Current Status and Future Promise of the Human Microbiome

The human-associated microbiota is diverse, varies between individuals and body sites, and is important in human health. Microbes in human body play an essential role in immunity, health, and disease. The human microbiome has been studies using the advances of next-generation sequencing and its metagenomic applications. This has allowed investigation of the microbial composition in the human body, and identification of the functional genes expressed by this microbial community. The gut microbes have been found to be the most diverse and constitute the densest cell number in the human microbiota; thus, it has been studied more than other sites. Early results have indicated that the imbalances in gut microbiota are related to numerous disorders, such as inflammatory bowel disease, colorectal cancer, diabetes, and atopy. Clinical therapy involving modulating of the microbiota, such as fecal transplantation, has been applied, and its effects investigated in some diseases. Human microbiome studies form part of human genome projects, and understanding gleaned from studies increase the possibility of various applications including personalized medicine.

[1]  R. Knight,et al.  Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns , 2010, Proceedings of the National Academy of Sciences.

[2]  Fiona Powrie,et al.  Microbiota, Disease, and Back to Health: A Metastable Journey , 2012, Science Translational Medicine.

[3]  E. Purdom,et al.  Diversity of the Human Intestinal Microbial Flora , 2005, Science.

[4]  C. Neut,et al.  Self inflicted rectal ulcer: hearing is believing , 2003, Gut.

[5]  B. Roe,et al.  A core gut microbiome in obese and lean twins , 2008, Nature.

[6]  R. Lorenz,et al.  Gut Microbiota and Obesity , 2012, Current Obesity Reports.

[7]  Ruth E Ley,et al.  Obesity and the human microbiome , 2010, Current opinion in gastroenterology.

[8]  D. Relman,et al.  Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation , 2010, Proceedings of the National Academy of Sciences.

[9]  V. Mathan,et al.  Colonic dysfunction in acute diarrhoea: the role of luminal short chain fatty acids. , 1993, Gut.

[10]  F. Bäckhed,et al.  Host-Bacterial Mutualism in the Human Intestine , 2005, Science.

[11]  T. Borody,et al.  Fecal microbiota transplantation: a new standard treatment option for Clostridium difficile infection , 2013, Expert review of anti-infective therapy.

[12]  Matthew W. Johnson,et al.  The Bacteriology of Pouchitis: A Molecular Phylogenetic Analysis Using 16S rRNA Gene Cloning and Sequencing , 2010, Annals of surgery.

[13]  Roderic Guigo,et al.  A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library , 2008, Nucleic acids research.

[14]  B. Leggett,et al.  The Effects from DNA Extraction Methods on the Evaluation of Microbial Diversity Associated with Human Colonic Tissue , 2011, Microbial Ecology.

[15]  Henrik Svanström,et al.  Antibiotic use and inflammatory bowel diseases in childhood , 2010, Gut.

[16]  S. Wilhelm,et al.  Role of Lactobacillus in the Prevention of Antibiotic‐Associated Diarrhea: A Meta‐analysis , 2010, Pharmacotherapy.

[17]  L. Morelli,et al.  Mode of delivery affects the bacterial community in the newborn gut. , 2010, Early human development.

[18]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[19]  Ateequr Rehman,et al.  Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. , 2011, Gastroenterology.

[20]  H. Harmsen,et al.  Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. , 2000, Journal of pediatric gastroenterology and nutrition.

[21]  D. Gevers,et al.  The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. , 2012, The Journal of allergy and clinical immunology.

[22]  R Balfour Sartor,et al.  Microbial influences in inflammatory bowel diseases. , 2008, Gastroenterology.

[23]  C. Manichanh,et al.  Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach , 2005, Gut.

[24]  William A. Walters,et al.  Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. , 2012, Cell host & microbe.

[25]  M. Bulsara,et al.  Updated Meta-analysis of Probiotics for Preventing Necrotizing Enterocolitis in Preterm Neonates , 2010, Pediatrics.

[26]  P. Chain,et al.  Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. , 2012, Current opinion in biotechnology.

[27]  Miguel Pignatelli,et al.  Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota , 2011, PloS one.

[28]  P. Turnbaugh,et al.  An Invitation to the Marriage of Metagenomics and Metabolomics , 2008, Cell.

[29]  R. Knight,et al.  Bacterial Community Variation in Human Body Habitats Across Space and Time , 2009, Science.

[30]  J. Clemente,et al.  Human gut microbiome viewed across age and geography , 2012, Nature.

[31]  William A. Walters,et al.  Experimental and analytical tools for studying the human microbiome , 2011, Nature Reviews Genetics.

[32]  Cecilia Jernberg,et al.  Long-term impacts of antibiotic exposure on the human intestinal microbiota. , 2010, Microbiology.

[33]  J. Doré,et al.  Low counts of Faecalibacterium prausnitzii in colitis microbiota , 2009, Inflammatory bowel diseases.

[34]  G. Macfarlane,et al.  Nondigestible Oligosaccharides Enhance Bacterial Colonization Resistance against Clostridium difficile In Vitro , 2003, Applied and Environmental Microbiology.

[35]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[36]  H. Dupont,et al.  The intestinal microbiota and chronic disorders of the gut , 2011, Nature Reviews Gastroenterology &Hepatology.

[37]  Pierre Ernst,et al.  Increased risk of childhood asthma from antibiotic use in early life. , 2007, Chest.

[38]  Maria Karlsson,et al.  Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. , 2010, Cell host & microbe.

[39]  J. Bakken,et al.  Treating Clostridium difficile infection with fecal microbiota transplantation. , 2011, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

[40]  George Casella,et al.  Fecal Microbiota in Premature Infants Prior to Necrotizing Enterocolitis , 2011, PloS one.

[41]  R. Knight,et al.  Microbiota restoration: natural and supplemented recovery of human microbial communities , 2011, Nature Reviews Microbiology.

[42]  J. Gordon,et al.  How host-microbial interactions shape the nutrient environment of the mammalian intestine. , 2002, Annual review of nutrition.

[43]  P. Turnbaugh,et al.  Microbial ecology: Human gut microbes associated with obesity , 2006, Nature.

[44]  Adam Godzik,et al.  Shotgun metaproteomics of the human distal gut microbiota , 2008, The ISME Journal.

[45]  L. T. Angenent,et al.  Succession of microbial consortia in the developing infant gut microbiome , 2010, Proceedings of the National Academy of Sciences.

[46]  M. Hartmann,et al.  Early life antibiotic‐driven changes in microbiota enhance susceptibility to allergic asthma , 2012, EMBO reports.

[47]  P. Bork,et al.  Enterotypes of the human gut microbiome , 2011, Nature.

[48]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[49]  B. Finlay,et al.  Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. , 2007, Cell host & microbe.

[50]  J. Sung,et al.  Comparison of the Gut Microbiotas of Healthy Adult Twins Living in South Korea and the United States , 2011, Applied and Environmental Microbiology.

[51]  Katherine H. Huang,et al.  A framework for human microbiome research , 2012, Nature.

[52]  Jeroen Raes,et al.  A metagenomic insight into our gut's microbiome , 2012, Gut.

[53]  U. Göbel,et al.  Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. , 1997, FEMS microbiology reviews.

[54]  V. Tremaroli,et al.  Functional interactions between the gut microbiota and host metabolism , 2012, Nature.

[55]  T. Borody,et al.  Fecal microbiota transplantation and emerging applications , 2012, Nature Reviews Gastroenterology &Hepatology.

[56]  J. Handelsman,et al.  Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. , 1998, Chemistry & biology.

[57]  R. Hunt,et al.  Fecal Microbiota Transplantation for Clostridium difficile Infection: Systematic Review and Meta-Analysis , 2013, The American Journal of Gastroenterology.

[58]  M. Kachrimanidou,et al.  Clostridium difficile Infection: A Comprehensive Review , 2011, Critical reviews in microbiology.