451
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Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J Clin Microbiol 2013; 51:2884-92. [PMID: 23804381 DOI: 10.1128/jcm.00845-13] [Citation(s) in RCA: 349] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Clostridium difficile infection (CDI) causes nearly half a million cases of diarrhea and colitis in the United States each year. Although the importance of the gut microbiota in C. difficile pathogenesis is well recognized, components of the human gut flora critical for colonization resistance are not known. Culture-independent high-density Roche 454 pyrosequencing was used to survey the distal gut microbiota for 39 individuals with CDI, 36 subjects with C. difficile-negative nosocomial diarrhea (CDN), and 40 healthy control subjects. A total of 526,071 partial 16S rRNA sequence reads of the V1 to V3 regions were aligned with 16S databases, identifying 3,531 bacterial phylotypes from 115 fecal samples. Genomic analysis revealed significant alterations of organism lineages in both the CDI and CDN groups, which were accompanied by marked decreases in microbial diversity and species richness driven primarily by a paucity of phylotypes within the Firmicutes phylum. Normally abundant gut commensal organisms, including the Ruminococcaceae and Lachnospiraceae families and butyrate-producing C2 to C4 anaerobic fermenters, were significantly depleted in the CDI and CDN groups. These data demonstrate associations between the depletion of Ruminococcaceae, Lachnospiraceae, and butyrogenic bacteria in the gut microbiota and nosocomial diarrhea, including C. difficile infection. Mechanistic studies focusing on the functional roles of these organisms in diarrheal diseases and resistance against C. difficile colonization are warranted.
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452
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Microbial brokers of insect-plant interactions revisited. J Chem Ecol 2013; 39:952-61. [PMID: 23793897 DOI: 10.1007/s10886-013-0308-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/01/2013] [Accepted: 06/06/2013] [Indexed: 12/22/2022]
Abstract
Recent advances in sequencing methods have transformed the field of microbial ecology, making it possible to determine the composition and functional capabilities of uncultured microorganisms. These technologies have been instrumental in the recognition that resident microorganisms can have profound effects on the phenotype and fitness of their animal hosts by modulating the animal signaling networks that regulate growth, development, behavior, etc. Against this backdrop, this review assesses the impact of microorganisms on insect-plant interactions, in the context of the hypothesis that microorganisms are biochemical brokers of plant utilization by insects. There is now overwhelming evidence for a microbial role in insect utilization of certain plant diets with an extremely low or unbalanced nutrient content. Specifically, microorganisms enable insect utilization of plant sap by synthesizing essential amino acids. They also can broker insect utilization of plant products of extremely high lignocellulose content, by enzymatic breakdown of complex plant polysaccharides, nitrogen fixation, and sterol synthesis. However, the experimental evidence for microbial-mediated detoxification of plant allelochemicals is limited. The significance of microorganisms as brokers of plant utilization by insects is predicted to vary, possibly widely, as a result of potentially complex interactions between the composition of the microbiota and the diet and insect developmental age or genotype. For every insect species feeding on plant material, the role of resident microbiota as biochemical brokers of plant utilization is a testable hypothesis.
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453
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Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 2013; 499:219-22. [PMID: 23748443 PMCID: PMC3710538 DOI: 10.1038/nature12212] [Citation(s) in RCA: 359] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 04/22/2013] [Indexed: 12/16/2022]
Abstract
The mammalian gut ecosystem has significant influence on host physiology1–4, but the mechanisms that sustain this complex environment in the face of different stresses remain obscure. Perturbations to this ecosystem, such as through antibiotic treatment or diet, are currently interpreted at the level of bacterial phylogeny5–7. Less is known about the contributions of the abundant population of phage to this ecological network. Here, we explore the phageome as a potential genetic reservoir for bacterial adaptation by sequencing murine fecal phage populations following antibiotic perturbation. We show that antibiotic treatment leads to the enrichment of phage-encoded genes that confer resistance via disparate mechanisms to the administered drug as well as genes that confer resistance to antibiotics unrelated to the administered drug, and we demonstrate experimentally that phage from treated mice afford aerobically cultured naïve microbiota increased resistance. Systems-wide analyses uncover post-treatment phage-encoded processes related to host colonization and growth adaptation, indicating that the phageome broadly enriches for functionally beneficial genes under stress-related conditions. We also show that antibiotic treatment expands the interactions between phage and bacterial species, leading to a more highly connected phage-bacterial network for gene exchange. Our work implicates the phageome in the emergence of multidrug resistance and indicates that the adaptive capacity of the phageome may represent a community-based mechanism for protecting the gut microflora, preserving its functional robustness during antibiotic stress.
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454
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Marcobal A, Kashyap PC, Nelson TA, Aronov PA, Donia MS, Spormann A, Fischbach MA, Sonnenburg JL. A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice. ISME JOURNAL 2013; 7:1933-43. [PMID: 23739052 DOI: 10.1038/ismej.2013.89] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/21/2013] [Accepted: 04/24/2013] [Indexed: 12/21/2022]
Abstract
Defining the functional status of host-associated microbial ecosystems has proven challenging owing to the vast number of predicted genes within the microbiome and relatively poor understanding of community dynamics and community-host interaction. Metabolomic approaches, in which a large number of small molecule metabolites can be defined in a biological sample, offer a promising avenue to 'fingerprint' microbiota functional status. Here, we examined the effects of the human gut microbiota on the fecal and urinary metabolome of a humanized (HUM) mouse using an optimized ultra performance liquid chromatography-mass spectrometry-based method. Differences between HUM and conventional mouse urine and fecal metabolomic profiles support host-specific aspects of the microbiota's metabolomic contribution, consistent with distinct microbial compositions. Comparison of microbiota composition and metabolome of mice humanized with different human donors revealed that the vast majority of metabolomic features observed in donor samples are produced in the corresponding HUM mice, and individual-specific features suggest 'personalized' aspects of functionality can be reconstituted in mice. Feeding the mice a defined, custom diet resulted in modification of the metabolite signatures, illustrating that host diet provides an avenue for altering gut microbiota functionality, which in turn can be monitored via metabolomics. Using a defined model microbiota consisting of one or two species, we show that simplified communities can drive major changes in the host metabolomic profile. Our results demonstrate that metabolomics constitutes a powerful avenue for functional characterization of the intestinal microbiota and its interaction with the host.
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Affiliation(s)
- A Marcobal
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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455
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Choi JJ, Eum SY, Rampersaud E, Daunert S, Abreu MT, Toborek M. Exercise attenuates PCB-induced changes in the mouse gut microbiome. ENVIRONMENTAL HEALTH PERSPECTIVES 2013; 121:725-30. [PMID: 23632211 PMCID: PMC3672930 DOI: 10.1289/ehp.1306534] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/23/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND The gut microbiome, a dynamic bacterial community that interacts with the host, is integral to human health because it regulates energy metabolism and immune functions. The gut microbiome may also play a role in risks from environmental toxicants. OBJECTIVES We investigated the effects of polychlorinated biphenyls (PCBs) and exercise on the composition and structure of the gut microbiome in mice. METHODS After mice exercised voluntarily for 5 weeks, they were treated by oral gavage with a mixture of environmentally relevant PCB congeners (PCB153, PCB138, and PCB180; total PCB dose, 150 µmol/kg) for 2 days. We then assessed the microbiome by determination of 16S rRNA using microarray analysis. RESULTS Oral exposure to PCBs significantly altered the abundance of the gut microbiome in mice primarily by decreasing the levels of Proteobacteria. The activity level of the mice correlated with a substantial shift in abundance, biodiversity, and composition of the microbiome. Importantly, exercise attenuated PCB-induced changes in the gut microbiome. CONCLUSIONS Our results show that oral exposure to PCBs can induce substantial changes in the gut microbiome, which may then influence their systemic toxicity. These changes can be attenuated by behavioral factors, such as voluntary exercise.
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Affiliation(s)
- Jeong June Choi
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, Florida 33136, USA
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456
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Divergent mechanisms of interaction of Helicobacter pylori and Campylobacter jejuni with mucus and mucins. Infect Immun 2013; 81:2838-50. [PMID: 23716616 DOI: 10.1128/iai.00415-13] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Helicobacter pylori and Campylobacter jejuni colonize the stomach and intestinal mucus, respectively. Using a combination of mucus-secreting cells, purified mucins, and a novel mucin microarray platform, we examined the interactions of these two organisms with mucus and mucins. H. pylori and C. jejuni bound to distinctly different mucins. C. jejuni displayed a striking tropism for chicken gastrointestinal mucins compared to mucins from other animals and preferentially bound mucins from specific avian intestinal sites (in order of descending preference: the large intestine, proximal small intestine, and cecum). H. pylori bound to a number of animal mucins, including porcine stomach mucin, but with less avidity than that of C. jejuni for chicken mucin. The strengths of interaction of various wild-type strains of H. pylori with different animal mucins were comparable, even though they did not all express the same adhesins. The production of mucus by HT29-MTX-E12 cells promoted higher levels of infection by C. jejuni and H. pylori than those for the non-mucus-producing parental cell lines. Both C. jejuni and H. pylori bound to HT29-MTX-E12 mucus, and while both organisms bound to glycosylated epitopes in the glycolipid fraction of the mucus, only C. jejuni bound to purified mucin. This study highlights the role of mucus in promoting bacterial infection and emphasizes the potential for even closely related bacteria to interact with mucus in different ways to establish successful infections.
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457
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Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C. Computational meta'omics for microbial community studies. Mol Syst Biol 2013; 9:666. [PMID: 23670539 PMCID: PMC4039370 DOI: 10.1038/msb.2013.22] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/03/2013] [Indexed: 12/16/2022] Open
Abstract
Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges.
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Affiliation(s)
- Nicola Segata
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- Present address: Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Daniela Boernigen
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy L Tickle
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xochitl C Morgan
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy S Garrett
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Curtis Huttenhower
- Biostatistics Department, Harvard School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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458
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Meyer F, Trimble WL, Chang EB, Handley KM. Functional predictions from inference and observation in sequence-based inflammatory bowel disease research. Genome Biol 2013. [PMID: 23013527 PMCID: PMC3491387 DOI: 10.1186/gb-2012-13-9-169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Meta-omics approaches such as metagenomics, metatranscriptomics and metaproteogenomics have the potential to improve our understanding of how the human microbiome affects digestive health and disease. See research article http://www.genomebiology.com/2012/13/9/R79
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Affiliation(s)
- Folker Meyer
- Institute for Genomics and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA.
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459
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Meyer F, Trimble WL, Chang EB, Handley KM. Functional predictions from inference and observation in sequence-based inflammatory bowel disease research. Genome Biol 2013; 13:169. [PMID: 23013527 DOI: 10.1186/gb4042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Meta-omics approaches such as metagenomics, metatranscriptomics and metaproteogenomics have the potential to improve our understanding of how the human microbiome affects digestive health and disease.
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Affiliation(s)
- Folker Meyer
- Institute for Genomics and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA.
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460
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Reigstad CS, Kashyap PC. Beyond phylotyping: understanding the impact of gut microbiota on host biology. Neurogastroenterol Motil 2013; 25:358-72. [PMID: 23594242 PMCID: PMC4524550 DOI: 10.1111/nmo.12134] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 03/19/2013] [Indexed: 12/14/2022]
Abstract
BACKGROUND Microbial constituents of the gut microbiome interact with each other and the host to alter the luminal environment and impact development, motility, and homeostasis of the gut. Powerful methods are becoming available to investigate connections between the gut microbiome and human health. While high-throughput sequencing of 16S rRNA genes can be used to identify and enumerate microbes in the gut, advances in several techniques (e.g., metagenomics, metatranscriptomics, metabolomics, and metaproteomics) are providing a clearer view as to the specific activities of the microbiota in the context of functional host-microbe interactions. Testing emergent hypotheses regarding microbial effects on host biology, which arise from analyses of 'Big Data' generated from massive parallel high-throughput sequencing technology and spectroscopic techniques, to guide translational research is an important goal for the future. Insights regarding the fundamental operating principles of the gut microbiota should lay the foundation for rational manipulation of the microbiota to promote human health. PURPOSE In this review, we provide an overview of current research on the gut microbiome emphasizing current state-of-the-art technologies, approaches, and directions for improvement of our understanding of the impact of the gut microbiota with specific focus on gastrointestinal motility disorders.
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Affiliation(s)
- Christopher S. Reigstad
- Department of Gastroenterology and Hepatology; Enteric Neuroscience Program; Mayo Clinic; Rochester; MN; USA
| | - Purna C. Kashyap
- Department of Gastroenterology and Hepatology; Enteric Neuroscience Program; Mayo Clinic; Rochester; MN; USA
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461
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Abstract
Easy access to next generation sequencing has enabled the rapid analysis of complex microbial populations. To take full advantage of these technologies, animal models enabling the manipulation of human microbiomes and the study of the impact of such perturbations on the host are needed. To this aim we are developing experimentally tractable and clinically relevant pig models of the human adult and infant gastro-intestinal tract. The intestine of germ-free piglets was populated with human adult or infant fecal microbial populations, and the piglets were maintained on solid or milk diet, respectively. Amplicons of 16S rRNA V6 region were deep-sequenced to monitor to what extent the transplanted human microbiomes changed in the pig. Within 24 h of transfer of human fecal microbiome to pigs, bacterial microbiomes rich in Proteobacteria emerged. These populations evolved toward a more diverse composition rich in Bacteroidetes and Firmicutes. In the experiment where infant microbiome was used, the phylogenetic composition of the transplanted bacterial population converged toward that of the human inoculum. A majority of sequences belonged to a relatively small number of operational taxonomic units, whereas at the other end of the abundance spectrum, a large number of rare and transient OTUs were detected. Analysis of fecal and colonic microbiomes originating from the same animal indicate that feces closely replicate the colonic microbiome. We conclude that the pig intestine can be colonized with human fecal microbiomes to generate a realistic model of the human GI tract.
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462
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Maurice CF, Turnbaugh PJ. Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales. FEMS Microbiol Rev 2013; 37:830-48. [PMID: 23550823 DOI: 10.1111/1574-6976.12022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/18/2013] [Accepted: 03/19/2013] [Indexed: 12/15/2022] Open
Abstract
Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small-to-moderate-sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single-cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities.
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Affiliation(s)
- Corinne F Maurice
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, 02138, USA
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463
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Functional screening of a metagenomic library reveals operons responsible for enhanced intestinal colonization by gut commensal microbes. Appl Environ Microbiol 2013; 79:3829-38. [PMID: 23584783 DOI: 10.1128/aem.00581-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Evidence suggests that gut microbes colonize the mammalian intestine through propagation as an adhesive microbial community. A bacterial artificial chromosome (BAC) library of murine bowel microbiota DNA in the surrogate host Escherichia coli DH10B was screened for enhanced adherence capability. Two out of 5,472 DH10B clones, 10G6 and 25G1, exhibited enhanced capabilities to adhere to inanimate surfaces in functional screens. DNA segments inserted into the 10G6 and 25G1 clones were 52 and 41 kb and included 47 and 41 protein-coding open reading frames (ORFs), respectively. DNA sequence alignments, tetranucleotide frequency, and codon usage analysis strongly suggest that these two DNA fragments are derived from species belonging to the genus Bacteroides. Consistent with this finding, a large portion of the predicted gene products were highly homologous to those of Bacteroides spp. Transposon mutagenesis and subsequent experiments that involved heterologous expression identified two operons associated with enhanced adherence. E. coli strains transformed with the 10a or 25b operon adhered to the surface of intestinal epithelium and colonized the mouse intestine more vigorously than did the control strain. This study has revealed the genetic determinants of unknown commensals (probably resembling Bacteroides species) that enhance the ability of the bacteria to colonize the murine bowel.
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464
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de Vos WM. Fame and future of faecal transplantations--developing next-generation therapies with synthetic microbiomes. Microb Biotechnol 2013. [PMID: 23574632 DOI: 10.1111/1751-7915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
While practised for over thousand years, there is presently a renaissance in the interest of using of faecal transplantations to modify the intestinal microbiota of patients. This clinical practice consists of delivering large amounts of bowel microbes in various forms into the intestinal tract of the recipient that usually has been cleared previously. The major reason for the popularity of faecal transplantations is their effectiveness in treating a variety of diseases. Hence, there is a need to develop this procedure to the next level. While there are various developments to select, standardize and store the donor microbiota, it is more challenging to understand the intestinal microbial communities and develop ways to deliver these via robust biotechnological processes. The various approaches that have been followed to do so are discussed in this contribution that is also addressing the concept of the minimal microbiome as well as the production of the synthetic communities that can be instrumental in new therapeutic avenues to modify the intestinal microbiota.
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Affiliation(s)
- Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.
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465
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Cahenzli J, Balmer ML, McCoy KD. Microbial-immune cross-talk and regulation of the immune system. Immunology 2013; 138:12-22. [PMID: 22804726 DOI: 10.1111/j.1365-2567.2012.03624.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/14/2012] [Accepted: 07/10/2012] [Indexed: 12/13/2022] Open
Abstract
We are all born germ-free. Following birth we enter into a lifelong relationship with microbes residing on our body's surfaces. The lower intestine is home to the highest microbial density in our body, which is also the highest microbial density known on Earth (up to 10(12) /g of luminal contents). With our indigenous microbial cells outnumbering our human cells by an order of magnitude our body is more microbial than human. Numerous immune adaptations confine these microbes within the mucosa, enabling most of us to live in peaceful homeostasis with our intestinal symbionts. Intestinal epithelial cells not only form a physical barrier between the bacteria-laden lumen and the rest of the body but also function as multi-tasking immune cells that sense the prevailing microbial (apical) and immune (basolateral) milieus, instruct the underlying immune cells, and adapt functionally. In the constant effort to ensure intestinal homeostasis, the immune system becomes educated to respond appropriately and in turn immune status can shape the microbial consortia. Here we review how the dynamic immune-microbial dialogue underlies maturation and regulation of the immune system and discuss recent findings on the impact of diet on both microbial ecology and immune function.
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Affiliation(s)
- Julia Cahenzli
- Department of Clinical Research, Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
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466
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Lawley TD, Walker AW. Intestinal colonization resistance. Immunology 2013; 138:1-11. [PMID: 23240815 DOI: 10.1111/j.1365-2567.2012.03616.x] [Citation(s) in RCA: 368] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/12/2012] [Accepted: 06/13/2012] [Indexed: 12/16/2022] Open
Abstract
Dense, complex microbial communities, collectively termed the microbiota, occupy a diverse array of niches along the length of the mammalian intestinal tract. During health and in the absence of antibiotic exposure the microbiota can effectively inhibit colonization and overgrowth by invading microbes such as pathogens. This phenomenon is called 'colonization resistance' and is associated with a stable and diverse microbiota in tandem with a controlled lack of inflammation, and involves specific interactions between the mucosal immune system and the microbiota. Here we overview the microbial ecology of the healthy mammalian intestinal tract and highlight the microbe-microbe and microbe-host interactions that promote colonization resistance. Emerging themes highlight immunological (T helper type 17/regulatory T-cell balance), microbiota (diverse and abundant) and metabolic (short-chain fatty acid) signatures of intestinal health and colonization resistance. Intestinal pathogens use specific virulence factors or exploit antibiotic use to subvert colonization resistance for their own benefit by triggering inflammation to disrupt the harmony of the intestinal ecosystem. A holistic view that incorporates immunological and microbiological facets of the intestinal ecosystem should facilitate the development of immunomodulatory and microbe-modulatory therapies that promote intestinal homeostasis and colonization resistance.
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Affiliation(s)
- Trevor D Lawley
- Bacterial Pathogenesis Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK.
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467
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Hisamatsu T, Kanai T, Mikami Y, Yoneno K, Matsuoka K, Hibi T. Immune aspects of the pathogenesis of inflammatory bowel disease. Pharmacol Ther 2013; 137:283-97. [PMID: 23103332 DOI: 10.1016/j.pharmthera.2012.10.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 10/11/2012] [Indexed: 12/11/2022]
Abstract
Although the precise etiologies of inflammatory bowel disease (IBD) (ulcerative colitis and Crohn's disease) remain obscure, several reports have indicated that dysfunction of the mucosal immune system plays an important role in its pathogenesis. Recent progress with genome-wide association studies has identified many IBD susceptibility genes. In individuals with genetic risk, abnormal interactions between the host immune system and gut flora, and dysregulation of cellular responses such as autophagy and ER stress, induce an abnormal host immune response in the gut resulting in intestinal inflammation. Research progress animal models in IBD, and in human IBD, has identified several key molecules in IBD pathogenesis such as TNFα and adhesion molecules, and molecular targeting therapies based on these molecules have been developed. Here, we review immunological aspects in IBD pathogenesis and the development of immunoregulatory therapy.
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Affiliation(s)
- Tadakazu Hisamatsu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
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468
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Nelson AM, Elftman MD, Pinto AK, Baldridge M, Hooper P, Kuczynski J, Petrosino JF, Young VB, Wobus CE. Murine norovirus infection does not cause major disruptions in the murine intestinal microbiota. MICROBIOME 2013; 1:7. [PMID: 24451302 PMCID: PMC4177540 DOI: 10.1186/2049-2618-1-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 01/09/2013] [Indexed: 06/03/2023]
Abstract
BACKGROUND Murine norovirus (MNV) is the most common gastrointestinal pathogen of research mice and can alter research outcomes in biomedical mouse models of inflammatory bowel disease (IBD). Despite indications that an altered microbiota is a risk factor for IBD, the response of the murine intestinal microbiota to MNV infection has not been examined. Microbiota disruption caused by MNV infection could introduce the confounding effects observed in research experiments. Therefore, this study investigated the effects of MNV infection on the intestinal microbiota of wild-type mice. RESULTS The composition of the intestinal microbiota was assessed over time in both outbred Swiss Webster and inbred C57BL/6 mice following MNV infection. Mice were infected with both persistent and non-persistent MNV strains and tissue-associated or fecal-associated microbiota was analyzed by 16S rRNA-encoding gene pyrosequencing. Analysis of intestinal bacterial communities in infected mice at the phylum and family level showed no major differences to uninfected controls, both in tissue-associated samples and feces, and also over time following infection, demonstrating that the intestinal microbiota of wild-type mice is highly resistant to disruption following MNV infection. CONCLUSIONS This is the first study to describe the intestinal microbiota following MNV infection and demonstrates that acute or persistent MNV infection is not associated with major disruptions of microbial communities in Swiss Webster and C57BL/6 mice.
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Affiliation(s)
- Adam M Nelson
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael D Elftman
- Department of Microbiology and Immunology, University of Michigan Medical School, 5622 Medical Sciences Bldg. II, 1150 West Medical Center Drive, 48109-5620, Ann Arbor, USA
| | - Amelia K Pinto
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Megan Baldridge
- Department of Pathology and Immunology, Washington University School of Medicine, MO, St Louis, USA
| | - Patrick Hooper
- Department of Microbiology and Immunology, University of Michigan Medical School, 5622 Medical Sciences Bldg. II, 1150 West Medical Center Drive, 48109-5620, Ann Arbor, USA
| | - Justin Kuczynski
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research Department of Molecular Virology and Microbiology, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, 5622 Medical Sciences Bldg. II, 1150 West Medical Center Drive, 48109-5620, Ann Arbor, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, 5622 Medical Sciences Bldg. II, 1150 West Medical Center Drive, 48109-5620, Ann Arbor, USA
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469
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Singh S, Eldin C, Kowalczewska M, Raoult D. Axenic culture of fastidious and intracellular bacteria. Trends Microbiol 2013. [DOI: 10.1016/j.tim.2012.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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470
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Hildebrand F, Nguyen TLA, Brinkman B, Yunta RG, Cauwe B, Vandenabeele P, Liston A, Raes J. Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol 2013; 14:R4. [PMID: 23347395 PMCID: PMC4053703 DOI: 10.1186/gb-2013-14-1-r4] [Citation(s) in RCA: 335] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 01/08/2013] [Accepted: 01/24/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Murine models are a crucial component of gut microbiome research. Unfortunately, a multitude of genetic backgrounds and experimental setups, together with inter-individual variation, complicates cross-study comparisons and a global understanding of the mouse microbiota landscape. Here, we investigate the variability of the healthy mouse microbiota of five common lab mouse strains using 16S rDNA pyrosequencing. RESULTS We find initial evidence for richness-driven, strain-independent murine enterotypes that show a striking resemblance to those in human, and which associate with calprotectin levels, a marker for intestinal inflammation. After enterotype stratification, we find that genetic, caging and inter-individual variation contribute on average 19%, 31.7% and 45.5%, respectively, to the variance in the murine gut microbiota composition. Genetic distance correlates positively to microbiota distance, so that genetically similar strains have more similar microbiota than genetically distant ones. Specific mouse strains are enriched for specific operational taxonomic units and taxonomic groups, while the 'cage effect' can occur across mouse strain boundaries and is mainly driven by Helicobacter infections. CONCLUSIONS The detection of enterotypes suggests a common ecological cause, possibly low-grade inflammation that might drive differences among gut microbiota composition in mammals. Furthermore, the observed environmental and genetic effects have important consequences for experimental design in mouse microbiome research.
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Affiliation(s)
- Falk Hildebrand
- Department of Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Thi Loan Anh Nguyen
- Department of Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Autoimmune Genetics Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium
- Katholieke Universiteit Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Brigitta Brinkman
- Department for Molecular Biomedical Research, VIB, Technologiepark Zwijnaarde 927, 9052 Ghent, Belgium
- Department for Molecular Biomedical Research, GhentUniversity, Technologiepark Zwijnaarde 927, 9052 Ghent, Belgium
| | - Roberto Garcia Yunta
- Department of Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Benedicte Cauwe
- Autoimmune Genetics Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium
- Katholieke Universiteit Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Peter Vandenabeele
- Department for Molecular Biomedical Research, VIB, Technologiepark Zwijnaarde 927, 9052 Ghent, Belgium
- Department for Molecular Biomedical Research, GhentUniversity, Technologiepark Zwijnaarde 927, 9052 Ghent, Belgium
| | - Adrian Liston
- Autoimmune Genetics Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium
- Katholieke Universiteit Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Jeroen Raes
- Department of Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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471
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Relman DA. Restoration of the gut microbial habitat as a disease therapy. Nat Biotechnol 2013; 31:35-7. [DOI: 10.1038/nbt.2475] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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472
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Hemarajata P, Versalovic J. Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Therap Adv Gastroenterol 2013; 6:39-51. [PMID: 23320049 PMCID: PMC3539293 DOI: 10.1177/1756283x12459294] [Citation(s) in RCA: 552] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Recent explorations of the human gut microbiota suggest that perturbations of microbial communities may increase predisposition to different disease phenotypes. Dietary nutrients may be converted into metabolites by intestinal microbes that serve as biologically active molecules affecting regulatory functions in the host. Probiotics may restore the composition of the gut microbiome and introduce beneficial functions to gut microbial communities, resulting in amelioration or prevention of gut inflammation and other intestinal or systemic disease phenotypes. This review describes how diet and intestinal luminal conversion by gut microbes play a role in shaping the structure and function of intestinal microbial communities. Proposed mechanisms of probiosis include alterations of composition and function of the human gut microbiome, and corresponding effects on immunity and neurobiology.
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Affiliation(s)
- Peera Hemarajata
- Department of Molecular Virology and Microbiology and Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine and Texas Children’s Hospital, 1102 Bates Street, Feigin Center 830, Houston, TX 77030, USA
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473
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Xu X, Xu P, Ma C, Tang J, Zhang X. Gut microbiota, host health, and polysaccharides. Biotechnol Adv 2012; 31:318-37. [PMID: 23280014 DOI: 10.1016/j.biotechadv.2012.12.009] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 12/20/2012] [Accepted: 12/21/2012] [Indexed: 02/07/2023]
Abstract
The intestinal microbiota is a complicated ecosystem that influences many aspects of host physiology (i.e. diet, disease development, drug metabolism, and regulation of the immune system). It also exhibits spatial patterning and temporal dynamics. In this review, the effects of internal and external (environmental) factors on intestinal microbiota are discussed. We describe the roles of the gut microbiota in maintaining intestinal and immune system homeostasis and the relationship between gut microbiota and diseases. In particular, the contributions of polysaccharides, as the most abundant diet components in intestinal microbiota and host health are presented. Finally, perspectives for research avenues relating to gut microbiota are also discussed.
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Affiliation(s)
- Xiaofei Xu
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
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474
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Lawley B, Tannock GW. Nucleic acid-based methods to assess the composition and function of the bowel microbiota. Gastroenterol Clin North Am 2012; 41:855-68. [PMID: 23101691 DOI: 10.1016/j.gtc.2012.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This article describes nucleic acid-based methods to assess the composition and function of the bowel microbiota. The methods range from the relatively simple (polymerase chain reaction) to the technically sophisticated (metatranscriptomics). Not all are accessible to the majority of laboratories, but a core of validated (used in more than 1 study) tools is readily available to most researchers. Reliance on a single methodology per human study is not recommended. Generally, a study could commence with a screening of samples to determine whether it will be worthwhile expending further time and money on an in-depth analysis.
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Affiliation(s)
- Blair Lawley
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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475
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Abstract
Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Understanding the factors that underlie changes in the composition and function of the gut microbiota will aid in the design of therapies that target it. This goal is formidable. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time - especially during disease and early development. Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.
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476
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Lagier JC, Million M, Hugon P, Armougom F, Raoult D. Human gut microbiota: repertoire and variations. Front Cell Infect Microbiol 2012; 2:136. [PMID: 23130351 PMCID: PMC3487222 DOI: 10.3389/fcimb.2012.00136] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/16/2012] [Indexed: 12/28/2022] Open
Abstract
The composition of human gut microbiota and their relationship with the host and, consequently, with human health and disease, presents several challenges to microbiologists. Originally dominated by culture-dependent methods for exploring this ecosystem, the advent of molecular tools has revolutionized our ability to investigate these relationships. However, many biases that have led to contradictory results have been identified. Microbial culturomics, a recent concept based on a use of several culture conditions with identification by MALDI-TOF followed by the genome sequencing of the new species cultured had allowed a complementarity with metagenomics. Culturomics allowed to isolate 31 new bacterial species, the largest human virus, the largest bacteria, and the largest Archaea from human. Moreover, some members of this ecosystem, such as Eukaryotes, giant viruses, Archaea, and Planctomycetes, have been neglected by the majority of studies. In addition, numerous factors, such as age, geographic provenance, dietary habits, antibiotics, or probiotics, can influence the composition of the microbiota. Finally, in addition to the countless biases associated with the study techniques, a considerable limitation to the interpretation of studies of human gut microbiota is associated with funding sources and transparency disclosures. In the future, studies independent of food industry funding and using complementary methods from a broad range of both culture-based and molecular tools will increase our knowledge of the repertoire of this complex ecosystem and host-microbiota mutualism.
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Affiliation(s)
- Jean-Christophe Lagier
- URMITE, UM63, CNRS 7278, L'Institut de Recherche pour le Développement 198, INSERM 1095, Aix-Marseille Université Marseille, France
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477
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Bibiloni R. Rodent models to study the relationships between mammals and their bacterial inhabitants. Gut Microbes 2012; 3:536-43. [PMID: 22918304 PMCID: PMC3495791 DOI: 10.4161/gmic.21905] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Laboratory rodents have been instrumental in helping researchers to unravel the complex interactions that mammals have with their microbial commensals. Progress in defining these interactions has also been possible thanks to the development of culture-independent methods for describing the microbiota associated to body surfaces. Understanding the mechanisms that govern this relationship at the molecular, cellular, and ecological levels is central to both health and disease. The present review of rodent models commonly used to investigate microbial-host "conversations" is focused on those complex bacterial communities residing in the lower gut. Although many types of pathology have been studied using gnotobiotic animals, only the models relevant to commensal bacteria will be described.
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478
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Haange SB, Oberbach A, Schlichting N, Hugenholtz F, Smidt H, von Bergen M, Till H, Seifert J. Metaproteome Analysis and Molecular Genetics of Rat Intestinal Microbiota Reveals Section and Localization Resolved Species Distribution and Enzymatic Functionalities. J Proteome Res 2012; 11:5406-17. [DOI: 10.1021/pr3006364] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sven-Bastiaan Haange
- Department of Pediatric Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Proteomics, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Andreas Oberbach
- Department of Pediatric Surgery, University Hospital of Leipzig, Leipzig, Germany
- Integrated Research and Treatment
Center (IFB) Adiposity Diseases, Leipzig University Medical Centre, Leipzig, Germany
| | - Nadine Schlichting
- Department of Pediatric Surgery, University Hospital of Leipzig, Leipzig, Germany
- Integrated Research and Treatment
Center (IFB) Adiposity Diseases, Leipzig University Medical Centre, Leipzig, Germany
| | - Floor Hugenholtz
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Martin von Bergen
- Department of Proteomics, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
- Department of Metabolomics, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Holger Till
- Department of Pediatric Surgery, University Hospital of Leipzig, Leipzig, Germany
- Integrated Research and Treatment
Center (IFB) Adiposity Diseases, Leipzig University Medical Centre, Leipzig, Germany
| | - Jana Seifert
- Department of Proteomics, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
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479
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Vamanu E, Pelinescu D, Avram I, Niță S, Vamanu A. Study of PROBAC product influence on infant microbiota in a single-chamber colonic fermentation model GIS1. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0558-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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480
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Abstract
The human gut is home to vast numbers of bacteria (gut microbiota), which outnumber the cells in the human body by an order of magnitude. The gut microbiota has coevolved with humans and can be considered an organ of similar size as the liver, containing more than 1,000 cell types (bacterial species) and encoding 150-fold more genes than are present in the human genome. Accordingly, the gut microbiota may have profound effects on various host responses, either directly or indirectly, by modifying food components or endogenously produced molecules into signaling molecules. Recent findings suggest that an altered gut microbial composition is associated with inflammatory bowel disease and obesity, indicating that the gut microbiota should be considered a contributing factor in several common diseases.
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Affiliation(s)
- Fredrik Bäckhed
- Sahlgrenska Center for Cardiovascular and Metabolic Research/Wallenberg Laboratory and Department of Molecular and Clinical Medicine, University of Gothenburg, S-413 45 Gothenburg, Sweden.
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481
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Clavel T, Charrier C, Haller D. Streptococcus danieliae sp. nov., a novel bacterium isolated from the caecum of a mouse. Arch Microbiol 2012; 195:43-9. [DOI: 10.1007/s00203-012-0846-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/22/2012] [Accepted: 09/25/2012] [Indexed: 12/21/2022]
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482
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Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, Trape JF, Koonin EV, La Scola B, Raoult D. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012; 18:1185-93. [PMID: 23033984 DOI: 10.1111/1469-0691.12023] [Citation(s) in RCA: 749] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Comprehensive determination of the microbial composition of the gut microbiota and the relationships with health and disease are major challenges in the 21st century. Metagenomic analysis of the human gut microbiota detects mostly uncultured bacteria. We studied stools from two lean Africans and one obese European, using 212 different culture conditions (microbial culturomics), and tested the colonies by using mass spectrometry and 16S rRNA amplification and sequencing. In parallel, we analysed the same three samples by pyrosequencing 16S rRNA amplicons targeting the V6 region. The 32 500 colonies obtained by culturomics have yielded 340 species of bacteria from seven phyla and 117 genera, including two species from rare phyla (Deinococcus-Thermus and Synergistetes, five fungi, and a giant virus (Senegalvirus). The microbiome identified by culturomics included 174 species never described previously in the human gut, including 31 new species and genera for which the genomes were sequenced, generating c. 10 000 new unknown genes (ORFans), which will help in future molecular studies. Among these, the new species Microvirga massiliensis has the largest bacterial genome so far obtained from a human, and Senegalvirus is the largest virus reported in the human gut. Concurrent metagenomic analysis of the same samples produced 698 phylotypes, including 282 known species, 51 of which overlapped with the microbiome identified by culturomics. Thus, culturomics complements metagenomics by overcoming the depth bias inherent in metagenomic approaches.
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Affiliation(s)
- J-C Lagier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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483
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Gordon JI, Dewey KG, Mills DA, Medzhitov RM. The human gut microbiota and undernutrition. Sci Transl Med 2012; 4:137ps12. [PMID: 22674549 DOI: 10.1126/scitranslmed.3004347] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Childhood malnutrition is a global health problem that cannot be attributed to food insecurity alone. The gut microbiota may contribute to this devastating health disorder. In this Perspective, we call for the application of tools and concepts emerging from studies of the human gut microbiota to better understand the nutritional needs of infants and children and the role of the microbiota in the pathogenesis and treatment of undernutrition. This effort will require elucidation of the interrelationships between breast milk composition and the development of the microbiota and immune system in the context of the maternal-infant dyad.
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Affiliation(s)
- Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
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484
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Lebeis SL, Rott M, Dangl JL, Schulze-Lefert P. Culturing a plant microbiome community at the cross-Rhodes. THE NEW PHYTOLOGIST 2012; 196:341-344. [PMID: 22978611 DOI: 10.1111/j.1469-8137.2012.04336.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Sarah L Lebeis
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Matthias Rott
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
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485
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Hickey RJ, Zhou X, Pierson JD, Ravel J, Forney LJ. Understanding vaginal microbiome complexity from an ecological perspective. Transl Res 2012; 160:267-82. [PMID: 22683415 PMCID: PMC3444549 DOI: 10.1016/j.trsl.2012.02.008] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/13/2012] [Accepted: 02/14/2012] [Indexed: 12/31/2022]
Abstract
The various microbiota normally associated with the human body have an important influence on human development, physiology, immunity, and nutrition. This is certainly true for the vagina wherein communities of mutualistic bacteria constitute the first line of defense for the host by excluding invasive, nonindigenous organisms that may cause disease. In recent years much has been learned about the bacterial species composition of these communities and how they differ between individuals of different ages and ethnicities. A deeper understanding of their origins and the interrelationships of constituent species is needed to understand how and why they change over time or in response to changes in the host environment. Moreover, there are few unifying theories to explain the ecological dynamics of vaginal ecosystems as they respond to disturbances caused by menses and human activities such as intercourse, douching, and other habits and practices. This fundamental knowledge is needed to diagnose and assess risk to disease. Here we summarize what is known about the species composition, structure, and function of bacterial communities in the human vagina and the applicability of ecological models of community structure and function to understanding the dynamics of this and other ecosystems that comprise the human microbiome.
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Affiliation(s)
- Roxana J Hickey
- Institute for Bioinformatics and Evolutionary Studies-IBEST, University of Idaho, Moscow, ID, USA
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486
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Abstract
The microbial communities that colonize different regions of the human gut influence many aspects of health. In the healthy state, they contribute nutrients and energy to the host via the fermentation of nondigestible dietary components in the large intestine, and a balance is maintained with the host's metabolism and immune system. Negative consequences, however, can include acting as sources of inflammation and infection, involvement in gastrointestinal diseases, and possible contributions to diabetes mellitus and obesity. Major progress has been made in defining some of the dominant members of the microbial community in the healthy large intestine, and in identifying their roles in gut metabolism. Furthermore, it has become clear that diet can have a major influence on microbial community composition both in the short and long term, which should open up new possibilities for health manipulation via diet. Achieving better definition of those dominant commensal bacteria, community profiles and system characteristics that produce stable gut communities beneficial to health is important. The extent of interindividual variation in microbiota composition within the population has also become apparent, and probably influences individual responses to drug administration and dietary manipulation. This Review considers the complex interplay between the gut microbiota, diet and health.
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487
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Chen L, Teasdale MT, Kaczmarczyk MM, Freund GG, Miller MJ. Development of a Lactobacillus specific T-RFLP method to determine lactobacilli diversity in complex samples. J Microbiol Methods 2012; 91:262-8. [PMID: 22981747 DOI: 10.1016/j.mimet.2012.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 08/06/2012] [Accepted: 08/07/2012] [Indexed: 11/29/2022]
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) analysis has been widely used for studying microbial communities. However, most T-RFLP assays use 16S rDNA as the target and are unable to accurately characterize a microbial subpopulation. In this study, we developed a novel T-RFLP protocol based on Lactobacillus hsp60 to rapidly characterize and compare lactobacilli composition. The theoretical terminal restriction fragment (TRF) profiles were calculated from 769 Lactobacillus hsp60 sequences from online databases. In silico digestion with restriction endonucleases AluI and TacI on hsp60 amplicons generated 83 distinct TRF patterns, of which, 70 were species specific. To validate the assay, five previously sequenced lactobacilli were cultured independently, mixed at known concentrations and subjected to analysis by T-RFLP. All five strains generated the predicted TRFs and a qualitative consistent relationship was revealed. We performed the T-RFLP protocol on fecal samples from mice fed 6 different diets (n=4). Principal component analysis and agglomerative hierarchical clustering revealed that the lactobacilli community was strongly connected to dietary supplementation. Our study demonstrates the potential for using Lactobacillus specific T-RFLP to characterize lactobacilli communities in complex samples.
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Affiliation(s)
- Long Chen
- Department of Food Science & Human Nutrition, University of Illinois, Urbana, IL 61801, United States
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488
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Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature 2012. [PMID: 22972295 DOI: 10.1038/nature11550.diversity] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Understanding the factors that underlie changes in the composition and function of the gut microbiota will aid in the design of therapies that target it. This goal is formidable. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time - especially during disease and early development. Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.
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Affiliation(s)
- Catherine A Lozupone
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
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489
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Dantas G, Sommer MOA. Context matters - the complex interplay between resistome genotypes and resistance phenotypes. Curr Opin Microbiol 2012; 15:577-82. [PMID: 22954750 DOI: 10.1016/j.mib.2012.07.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 07/11/2012] [Accepted: 07/13/2012] [Indexed: 12/13/2022]
Abstract
Application of metagenomic functional selections to study antibiotic resistance genes is revealing a highly diverse and complex network of genetic exchange between bacterial pathogens and environmental reservoirs, which likely contributes significantly to increasing resistance levels in pathogens. In some cases, clinically relevant resistance genes have been acquired from organisms where their native function is not antibiotic resistance, and which may not even confer a resistance phenotype in their native context. In this review, we attempt to distinguish the resistance phenotype from the resistome genotype, and we highlight examples of genes and their hosts where this distinction becomes important in order to understand the relevance of environmental niches that contribute most to clinical problems associated with antibiotic resistance.
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Affiliation(s)
- Gautam Dantas
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
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490
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Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol 2012; 10:607-17. [PMID: 22864264 DOI: 10.1038/nrmicro2853] [Citation(s) in RCA: 302] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere. Here, we briefly review the incipient rise of a phage biology renaissance, which has been catalysed by advances in next-generation sequencing. We explore how work characterizing phage diversity and lifestyles in the human gut is changing our view of ourselves as supra-organisms. Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes.
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491
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Harley ITW, Karp CL. Obesity and the gut microbiome: Striving for causality. Mol Metab 2012; 1:21-31. [PMID: 24024115 DOI: 10.1016/j.molmet.2012.07.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 12/15/2022] Open
Abstract
The gut microbiome has been proposed to play a causal role in obesity. Here, we review the historical context for this hypothesis, highlight recent key findings, and critically discuss issues central to further progress in the field, including the central epistemological problem for the field: how to define causality in the relationship between microbiota and obesity phenotypes. Definition of such will be critical for the field to move forward.
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Affiliation(s)
- Isaac T W Harley
- Division of Molecular Immunology, Cincinnati Children's Hospital Research Foundation, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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492
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Discussion from the 24th Marabou Symposium: Nutrition and the human microbiome. Nutr Rev 2012; 70 Suppl 1:S57-86. [DOI: 10.1111/j.1753-4887.2012.00501.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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493
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Shade A, Hogan CS, Klimowicz AK, Linske M, McManus PS, Handelsman J. Culturing captures members of the soil rare biosphere. Environ Microbiol 2012; 14:2247-52. [PMID: 22788977 PMCID: PMC3466410 DOI: 10.1111/j.1462-2920.2012.02817.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The ecological significance of rare microorganisms within microbial communities remains an important, unanswered question. Microorganisms of extremely low abundance (the 'rare biosphere') are believed to be largely inaccessible and unknown. To understand the structure of complex environmental microbial communities, including the representation of rare and prevalent community members, we coupled traditional cultivation with pyrosequencing. We compared cultured and uncultured bacterial members of the same agricultural soil, including eight locations within one apple orchard and four time points. Our analysis revealed that soil bacteria captured by culturing were in very low abundance or absent in the culture-independent community, demonstrating unexpected accessibility of the rare biosphere by culturing.
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Affiliation(s)
- Ashley Shade
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityKline Biology Tower, 219 Prospect St, New Haven, CT 06520, USA
| | - Clifford S Hogan
- Department of Plant Pathology, University of Wisconsin-Madison1630 Linden Drive, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-MadisonMicrobial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
| | - Amy K Klimowicz
- Department of Plant Pathology, University of Wisconsin-Madison1630 Linden Drive, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-MadisonMicrobial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
| | - Matthew Linske
- Department of Plant Pathology, University of Wisconsin-Madison1630 Linden Drive, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-MadisonMicrobial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
| | - Patricia S McManus
- Department of Plant Pathology, University of Wisconsin-Madison1630 Linden Drive, Madison, WI 53706, USA
| | - Jo Handelsman
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityKline Biology Tower, 219 Prospect St, New Haven, CT 06520, USA
- *For correspondence. E-mail ; Tel. (+1) 203 432 9119; Fax (+1) 203 432 6161
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494
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Abstract
With the rapid advances in sequencing technologies in recent years, the human genome is now considered incomplete without the complementing microbiome, which outnumbers human genes by a factor of one hundred. The human microbiome, and more specifically the gut microbiome, has received considerable attention and research efforts over the past decade. Many studies have identified and quantified "who is there?," while others have determined some of their functional capacity, or "what are they doing?" In a recent study, we identified novel salt-tolerance loci from the human gut microbiome using combined functional metagenomic and bioinformatics based approaches. Herein, we discuss the identified loci, their role in salt-tolerance and their importance in the context of the gut environment. We also consider the utility and power of functional metagenomics for mining such environments for novel genes and proteins, as well as the implications and possible applications for future research.
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Affiliation(s)
- Eamonn P. Culligan
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland,Department of Microbiology; University College Cork; Cork, Ireland
| | - Julian R. Marchesi
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland,Cardiff School of Biosciences; Cardiff University; Cardiff, UK,Correspondence to: Julian R. Marchesi, and Colin Hill, and Roy D. Sleator,
| | - Colin Hill
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland,Department of Microbiology; University College Cork; Cork, Ireland,Correspondence to: Julian R. Marchesi, and Colin Hill, and Roy D. Sleator,
| | - Roy D. Sleator
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland,Correspondence to: Julian R. Marchesi, and Colin Hill, and Roy D. Sleator,
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495
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Chen W, Liu F, Ling Z, Tong X, Xiang C. Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One 2012; 7:e39743. [PMID: 22761885 PMCID: PMC3386193 DOI: 10.1371/journal.pone.0039743] [Citation(s) in RCA: 668] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 05/25/2012] [Indexed: 12/12/2022] Open
Abstract
Recent reports have suggested the involvement of gut microbiota in the progression of colorectal cancer (CRC). We utilized pyrosequencing based analysis of 16S rRNA genes to determine the overall structure of microbiota in patients with colorectal cancer and healthy controls; we investigated microbiota of the intestinal lumen, the cancerous tissue and matched noncancerous normal tissue. Moreover, we investigated the mucosa-adherent microbial composition using rectal swab samples because the structure of the tissue-adherent bacterial community is potentially altered following bowel cleansing. Our findings indicated that the microbial structure of the intestinal lumen and cancerous tissue differed significantly. Phylotypes that enhance energy harvest from diets or perform metabolic exchange with the host were more abundant in the lumen. There were more abundant Firmicutes and less abundant Bacteroidetes and Proteobacteria in lumen. The overall microbial structures of cancerous tissue and noncancerous tissue were similar; howerer the tumor microbiota exhibited lower diversity. The structures of the intestinal lumen microbiota and mucosa-adherent microbiota were different in CRC patients compared to matched microbiota in healthy individuals. Lactobacillales was enriched in cancerous tissue, whereas Faecalibacterium was reduced. In the mucosa-adherent microbiota, Bifidobacterium, Faecalibacterium, and Blautia were reduced in CRC patients, whereas Fusobacterium, Porphyromonas, Peptostreptococcus, and Mogibacterium were enriched. In the lumen, predominant phylotypes related to metabolic disorders or metabolic exchange with the host, Erysipelotrichaceae, Prevotellaceae, and Coriobacteriaceae were increased in cancer patients. Coupled with previous reports, these results suggest that the intestinal microbiota is associated with CRC risk and that intestinal lumen microflora potentially influence CRC risk via cometabolism or metabolic exchange with the host. However, mucosa-associated microbiota potentially affects CRC risk primarily through direct interaction with the host.
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Affiliation(s)
- Weiguang Chen
- State Key Laboratory for Infectious Diseases Diagnostics and Treatment, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Fanlong Liu
- Department of Anus and Intestine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zongxin Ling
- State Key Laboratory for Infectious Diseases Diagnostics and Treatment, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaojuan Tong
- State Key Laboratory for Infectious Diseases Diagnostics and Treatment, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Charlie Xiang
- State Key Laboratory for Infectious Diseases Diagnostics and Treatment, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- * E-mail:
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496
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Ji YS, Kim HN, Park HJ, Lee JE, Yeo SY, Yang JS, Park SY, Yoon HS, Cho GS, Franz CMAP, Bomba A, Shin HK, Holzapfel WH. Modulation of the murine microbiome with a concomitant anti-obesity effect by Lactobacillus rhamnosus GG and Lactobacillus sakei NR28. Benef Microbes 2012; 3:13-22. [PMID: 22348905 DOI: 10.3920/bm2011.0046] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The microbiota of the gastrointestinal tract (GIT) constitutes the major part of the total human microbiome and is considered to be an important regulator of human health and host metabolism. Numerous investigations in recent years have focused on the connection between the human microbiota and metabolic diseases such as obesity, type II diabetes and atherosclerosis. Yet, little is known about the impact of probiotic consumption on the GIT microbial population and the potential effect on chronic diseases. In this study, the modulation of the microbial community in the murine small intestine resulting from probiotic feeding was investigated and was found to be associated with an anti-obesity effect. Changes in the microbiota of the mouse faeces and small intestine were monitored using quantitative real-time PCR and by following the mRNA expression levels of various obesity-related biomarkers following probiotic feeding in a mouse model. Lactobacillus rhamnosus GG and Lactobacillus sakei NR28 (a putative probiotic strain isolated from kimchi) were administered at a daily level of approximately 1×10(8) viable bacteria per mouse (C57BL/6J mice) for up to three weeks. Feeding these strains resulted in a significant reduction of epididymal fat mass, as well as obesity-related biomarkers like acetyl-CoA carboxylase, fatty acid synthase, and stearoyl-CoA desaturase-1 in the liver. The total number and ratio of the microbial groups, i.e. Firmicutes, Bacteroidetes, Clostridium cluster I and XIVab, and Lactobacillus spp. were modulated in the small intestine, and the Firmicutes:Bacteroidetes ratio was decreased. In contrast, no noticeable effect of probiotic feeding could be detected on the faecal microbiota, neither quantitatively, nor with regard to the bacterial groups (Firmicutes, Bacteroidetes, Clostridium cluster I and XIVab, and Lactobacillus spp.) studied.
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Affiliation(s)
- Y S Ji
- School of Life Science, Handong Global University, Pohang, Gyungbuk, Republic of Korea
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497
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Abstract
The large numbers of microorganisms that inhabit mammalian body surfaces have a highly coevolved relationship with the immune system. Although many of these microbes carry out functions that are critical for host physiology, they nevertheless pose the threat of breach with ensuing pathologies. The mammalian immune system plays an essential role in maintaining homeostasis with resident microbial communities, thus ensuring that the mutualistic nature of the host-microbial relationship is maintained. At the same time, resident bacteria profoundly shape mammalian immunity. Here, we review advances in our understanding of the interactions between resident microbes and the immune system and the implications of these findings for human health.
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Affiliation(s)
- Lora V. Hooper
- The Howard Hughes Medical Institute and Department of Immunology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390
| | - Dan R. Littman
- Howard Hughes Medical Institute and Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Andrew J. Macpherson
- Mucosal Immunology Lab, Maurice Müller Laboratories, University Clinic for Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
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498
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499
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Pfeiffer N, Desmarchelier C, Blaut M, Daniel H, Haller D, Clavel T. Acetatifactor muris gen. nov., sp. nov., a novel bacterium isolated from the intestine of an obese mouse. Arch Microbiol 2012; 194:901-7. [PMID: 22659832 DOI: 10.1007/s00203-012-0822-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 05/10/2012] [Accepted: 05/11/2012] [Indexed: 11/30/2022]
Abstract
We used selective agar media for culturing bacteria from the caecum of mice fed a high calorie diet. In addition to the isolation of Enterobacteriaceae growing on a medium containing cholesterol and bile salts, we focused on the characterization of strain CT-m2(T), which, based on 16S rDNA analysis, did not appear to correspond to any currently described organisms. The isolate belongs to the Clostridium cluster XIV and is most closely related to members of the Lachnospiraceae, including the genera Anaerostipes, Blautia, Butyrivibrio, Clostridium, Coprococcus, Eubacterium, Robinsoniella, Roseburia, Ruminococcus and Syntrophococcus (≤90 % similarity). Strain CT-m2(T) is a non-motile Gram-positive rod that does not form spores and has a G + C content of DNA of 48.5 %. Cells grow under strictly anoxic conditions (100 % N₂) and produce acetate and butyrate after growth in reduced WCA broth. In contrast to related species, the new bacterium does not metabolize glucose and is positive for phenylalanine arylamidase, and its major cellular fatty acid is C₁₄:₀. Based on phylogenetic and phenotypic studies, the isolate merits recognition as a member of a novel genus and species, for which the name Acetatifactor muris is proposed. The type strain is CT-m2(T) (= DSM 23669(T) = ATCC BAA-2170(T)).
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Affiliation(s)
- Nora Pfeiffer
- Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
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500
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Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R. Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res 2012; 22:1974-84. [PMID: 22665442 PMCID: PMC3460192 DOI: 10.1101/gr.138198.112] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We lack a deep understanding of genetic and metabolic attributes specializing in microbial consortia for initial and subsequent waves of colonization of our body habitats. Here we show that phylogenetically interspersed bacteria in Clostridium cluster XIVa, an abundant group of bacteria in the adult human gut also known as the Clostridium coccoides or Eubacterium rectale group, contains species that have evolved distribution patterns consistent with either early successional or stable gut communities. The species that specialize to the infant gut are more likely to associate with systemic infections and can reach high abundances in individuals with Inflammatory Bowel Disease (IBD), indicating that a subset of the microbiota that have adapted to pioneer/opportunistic lifestyles may do well in both early development and with disease. We identified genes likely selected during adaptation to pioneer/opportunistic lifestyles as those for which early succession association and not phylogenetic relationships explain genomic abundance. These genes reveal potential mechanisms by which opportunistic gut bacteria tolerate osmotic and oxidative stress and potentially important aspects of their metabolism. These genes may not only be biomarkers of properties associated with adaptation to early succession and disturbance, but also leads for developing therapies aimed at promoting reestablishment of stable gut communities following physiologic or pathologic disturbances.
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Affiliation(s)
- Catherine Lozupone
- Department of Chemistry & Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
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