota-derived molecules are discovered in the future and consider the challenges inherent in finding specific molecules that are critical for driving microbe-host and microbe-microbe interactions and understanding their biological relevance.

[1]  P. Gérard Metabolism of Cholesterol and Bile Acids by the Gut Microbiota , 2013, Pathogens.

[2]  Wendy S. Garrett,et al.  Cancer and the microbiota , 2015, Science.

[3]  N. Moran,et al.  Parallel genomic evolution and metabolic interdependence in an ancient symbiosis , 2007, Proceedings of the National Academy of Sciences.

[4]  M. Fischbach,et al.  A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice , 2013, The ISME Journal.

[5]  Krystle L. Chavarria,et al.  Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora , 2014, Proceedings of the National Academy of Sciences.

[6]  J. Nicholson,et al.  Therapeutic Modulation of Microbiota-Host Metabolic Interactions , 2012, Science Translational Medicine.

[7]  M. Daffé,et al.  Mycolic acids: structures, biosynthesis, and beyond. , 2014, Chemistry & biology.

[8]  Peter Cimermancic,et al.  A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics , 2014, Cell.

[9]  O. Kuipers,et al.  Evaluating the feasibility of lantibiotics as an alternative therapy against bacterial infections in humans , 2011, Expert opinion on drug metabolism & toxicology.

[10]  C. J. Moore,et al.  Production of the Lantibiotic Salivaricin A and Its Variants by Oral Streptococci and Use of a Specific Induction Assay To Detect Their Presence in Human Saliva , 2006, Applied and Environmental Microbiology.

[11]  T. Meyer,et al.  The production of p-cresol sulfate and indoxyl sulfate in vegetarians versus omnivores. , 2012, Clinical journal of the American Society of Nephrology : CJASN.

[12]  E. Mayer,et al.  Gut/brain axis and the microbiota. , 2015, The Journal of clinical investigation.

[13]  K. Hase,et al.  Gut microbiota-generated metabolites in animal health and disease. , 2014, Nature chemical biology.

[14]  T. Natori,et al.  Synthesis and stereochemistry of agelasphin-9b , 1993 .

[15]  B. Reinhold,et al.  Structural requirements for glycolipid antigen recognition by CD1b-restricted T cells. , 1997, Science.

[16]  R. P. Ross,et al.  Streptolysin S-like virulence factors: the continuing sagA , 2011, Nature Reviews Microbiology.

[17]  J. Faith,et al.  Identifying Gut Microbe–Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice , 2014, Science Translational Medicine.

[18]  M. Fischbach,et al.  A family of pyrazinone natural products from a conserved nonribosomal peptide synthetase in Staphylococcus aureus. , 2010, Chemistry & biology.

[19]  Bernard Henrissat,et al.  The abundance and variety of carbohydrate-active enzymes in the human gut microbiota , 2013, Nature Reviews Microbiology.

[20]  Masahira Hattori,et al.  Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome , 2013, Nature.

[21]  M. Rohde,et al.  Cross-feeding and interkingdom communication in dual-species biofilms of Streptococcus mutans and Candida albicans , 2014, The ISME Journal.

[22]  Philipp Engel,et al.  Comparative Metabolomics and Structural Characterizations Illuminate Colibactin Pathway-Dependent Small Molecules , 2014, Journal of the American Chemical Society.

[23]  H. Sahl,et al.  Lantibiotic-mediated anti-lactobacillus activity of a vaginal Staphylococcus aureus isolate. , 1992, FEMS microbiology letters.

[24]  F. Portaels,et al.  Heterogeneity of Mycolactones Produced by Clinical Isolates of Mycobacterium ulcerans: Implications for Virulence , 2003, Infection and Immunity.

[25]  T. Meyer,et al.  Colonic contribution to uremic solutes. , 2011, Journal of the American Society of Nephrology : JASN.

[26]  H. Bouwmeester,et al.  Engineering the plant rhizosphere. , 2015, Current opinion in biotechnology.

[27]  Hui Hong,et al.  Mycolactones: immunosuppressive and cytotoxic polyketides produced by aquatic mycobacteria , 2008, Natural product reports.

[28]  M. Fons,et al.  Ruminococcin C, a new anti-Clostridium perfringens bacteriocin produced in the gut by the commensal bacterium Ruminococcus gnavus E1. , 2011, Biochimie.

[29]  P. Dorrestein,et al.  Clostridiolysin S, a Post-translationally Modified Biotoxin from Clostridium botulinum* , 2010, The Journal of Biological Chemistry.

[30]  S. Mazmanian,et al.  A microbial symbiosis factor prevents intestinal inflammatory disease , 2008, Nature.

[31]  Michael A Fischbach,et al.  Eating for two: how metabolism establishes interspecies interactions in the gut. , 2011, Cell host & microbe.

[32]  B. Bachmann,et al.  Bioactive oligosaccharide natural products. , 2014, Natural product reports.

[33]  R. Cichewicz,et al.  Fungal biofilm inhibitors from a human oral microbiome-derived bacterium. , 2012, Organic & biomolecular chemistry.

[34]  Kai Blin,et al.  antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers , 2013, Nucleic Acids Res..

[35]  Jintae Lee,et al.  Indole as an intercellular signal in microbial communities. , 2010, FEMS microbiology reviews.

[36]  Y. Amoako,et al.  Kinetics of mycolactone in human subcutaneous tissue during antibiotic therapy for Mycobacterium ulcerans disease , 2014, BMC Infectious Diseases.

[37]  J. Tagg,et al.  Salivaricin G32, a Homolog of the Prototype Streptococcus pyogenes Nisin-Like Lantibiotic SA-FF22, Produced by the Commensal Species Streptococcus salivarius , 2012, International journal of microbiology.

[38]  Daniel Henrion,et al.  Mycobacterial Toxin Induces Analgesia in Buruli Ulcer by Targeting the Angiotensin Pathways , 2014, Cell.

[39]  S. Long Genes and signals in the rhizobium-legume symbiosis. , 2001, Plant physiology.

[40]  Chuan He,et al.  Aureusimines in Staphylococcus aureus Are Not Involved in Virulence , 2010, PloS one.

[41]  Jian Ding,et al.  Discovery of LFF571: an investigational agent for Clostridium difficile infection. , 2012, Journal of medicinal chemistry.

[42]  S. Akira,et al.  Direct recognition of the mycobacterial glycolipid, trehalose dimycolate, by C-type lectin Mincle , 2009, The Journal of experimental medicine.

[43]  Robert J. Palmer,et al.  Oral multispecies biofilm development and the key role of cell–cell distance , 2010, Nature Reviews Microbiology.

[44]  Simona Littnerová,et al.  Bacteriocin-encoding genes and ExPEC virulence determinants are associated in human fecal Escherichia coli strains , 2013, BMC Microbiology.

[45]  M. Chamaillard,et al.  Nod2 Is a General Sensor of Peptidoglycan through Muramyl Dipeptide (MDP) Detection* , 2003, The Journal of Biological Chemistry.

[46]  C. Hill,et al.  Listeriolysin S, a Novel Peptide Haemolysin Associated with a Subset of Lineage I Listeria monocytogenes , 2008, PLoS pathogens.

[47]  Hening Lin,et al.  How pathogenic bacteria evade mammalian sabotage in the battle for iron , 2006, Nature chemical biology.

[48]  Roger G. Linington,et al.  Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters , 2014, Cell.

[49]  B. Roe,et al.  Genomic Island TnSmu2 of Streptococcus mutans Harbors a Nonribosomal Peptide Synthetase-Polyketide Synthase Gene Cluster Responsible for the Biosynthesis of Pigments Involved in Oxygen and H2O2 Tolerance , 2010, Applied and Environmental Microbiology.

[50]  Jamie Rossjohn,et al.  A conserved human T cell population targets mycobacterial antigens presented by CD1b , 2013, Nature Immunology.

[51]  Morgan A. Wyatt,et al.  Staphylococcus aureus Nonribosomal Peptide Secondary Metabolites Regulate Virulence , 2010, Science.

[52]  Jason M Crawford,et al.  Bacterial symbionts and natural products. , 2011, Chemical communications.

[53]  S. Duquesne,et al.  Microcins, gene-encoded antibacterial peptides from enterobacteria. , 2007, Natural product reports.

[54]  P. G. Arnison,et al.  Erratum: Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature (Natural Product Reports (2013) 30 (108-160) DOI:10.1039/C2NP20085F) , 2013 .

[55]  Natalia N. Ivanova,et al.  Symbiosis insights through metagenomic analysis of a microbial consortium. , 2006, Nature Reviews Microbiology.

[56]  H. Sahl,et al.  Production, purification and chemical properties of an antistaphylococcal agent produced by Staphylococcus epidermidis. , 1981, Journal of general microbiology.

[57]  Jesse R. Zaneveld,et al.  Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences , 2013, Nature Biotechnology.

[58]  K. Honda,et al.  Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species , 2011, Science.

[59]  G. Besra,et al.  Mycolic Acid Modification by the mmaA4 Gene of M. tuberculosis Modulates IL-12 Production , 2008, PLoS pathogens.

[60]  박주홍,et al.  The Toll-Like Receptor 2 pathway Establishes Colonization by a Commensal of the Human Microbiota , 2011 .

[61]  K. Philip,et al.  Enhanced Production, Purification, Characterization and Mechanism of Action of Salivaricin 9 Lantibiotic Produced by Streptococcus salivarius NU10 , 2013, PloS one.

[62]  D. Garbers,et al.  Guanylyl cyclase is a heat-stable enterotoxin receptor , 1990, Cell.

[63]  M. Glickman,et al.  Mycobacterium tuberculosis Lacking All Mycolic Acid Cyclopropanation Is Viable but Highly Attenuated and Hyperinflammatory in Mice , 2012, Infection and Immunity.

[64]  H. Bode,et al.  Identification and bioanalysis of natural products from insect symbionts and pathogens. , 2013, Advances in biochemical engineering/biotechnology.

[65]  M. Gershon,et al.  Physiological responses of guinea-pig myenteric neurons secondary to the release of endogenous serotonin by tryptamine , 1985, Neuroscience.

[66]  S. Zeissig,et al.  Sphingolipids from a Symbiotic Microbe Regulate Homeostasis of Host Intestinal Natural Killer T Cells , 2014, Cell.

[67]  W. A. van der Donk,et al.  Biosynthesis of the antimicrobial peptide epilancin 15X and its N-terminal lactate. , 2011, Chemistry & biology.

[68]  T. Dinan,et al.  Microbiota regulation of the Mammalian gut-brain axis. , 2015, Advances in applied microbiology.

[69]  R. Kolter,et al.  From Peptide Precursors to Oxazole and Thiazole-Containing Peptide Antibiotics: Microcin B17 Synthase , 1996, Science.

[70]  J. H. Marshall,et al.  Pigments of Staphylococcus aureus, a series of triterpenoid carotenoids , 1981, Journal of bacteriology.

[71]  Dae-Joong Kang,et al.  Bile salt biotransformations by human intestinal bacteria Published, JLR Papers in Press, November 18, 2005. , 2006, Journal of Lipid Research.

[72]  P. G. Arnison,et al.  esized and post-translationally modi fi ed peptide natural products : overview and recommendations for a universal nomenclature , 2012 .

[73]  M. Mori,et al.  Structure of cereulide, a cyclic dodecadepsipeptide toxin from Bacillus cereus and studies on NMR characteristics of its alkali metal complexes including a conformational structure of the K+ complex , 1995 .

[74]  Christoph Wilhelm,et al.  Commensal–dendritic-cell interaction specifies a unique protective skin immune signature , 2015, Nature.

[75]  C. Ronson,et al.  Isolation and characterization of the lantibiotic salivaricin A and its structural gene salA from Streptococcus salivarius 20P3 , 1993, Applied and environmental microbiology.

[76]  C. Walsh,et al.  Maturation of an Escherichia coli ribosomal peptide antibiotic by ATP-consuming N-P bond formation in microcin C7. , 2008, Journal of the American Chemical Society.

[77]  Carmen Buchrieser,et al.  Escherichia coli Induces DNA Double-Strand Breaks in Eukaryotic Cells , 2006, Science.

[78]  Rustem F. Ismagilov,et al.  Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis , 2015, Cell.

[79]  P. Hylemon,et al.  Isolation and characterization of a bile acid inducible 7alpha-dehydroxylating operon in Clostridium hylemonae TN271. , 2010, Anaerobe.

[80]  Y. Lai,et al.  Genotoxic Klebsiella pneumoniae in Taiwan , 2014, PloS one.

[81]  Pieter C Dorrestein,et al.  Discovery of a widely distributed toxin biosynthetic gene cluster , 2008, Proceedings of the National Academy of Sciences.

[82]  M. Mori,et al.  A novel dodecadepsipeptide, cereulide, is an emetic toxin of Bacillus cereus. , 1995, FEMS microbiology letters.

[83]  G. Challis A Widely Distributed Bacterial Pathway for Siderophore Biosynthesis Independent of Nonribosomal Peptide Synthetases , 2005, Chembiochem : a European journal of chemical biology.

[84]  M. Fons,et al.  Ruminococcin A, a New Lantibiotic Produced by aRuminococcus gnavus Strain Isolated from Human Feces , 2001, Applied and Environmental Microbiology.

[85]  W. R. Wikoff,et al.  Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites , 2009, Proceedings of the National Academy of Sciences.

[86]  Albert Bendelac,et al.  The biology of NKT cells. , 2007, Annual review of immunology.

[87]  Anahita Z Mostafavi,et al.  Biosynthetic assembly of the Bacteroides fragilis capsular polysaccharide A precursor bactoprenyl diphosphate-linked acetamido-4-amino-6-deoxygalactopyranose. , 2013, Biochemistry.

[88]  C. Whitfield,et al.  Biosynthesis and export of bacterial lipopolysaccharides. , 2014, Annual review of biochemistry.

[89]  A. Clara,et al.  Distribution of Genes Encoding the Trypsin-Dependent Lantibiotic Ruminococcin A among Bacteria Isolated from Human Fecal Microbiota , 2002, Applied and Environmental Microbiology.

[90]  Kai Blin,et al.  antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences , 2011, Nucleic Acids Res..

[91]  Christopher A. Voigt,et al.  Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca , 2012, Proceedings of the National Academy of Sciences.

[92]  Nicolas Blanchard,et al.  History, biology and chemistry of Mycobacterium ulcerans infections (Buruli ulcer disease). , 2013, Natural product reports.

[93]  R. P. Ross,et al.  Production of the Bsa Lantibiotic by Community-Acquired Staphylococcus aureus Strains , 2009, Journal of bacteriology.

[94]  J. Nicholson,et al.  Host-Gut Microbiota Metabolic Interactions , 2012, Science.

[95]  C. Walsh,et al.  Genetics and Assembly Line Enzymology of Siderophore Biosynthesis in Bacteria , 2002, Microbiology and Molecular Biology Reviews.

[96]  R. Ruoff The continuing saga , 1994, Nature.

[97]  H Kubota,et al.  Molecular structure of the toxin domain of heat-stable enterotoxin produced by a pathogenic strain of Escherichia coli. A putative binding site for a binding protein on rat intestinal epithelial cell membranes. , 1996, The Journal of biological chemistry.

[98]  J. Nicoli,et al.  Trypsin-dependent production of an antibacterial substance by a human Peptostreptococcus strain in gnotobiotic rats and in vitro , 1993, Applied and environmental microbiology.

[99]  S. Gringhuis,et al.  Signalling through C-type lectin receptors: shaping immune responses , 2009, Nature Reviews Immunology.

[100]  J. Czaplicki,et al.  Mycolic acids constitute a scaffold for mycobacterial lipid antigens stimulating CD1-restricted T cells. , 2009, Chemistry & biology.

[101]  Gustavo Glusman,et al.  Structural and Genetic Diversity of Group B Streptococcus Capsular Polysaccharides , 2005, Infection and Immunity.

[102]  D. Mitchell,et al.  Thiazole/oxazole-modified microcins: complex natural products from ribosomal templates. , 2011, Current opinion in chemical biology.

[103]  Andrew H. Van Benschoten,et al.  Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. , 2014, Cell host & microbe.

[104]  M. Schatz,et al.  Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis , 2011, Proceedings of the National Academy of Sciences.

[105]  K. Poralla,et al.  Genetic and biochemical analyses of the biosynthesis of the yellow carotenoid 4,4'-diaponeurosporene of Staphylococcus aureus , 1994, Journal of bacteriology.

[106]  M. Fons,et al.  Characterization and distribution of the gene cluster encoding RumC, an anti-Clostridium perfringens bacteriocin produced in the gut. , 2011, FEMS microbiology ecology.

[107]  Lynn Margulis,et al.  Symbiosis as a source of evolutionary innovation : speciation and morphogenesis , 1991 .

[108]  M. Salkinoja-Salonen,et al.  The higher toxicity of cereulide relative to valinomycin is due to its higher affinity for potassium at physiological plasma concentration. , 2006, Toxicology and applied pharmacology.

[109]  L. Margulis,et al.  Bellagio conference and book. Symbiosis as Source of Evolutionary Innovation: Speciation and Morphogenesis. Conference--June 25-30, 1989, Bellagio Conference Center, Italy. , 1991, Symbiosis.

[110]  M. Fischbach,et al.  Biosynthetic tailoring of microcin E492m: post-translational modification affords an antibacterial siderophore-peptide conjugate. , 2007, Journal of the American Chemical Society.

[111]  J. Merritt,et al.  Mutanobactin A from the human oral pathogen Streptococcus mutans is a cross-kingdom regulator of the yeast-mycelium transition. , 2010, Organic & biomolecular chemistry.

[112]  P. Flatt,et al.  Biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds. , 2007, Natural product reports.

[113]  F. Götz,et al.  Structure and Biosynthesis of Staphyloxanthin from Staphylococcus aureus* , 2005, Journal of Biological Chemistry.

[114]  G. Dalmasso,et al.  Bacterial genotoxin colibactin promotes colon tumour growth by inducing a senescence-associated secretory phenotype , 2014, Gut.

[115]  A. Peschel,et al.  Staphyloxanthin Plays a Role in the Fitness of Staphylococcus aureus and Its Ability To Cope with Oxidative Stress , 2006, Infection and Immunity.

[116]  M. Fischbach,et al.  Production of α-Galactosylceramide by a Prominent Member of the Human Gut Microbiota , 2013, PLoS biology.

[117]  M. Gilmore,et al.  The Enterococcus faecalis cytolysin: a novel toxin active against eukaryotic and prokaryotic cells , 2003, Cellular microbiology.

[118]  W. Garrett,et al.  The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis , 2013, Science.

[119]  Jörn Piel,et al.  Metabolites from symbiotic bacteria. , 2009, Natural product reports.

[120]  P. Poole,et al.  The rules of engagement in the legume-rhizobial symbiosis. , 2011, Annual review of genetics.

[121]  H. Weber,et al.  Enterotoxicity of a nonribosomal peptide causes antibiotic-associated colitis , 2014, Proceedings of the National Academy of Sciences.

[122]  S. B. Nascimento,et al.  Bacteriocins as alternative agents for control of multiresistant staphylococcal strains , 2006, Letters in applied microbiology.

[123]  J. Šmarda,et al.  Exoproducts of the Escherichia coli strain H22 inhibiting some enteric pathogens both in vitro and in vivo , 2006, Journal of applied microbiology.

[124]  G. Besra,et al.  Lipid length controls antigen entry into endosomal and nonendosomal pathways for CD1b presentation , 2002, Nature Immunology.

[125]  Sunita Sharma,et al.  Functional identification of a galactosyltransferase critical to Bacteroides fragilis Capsular Polysaccharide A biosynthesis. , 2014, Carbohydrate research.

[126]  N. Moran,et al.  Genomics and evolution of heritable bacterial symbionts. , 2008, Annual review of genetics.

[127]  K. Zimmermann,et al.  Identification and Characterization of Microcin S, a New Antibacterial Peptide Produced by Probiotic Escherichia coli G3/10 , 2012, PloS one.

[128]  N. V. van Nuland,et al.  Isolation and structural characterization of epilancin 15X, a novel lantibiotic from a clinical strain of Staphylococcus epidermidis , 2005, FEBS letters.

[129]  E. Lander,et al.  Development and Applications of CRISPR-Cas 9 for Genome Engineering , 2015 .

[130]  Yoshito Kishi,et al.  Chemistry of mycolactones, the causative toxins of Buruli ulcer , 2011, Proceedings of the National Academy of Sciences.

[131]  H. A. Barker,et al.  Amino acid degradation by anaerobic bacteria. , 1981, Annual review of biochemistry.

[132]  H. Sahl,et al.  Elucidation of the structure of SA-FF22, a lanthionine-containing antibacterial peptide produced by Streptococcus pyogenes strain FF22. , 1994, European journal of biochemistry.

[133]  E. Lander,et al.  Development and Applications of CRISPR-Cas9 for Genome Engineering , 2014, Cell.

[134]  C. Langner,et al.  Klebsiella oxytoca as a causative organism of antibiotic-associated hemorrhagic colitis. , 2006, The New England journal of medicine.

[135]  Harald Grallert,et al.  Cereulide synthetase gene cluster from emetic Bacillus cereus: Structure and location on a mega virulence plasmid related to Bacillus anthracis toxin plasmid pXO1 , 2006, BMC Microbiology.

[136]  J. Bertin,et al.  Nod1 Detects a Unique Muropeptide from Gram-Negative Bacterial Peptidoglycan , 2003, Science.

[137]  J. Šmarda,et al.  Bacteriocin synthesis in uropathogenic and commensal Escherichia coli: colicin E1 is a potential virulence factor , 2010, BMC Microbiology.

[138]  K. McKeage,et al.  Linaclotide: first global approval. , 2012, Drugs.

[139]  J. Crawford,et al.  The colibactin warhead crosslinks DNA , 2015, Nature chemistry.

[140]  A. Stewart,et al.  In Vivo Evidence for a Prodrug Activation Mechanism during Colibactin Maturation , 2013, Chembiochem : a European journal of chemical biology.

[141]  J. Tagg,et al.  Streptococcin A-FF22: Nisin-Like Antibiotic Substance Produced by a Group A Streptococcus , 1978, Antimicrobial Agents and Chemotherapy.

[142]  Zaid Abdo,et al.  Temporal Dynamics of the Human Vaginal Microbiota , 2012, Science Translational Medicine.

[143]  E. Oldfield,et al.  Role of rsbU and staphyloxanthin in phagocytosis and intracellular growth of Staphylococcus aureus in human macrophages and endothelial cells. , 2009, The Journal of infectious diseases.

[144]  E. Balskus,et al.  A prodrug resistance mechanism is involved in colibactin biosynthesis and cytotoxicity. , 2013, Journal of the American Chemical Society.

[145]  M. Hattori,et al.  Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota , 2013, Nature.

[146]  J. Petrosino,et al.  Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders , 2013, Cell.

[147]  W. Rabsch,et al.  Genetic Structure and Distribution of the Colibactin Genomic Island among Members of the Family Enterobacteriaceae , 2009, Infection and Immunity.

[148]  H. Sahl,et al.  Isolation, Characterization, and Heterologous Expression of the Novel Lantibiotic Epicidin 280 and Analysis of Its Biosynthetic Gene Cluster , 1998, Applied and Environmental Microbiology.

[149]  P. G. Arnison,et al.  Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. , 2013, Natural product reports.

[150]  Ascel Samba-Louaka,et al.  Escherichia coli Producing Colibactin Triggers Premature and Transmissible Senescence in Mammalian Cells , 2013, PloS one.

[151]  P. Gibbs,et al.  Inhibition of Salmonella typhimurium in the chicken intestinal tract by a transformed avirulent avian Escherichia coli. , 1999, Avian diseases.