gastrointestinal microbiome


Summary: All of the microbial organisms that naturally exist within the GASTROINTESTINAL TRACT.

Top Publications

  1. Marschall H, Backhed F. Could gut microbiota protect against sclerosing cholangitis?. Hepatology. 2016;63:26-7 pubmed publisher
  2. Piccolo B, Mercer K, Bhattacharyya S, Bowlin A, Saraf M, Pack L, et al. Early Postnatal Diets Affect the Bioregional Small Intestine Microbiome and Ileal Metabolome in Neonatal Pigs. J Nutr. 2017;147:1499-1509 pubmed publisher
    ..Regional effects may be important factors when considering gut tissue metabolism and development in the postnatal period. ..
  3. Martinez K, Leone V, Chang E. Microbial metabolites in health and disease: Navigating the unknown in search of function. J Biol Chem. 2017;292:8553-8559 pubmed publisher
    ..This review discusses the functional characterization of the microbiome, highlighting the advances in identifying bioactive microbial metabolites that have been directly linked to gastrointestinal and peripheral diseases. ..
  4. Lambert M, Thybo C, Lykkeboe S, Rasmussen L, Fretté X, Christensen L, et al. Combined bioavailable isoflavones and probiotics improve bone status and estrogen metabolism in postmenopausal osteopenic women: a randomized controlled trial. Am J Clin Nutr. 2017;106:909-920 pubmed publisher
    ..RCE intake combined with supplementation (calcium, magnesium, and calcitriol) was more effective than supplementation alone. This trial was registered at as NCT02174666. ..
  5. Varotto Boccazzi I, Ottoboni M, Martin E, Comandatore F, Vallone L, Spranghers T, et al. A survey of the mycobiota associated with larvae of the black soldier fly (Hermetia illucens) reared for feed production. PLoS ONE. 2017;12:e0182533 pubmed publisher
    ..Finally, the killer phenotype of isolated yeasts was tested, showing the inhibitory activity of just one species against sensitive strains, out of the 11 tested species. ..
  6. Hoffmann D, PALUMBO F, Ravel J, Roghmann M, Rowthorn V, von Rosenvinge E. Improving regulation of microbiota transplants. Science. 2017;358:1390-1391 pubmed publisher
  7. Rubinelli P, Kim S, Park S, Roto S, Ricke S. Sodium bisulfate and a sodium bisulfate/tannin mixture decreases pH when added to an in vitro incubated poultry cecal or fecal contents while reducing Salmonella Typhimurium marker strain survival and altering the microbiome. J Environ Sci Health B. 2017;52:607-615 pubmed publisher
    ..The antimicrobial action of feed-grade SBS may represent a potential pre-harvest control measure for Salmonella in poultry production. ..
  8. Ohtani N. [The role of SASP in tumor microenvironment.]. Clin Calcium. 2017;27:835-843 pubmed publisher
  9. Ost K, Round J. A Few Good Commensals: Gut Microbes Use IFN-? to Fight Salmonella. Immunity. 2017;46:977-979 pubmed publisher
    ..In a recent issue of Cell Host & Microbe, Thiemann et al. (2017) report the identification of specific gut bacteria that protect from Salmonella infection by priming host IFN-? responses. ..

More Information


  1. Bradford B, Tetlow L, Mabbott N. Prion disease pathogenesis in the absence of the commensal microbiota. J Gen Virol. 2017;98:1943-1952 pubmed publisher
  2. Wood M, Yu E, Mehta S. The Human Microbiome in the Fight Against Tuberculosis. Am J Trop Med Hyg. 2017;96:1274-1284 pubmed publisher
    ..Current evidence suggests that the gut and lung microbiome are associated with TB infection and disease. However, as studies are limited, etiological and longitudinal research is needed to determine clinical relevance. ..
  3. Talarico S, Santos F, Brandt K, Martinez M, Taddei C. Anaerobic bacteria in the intestinal microbiota of Brazilian children. Clinics (Sao Paulo). 2017;72:154-160 pubmed publisher
    ..coli. The presence of important anaerobic genera was observed in Brazilian infants living at a low socioeconomic level, a result that has already been well established for infants living in developed countries. ..
  4. Zhang S, Cao X, Huang H. Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research. Front Cell Infect Microbiol. 2017;7:51 pubmed publisher
    ..On the basis of this spatial model, this article also summarizes various sampling and processing strategies prior to and after DNA extraction and recommends guidelines for practical application in future research. ..
  5. Claesson M, Clooney A, O Toole P. A clinician's guide to microbiome analysis. Nat Rev Gastroenterol Hepatol. 2017;14:585-595 pubmed publisher
    ..We also offer perspectives on future applications of microbiome research, which we hope convey the promise of this technology for clinical applications. ..
  6. Masuoka H, Shimada K, Kiyosue Yasuda T, Kiyosue M, Oishi Y, Kimura S, et al. Transition of the intestinal microbiota of cats with age. PLoS ONE. 2017;12:e0181739 pubmed publisher
    ..We also identified lactobacilli and bifidobacteria at the species level based on 16S rRNA gene sequences and found that the species composition of Lactobacillus also changed with age. ..
  7. Needell J, Ir D, Robertson C, Kroehl M, Frank D, Zipris D. Maternal treatment with short-chain fatty acids modulates the intestinal microbiota and immunity and ameliorates type 1 diabetes in the offspring. PLoS ONE. 2017;12:e0183786 pubmed publisher
    ..These data demonstrate that short-chain fatty acids can reshape the intestinal microbiota and prevent virus-induced islet autoimmunity and may therefore represent a useful therapeutic strategy for disease prevention. ..
  8. Villa C, Ward W, Comelli E. Gut microbiota-bone axis. Crit Rev Food Sci Nutr. 2017;57:1664-1672 pubmed publisher
    ..Although auspicious, many questions regarding the GM-bone axis require consideration of potential mechanisms; sex-specific efficacy; effective dose of probiotics; and timing and duration of treatment. ..
  9. Zhang Q, Xiao X, Li M, Yu M, Ping F, Zheng J, et al. Vildagliptin increases butyrate-producing bacteria in the gut of diabetic rats. PLoS ONE. 2017;12:e0184735 pubmed publisher
    ..Moreover, Lachnospira abundance was significantly negatively correlated with fasting blood glucose levels. In conclusion, vildagliptin treatment could benefit the communities of the gut microbiota...
  10. Lokhov P, Lisitsa A, Archakov A. [Metabolomic blood test: purpose, implementation and interpretation of data]. Biomed Khim. 2017;63:232-240 pubmed publisher
  11. Zhang B, Lv Z, Li H, Guo S, Liu D, Guo Y. Dietary l-arginine inhibits intestinal Clostridium perfringens colonisation and attenuates intestinal mucosal injury in broiler chickens. Br J Nutr. 2017;118:321-332 pubmed publisher
    ..In conclusion, l-arginine supplementation could inhibit CP overgrowth and alleviate intestinal mucosal injury by modulating innate immune responses, enhancing barrier function and producing NO. ..
  12. Yang C, Liang C, Lin C, Hsiao C, Peng C, Lin H, et al. Impact of Enterobius vermicularis infection and mebendazole treatment on intestinal microbiota and host immune response. PLoS Negl Trop Dis. 2017;11:e0005963 pubmed publisher
    ..The interaction of Enterobius vermicularis infection in particular with gut microbiota and induced immune responses has never been thoroughly examined...
  13. Samuelson D, Shellito J, Maffei V, Tague E, Campagna S, Blanchard E, et al. Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae. PLoS Pathog. 2017;13:e1006426 pubmed publisher
    ..Collectively, these results suggest that alterations in the intestinal immune response as a consequence of alcohol-induced dysbiosis contribute to increased host susceptibility to Klebsiella pneumonia...
  14. Borton M, Sabag Daigle A, Wu J, Solden L, O Banion B, Daly R, et al. Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome. Microbiome. 2017;5:47 pubmed publisher
    ..These findings may prove informative with regard to prophylactic or therapeutic strategies to prevent disruption of microbial communities, or promote their restoration. ..
  15. Husted A, Trauelsen M, Rudenko O, Hjorth S, Schwartz T. GPCR-Mediated Signaling of Metabolites. Cell Metab. 2017;25:777-796 pubmed publisher
    ..The concept of key metabolites as ligands for specific GPCRs has broadened our understanding of metabolic signaling significantly and provides a number of novel potential drug targets. ..
  16. Lang M, Berry D, Passecker K, Mesteri I, Bhuju S, Ebner F, et al. HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis. Cancer Res. 2017;77:2424-2438 pubmed publisher
    ..Furthermore, our results offer a preclinical proof of concept for HuR inhibition as an effective means of FAP chemoprevention, with caution advised in the setting of IBD. Cancer Res; 77(9); 2424-38. ©2017 AACR. ..
  17. Liang C, Tseng H, Chen H, Wang W, Chiu C, Chang J, et al. Diversity and enterotype in gut bacterial community of adults in Taiwan. BMC Genomics. 2017;18:932 pubmed publisher
    ..We used NGS technology to characterize the microbiota and constructed a predictive model. The most significant finding was that Enterobacteriaceae, the predominant subtype, could be a new subtype of enterotypes in the Asian population. ..
  18. Scholz R, Langmann T. Gut flora connects obesity with pathological angiogenesis in the eye. EMBO Mol Med. 2016;8:1361-1363 pubmed publisher
  19. Guo Z, Jia X, Zhao B, Zeng S, Xiao J, Zheng B. C-type starches and their derivatives: structure and function. Ann N Y Acad Sci. 2017;1398:47-61 pubmed publisher
    ..We outline recent advances, potential applications, and limitations of C-type starches in industry, aiming to provide a theoretical basis for further research and to broaden the prospects of its applications. ..
  20. Nagashima K, Sawa S, Nitta T, Tsutsumi M, Okamura T, Penninger J, et al. Identification of subepithelial mesenchymal cells that induce IgA and diversify gut microbiota. Nat Immunol. 2017;18:675-682 pubmed publisher
    ..Thus, the subepithelial mesenchymal cells that serve as M cell inducers have a fundamental role in the maintenance of intestinal immune homeostasis. ..
  21. Schokker D, Jansman A, Veninga G, de Bruin N, Vastenhouw S, de Bree F, et al. Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development. BMC Genomics. 2017;18:241 pubmed publisher
  22. Cani P. Gut microbiota - at the intersection of everything?. Nat Rev Gastroenterol Hepatol. 2017;14:321-322 pubmed publisher
    ..However, is it reality? Or is the truth hidden in the shadow of several thousand publications a year with inflated expectations in almost any disease? ..
  23. Reed S, Neuman H, Glahn R, Koren O, Tako E. Characterizing the gut (Gallus gallus) microbiota following the consumption of an iron biofortified Rwandan cream seeded carioca (Phaseolus Vulgaris L.) bean-based diet. PLoS ONE. 2017;12:e0182431 pubmed publisher
    ..These results may be used to further improve the efficacy and safety of future biofortification efforts in eradicating global Fe deficiency. ..
  24. Maffei V, Kim S, Blanchard E, Luo M, Jazwinski S, Taylor C, et al. Biological Aging and the Human Gut Microbiota. J Gerontol A Biol Sci Med Sci. 2017;72:1474-1482 pubmed publisher
    ..We conclude that increasing biological age in community-dwelling adults is associated with gastrointestinal dysbiosis...
  25. Schickel J, Glauzy S, Ng Y, Chamberlain N, Massad C, Isnardi I, et al. Self-reactive VH4-34-expressing IgG B cells recognize commensal bacteria. J Exp Med. 2017;214:1991-2003 pubmed publisher
    ..Hence, B cells expressing germline-encoded self-reactive VH4-34 antibodies may represent an innate-like B cell population specialized in the containment of commensal bacteria when gut barriers are breached. ..
  26. Lukes J, Stensvold C, Jirků Pomajbíková K, Wegener Parfrey L. Are Human Intestinal Eukaryotes Beneficial or Commensals?. PLoS Pathog. 2015;11:e1005039 pubmed publisher
  27. Labus J, Hollister E, Jacobs J, Kirbach K, Oezguen N, Gupta A, et al. Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome. Microbiome. 2017;5:49 pubmed publisher
    ..They provide preliminary evidence for the involvement of specific microbes and their predicted metabolites in these correlations. ..
  28. Perez Muñoz M, Arrieta M, Ramer Tait A, Walter J. A critical assessment of the "sterile womb" and "in utero colonization" hypotheses: implications for research on the pioneer infant microbiome. Microbiome. 2017;5:48 pubmed publisher
  29. Coil D, Ettinger C, Eisen J. Gut Check: The evolution of an educational board game. PLoS Biol. 2017;15:e2001984 pubmed publisher
    ..Here we discuss the development of the game, some of the logistics of game development in this context, and offer suggestions for others thinking of similar projects. ..
  30. Xie C, Jiang C, Shi J, Gao X, Sun D, Sun L, et al. An Intestinal Farnesoid X Receptor-Ceramide Signaling Axis Modulates Hepatic Gluconeogenesis in Mice. Diabetes. 2017;66:613-626 pubmed publisher
    ..These results reveal a mechanism by which the dietary supplement CAPE and intestinal FXR regulates hepatic gluconeogenesis and suggest that inhibiting intestinal FXR is a strategy for treating hyperglycemia. ..
  31. Cui C, Li Y, Gao H, Zhang H, Han J, Zhang D, et al. Modulation of the gut microbiota by the mixture of fish oil and krill oil in high-fat diet-induced obesity mice. PLoS ONE. 2017;12:e0186216 pubmed publisher
    ..We proposed that further researches are needed to elucidate the causal relationship between obesity alleviation and gut microbiota modulation...
  32. Nakata K, Sugi Y, Narabayashi H, Kobayakawa T, Nakanishi Y, Tsuda M, et al. Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through the small GTPase ARF4. J Biol Chem. 2017;292:15426-15433 pubmed publisher
  33. Chung K. Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment?. J Allergy Clin Immunol. 2017;139:1071-1081 pubmed publisher
    ..A better understanding of the regulation of both the lung and gut microbiota to derive appropriate targets for prevention or treatment of asthma is needed. ..
  34. Richards E, Pepine C, Raizada M, Kim S. The Gut, Its Microbiome, and Hypertension. Curr Hypertens Rep. 2017;19:36 pubmed publisher
    ..Objective evidence and an understanding of mechanisms could have a major impact for new antihypertensive therapies and/or improved applications of current ones. ..
  35. Koppel N, Maini Rekdal V, Balskus E. Chemical transformation of xenobiotics by the human gut microbiota. Science. 2017;356: pubmed publisher
    ..Ultimately, a molecular understanding of gut microbial xenobiotic metabolism will guide personalized medicine and nutrition, inform toxicology risk assessment, and improve drug discovery and development. ..
  36. Stefanaki C, Peppa M, Mastorakos G, Chrousos G. Examining the gut bacteriome, virome, and mycobiome in glucose metabolism disorders: Are we on the right track?. Metabolism. 2017;73:52-66 pubmed publisher
    ..In this article, we attempt to reveal the interplay between human gut microbiota physiology, and hyperglycemic states, synthesizing, and interpreting findings from human studies. ..
  37. Sartor R. Gut microbiota: Optimal sampling of the intestinal microbiota for research. Nat Rev Gastroenterol Hepatol. 2015;12:253-4 pubmed publisher
  38. Krautkramer K, Dhillon R, Denu J, Carey H. Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin. Transl Res. 2017;189:30-50 pubmed publisher
    ..We also highlight key physiologic and disease settings where microbial metabolite-host chromatin interactions have been established and/or may be pertinent. ..
  39. Vizcarra J, Wilson Perez H, Espay A. The power in numbers: gut microbiota in Parkinson's disease. Mov Disord. 2015;30:296-8 pubmed publisher
  40. Liu R, Hong J, Xu X, Feng Q, Zhang D, Gu Y, et al. Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention. Nat Med. 2017;23:859-868 pubmed publisher
    ..Our findings identify previously unknown links between intestinal microbiota alterations, circulating amino acids and obesity, suggesting that it may be possible to intervene in obesity by targeting the gut microbiota. ..
  41. Han K, Bose S, Wang J, Lim S, Chin Y, Kim Y, et al. In vivo therapeutic effect of combination treatment with metformin and Scutellaria baicalensis on maintaining bile acid homeostasis. PLoS ONE. 2017;12:e0182467 pubmed publisher
    ..Further study is needed to find the specific strains of bacteria which contribute to FXR-related cholesterol and bile acid regulations. ..
  42. Ferrer M, Raczkowska B, Martínez Martínez M, Barbas C, Rojo D. Phenotyping of gut microbiota: Focus on capillary electrophoresis. Electrophoresis. 2017;38:2275-2286 pubmed publisher
  43. Williams A, Krych L, Fauzan Ahmad H, Nejsum P, Skovgaard K, Nielsen D, et al. A polyphenol-enriched diet and Ascaris suum infection modulate mucosal immune responses and gut microbiota composition in pigs. PLoS ONE. 2017;12:e0186546 pubmed publisher
    ..suum establishment, it significantly modulates the subsequent host response to helminth infection. Our results suggest an influence of diet on immune function which may potentially be exploited to enhance immunity to helminths...
  44. Irwin S, Fisher P, Graham E, Malek A, Robidoux A. Sulfites inhibit the growth of four species of beneficial gut bacteria at concentrations regarded as safe for food. PLoS ONE. 2017;12:e0186629 pubmed publisher
    ..thermophilus in 2000ppm NaHSO3 after 6 hours of exposure...
  45. Marzano V, Mancinelli L, Bracaglia G, del Chierico F, Vernocchi P, Di Girolamo F, et al. "Omic" investigations of protozoa and worms for a deeper understanding of the human gut "parasitome". PLoS Negl Trop Dis. 2017;11:e0005916 pubmed publisher
    ..Systems biology-based profiles of the gut "parasitome" under physiological and severe disease conditions can indeed contribute to the control of infectious diseases and offer a new perspective of omics-assisted tropical medicine...
  46. Parashar A, Udayabanu M. Gut microbiota: Implications in Parkinson's disease. Parkinsonism Relat Disord. 2017;38:1-7 pubmed publisher
    ..In this review, we try to connect the dots between GM and PD pathology using direct and indirect evidence. ..
  47. Elderman M, Sovran B, Hugenholtz F, Graversen K, Huijskes M, Houtsma E, et al. The effect of age on the intestinal mucus thickness, microbiota composition and immunity in relation to sex in mice. PLoS ONE. 2017;12:e0184274 pubmed publisher
    ..Our data contribute to a better understanding of the interplay between mucus-microbiota-and immune responses and ultimately may lead to more tailored design of strategies to modulate mucus production in targeted groups. ..
  48. Meng X, Lu S, Yang J, Jin D, Wang X, Bai X, et al. Metataxonomics reveal vultures as a reservoir for Clostridium perfringens. Emerg Microbes Infect. 2017;6:e9 pubmed publisher
    ..Our study suggests that the soil-related C. perfringens and other pathogens could have a reservoir in vultures and other animals. ..
  49. Roze J, Ancel P, Lepage P, Martin Marchand L, Al Nabhani Z, Delannoy J, et al. Nutritional strategies and gut microbiota composition as risk factors for necrotizing enterocolitis in very-preterm infants. Am J Clin Nutr. 2017;106:821-830 pubmed publisher
    ..For a given level of risk assessed by propensity score, colonization by C. neonatale and/or S. aureus is significantly associated with NEC. This trial (EPIFLORE study) was registered at as NCT01127698. ..
  50. Mulligan C, Friedman J. Maternal modifiers of the infant gut microbiota: metabolic consequences. J Endocrinol. 2017;235:R1-R12 pubmed publisher
    ..Comprehension of these pathways and mechanisms will elucidate our understanding of developmental programming and may expand the avenue of opportunities for novel therapeutics. ..
  51. Bornstein S, Moschetta M, Kawano Y, Sacco A, Huynh D, Brooks D, et al. Metformin Affects Cortical Bone Mass and Marrow Adiposity in Diet-Induced Obesity in Male Mice. Endocrinology. 2017;158:3369-3385 pubmed publisher
    ..Obesity was not detrimental to trabecular bone in growing mice, but bone marrow medullary expansion was observed, likely resulting from inhibition of osteoblastogenesis, and this was partially reversed by metformin treatment. ..
  52. Bendtsen K, Hansen C, Krych Ł, Skovgaard K, Kot W, Vogensen F, et al. Immunological effects of reduced mucosal integrity in the early life of BALB/c mice. PLoS ONE. 2017;12:e0176662 pubmed publisher
    ..DSS skewed the microbiota in favor of Gram negative phyla. Therefore, increased permeability induced tolerogenic immunity independent of microbiota, and this was enhanced by LPS stimulation. ..
  53. Giacomin P, Croese J, Krause L, Loukas A, Cantacessi C. Suppression of inflammation by helminths: a role for the gut microbiota?. Philos Trans R Soc Lond B Biol Sci. 2015;370: pubmed publisher