Human Gut Microbes

Human Gut Microbes The human gut is home to many bacteria, many of which are considered "commensal." This means that the bacteria are helped by their relationship with the host (the human) but the host is not affected.

According to a 2012 article:

"Under normal conditions, the gut “receives” a large amount of bacteria from the hands, pharyngeal and nasal secretions, water, food, and beverages. Neonates acquire the environmental flora very quickly after birth and in a few cases develop sepsis after translocation of this new flora. In healthy humans, the gut flora in each individual is surprisingly stable, and ingested pathogens are cleared fairly easily due to the presence of the commensal flora composed chiefly of anaerobes, most of which are very difficult to isolate. The ingestion of large inoculums of highly pathogenic bacteria (e.g., Vibrio cholerae, Salmonella spp, or staphylococci) or viruses (e.g., enteroviruses such as echovirus) can destabilise the normal gut microbiome, overwhelm natural defence mechanisms, and induce various clinical symptoms. Antibiotics also very efficiently destabilise the gut microbiome. Genetic studies show that even an extremely brief course of antibiotics such as macrolides can induce very long-lived changes in the gut flora, for up to 4 years."

Resources and articles

Related Sourcewatch articles

• Candida albicans
• Brain-Gut Axis

External Resources

• NIH Human Microbiome Project

External Articles

2014

• Lucock MD, Martin CE, Yates ZR, Veysey M, "Diet and our genetic legacy in the recent anthropocene: a darwinian perspective to nutritional health," J Evid Based Complementary Altern Med, January 2014.
• Suzuki M, Nishiumi S, Matsubara A, Azuma T, Yoshida M, "Metabolome analysis for discovering biomarkers of gastroenterological cancer," J Chromatogr B Analyt Technol Biomed Life Sci, March 1, 2014.
• Melanie R. Dorenkott, Laura E. Griffin, Katheryn M. Goodrich, Katherine A. Thompson-Witrick, Gabrielle Fundaro, Liyun Ye, Joseph R. Stevens, Mostafa Ali, Sean F. O’Keefe, Matthew W. Hulver, and Andrew P. Neilson, "Oligomeric Cocoa Procyanidins Possess Enhanced Bioactivity Compared to Monomeric and Polymeric Cocoa Procyanidins for Preventing the Development of Obesity, Insulin Resistance, and Impaired Glucose Tolerance during High-Fat Feeding," Journal of Agricultural and Food Chemistry, March 12, 2014.
• Farmer AD, Randall HA, Aziz Q, "It's a Gut Feeling - how the gut microbiota affects the state of mind," J Physiol, March 24, 2014.
• Evans CC, Lepard KJ, Kwak JW, Stancukas MC, Laskowski S, Dougherty J, Moulton L, Glawe A, Wang Y, Leone V, Antonopoulos DA, Smith D, Chang EB, Ciancio MJ, "Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity," PLoS One, March 26, 2014.
• Jean-Paul Lalles, "Luminal ATP: the missing link between intestinal alkaline phosphatase, the gut microbiota and inflammation?," American Journal of Physiology - Gastrointestinal and Liver Physiology, March 27, 2014.
• Likotrafiti E, Tuohy KM, Gibson GR, Rastall RA, "An in vitro study of the effect of probiotics, prebiotics and synbiotics on the elderly faecal microbiota," Anaerobe, March 28, 2014.
• Rodríguez-Gallego E, Guirro M, Riera-Borrull M, Hernández-Aguilera A, Mariné-Casadó R, Fernández-Arroyo S, Beltrán-Debón R, Sabench F, Hernández M, Del Castillo D, Menendez JA, Camps J, Ras R, Arola L, Joven J, "Mapping of the circulating metabolome reveals α-ketoglutarate as a predictor of morbid obesity-associated non-alcoholic fatty liver disease," Int J Obes (Lond), March 28, 2014.
• Comito D, Cascio A, Romano C, "Microbiota biodiversity in inflammatory bowel disease," Ital J Pediatr, March 31, 2014.
• Selkrig J, Wong P, Zhang X, Pettersson S, "Metabolic tinkering by the gut microbiome: Implications for brain development and function," Gut Microbes, March 31, 2014.
• Aloisio I, Mazzola G, Corvaglia LT, Tonti G, Faldella G, Biavati B, Di Gioia D, "Influence of intrapartum antibiotic prophylaxis against group B Streptococcus on the early newborn gut composition and evaluation of the anti-Streptococcus activity of Bifidobacterium strains," Appl Microbiol Biotechnol, April 1, 2014.
• Lyte M, "Microbial endocrinology: Host-microbiota neuroendocrine interactions influencing brain and behavior," Gut Microbes, April 1, 2014.
• Galley JD, Bailey MT, "Impact of stressor exposure on the interplay between commensal microbiota and host inflammation," Gut Microbes, April 1, 2014.
• Tyakht AV, Alexeev DG, Popenko AS, Govorun VM, "Rural and urban microbiota: To be or not to be?," Gut Microbes, April 1, 2014.
• Hansen CH, Krych L, Buschard K, Metzdorff SB, Nellemann C, Hansen LH, Nielsen DS, Frøkiær H, Skov S, Hansen AK, "A maternal gluten-free diet reduces inflammation and diabetes incidence in the offspring of NOD mice," Diabetes, April 2, 2014.
• Everard A, Lazarevic V, Gaïa N, Johansson M, Ståhlman M, Backhed F, Delzenne NM, Schrenzel J, François P, Cani PD, "Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity," ISME J, April 3, 2014.
• Kwok LY, Zhang J, Guo Z, Gesudu Q, Zheng Y, Qiao J, Huo D, Zhang H, "Characterization of Fecal Microbiota across Seven Chinese Ethnic Groups by Quantitative Polymerase Chain Reaction," PLoS One, April 3, 2014.
• Collins JW, Chervaux C, Raymond B, Derrien M, Brazeilles R, Kosta A, Chambaud I, Crepin VF, Frankel G, "Fermented dairy products modulate C. rodentium induced colonic hyperplasia," J Infect Dis, April 4, 2014.
• Staib L, Fuchs TM, "From food to cell: nutrient exploitation strategies of enteropathogens," Microbiology, April 4, 2014.
• Allegretti JR, Hamilton MJ, "Restoring the gut microbiome for the treatment of inflammatory bowel diseases," World J Gastroenterol, April 7, 2014.

2013

• Sepp E, Lõivukene K, Julge K, Voor T, Mikelsaar M, "The association of gut microbiota with body weight and body mass index in preschool children of Estonia," Microbial Ecology in Health and Disease, February 20, 2013.
• Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD, "Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents," PLoS One, June 17, 2013.
• Soyucen E, Gulcan A, Aktuglu-Zeybek AC, Onal H, Kiykim E, Aydin A, "Differences in the gut microbiota of healthy children and those with type 1 diabetes," Pediatr Int, November 1, 2013.

2012

• Hamad I, Sokhna C, Raoult D, Bittar F, "Molecular detection of eukaryotes in a single human stool sample from Senegal," PLoS One, 2012.
• Guarino A, Wudy A, Basile F, Ruberto E, Buccigrossi V, "Composition and roles of intestinal microbiota in children," J Matern Fetal Neonatal Med, April 2012.
• Claesson MJ, Jeffery IB, Conde S, Power SE, O'Connor EM, Cusack S, Harris HM, Coakley M, Lakshminarayanan B, O'Sullivan O, Fitzgerald GF, Deane J, O'Connor M, Harnedy N, O'Connor K, O'Mahony D, van Sinderen D, Wallace M, Brennan L, Stanton C, Marchesi JR, Fitzgerald AP, Shanahan F, Hill C, Ross RP, O'Toole PW, "Gut microbiota composition correlates with diet and health in the elderly," Nature, August 9, 2012.
• Jean Carlet, "The gut is the epicentre of antibiotic resistance," Antimicrobial Resistance and Infection Control, November 27, 2012.

2011

• Parfrey LW, Walters WA, Knight R, "Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions," Frontiers in Microbiology, 2011.
• Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD, "Linking long-term dietary patterns with gut microbial enterotypes," Science, October 7, 2011.

2010

• Marchesi JR, "Prokaryotic and eukaryotic diversity of the human gut," Adv Appl Microbiol, 2010.
• Church C, Neill A, Schotthoefer AM, "Intestinal infections in humans in the Rocky Mountain region, United States," J Parasitol, February 2010.
• Tezuka H, Ohteki T, "Regulation of intestinal homeostasis by dendritic cells," Immunol Rev, March 2010.
• Gillevet P, Sikaroodi M, Keshavarzian A, Mutlu EA, "Quantitative assessment of the human gut microbiome using multitag pyrosequencing," Chemistry & Biodiviersity, May 2010.

2000s

• Hooper LV, Midtvedt T, Gordon JI, "How host-microbial interactions shape the nutrient environment of the mammalian intestine," Annu Rev Nutr, 2002.
• Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI, "Host-bacterial mutualism in the human intestine," Science, March 25, 2005.
• Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al, "Diversity of the human intestinal microbial flora," Science, June 10, 2005.
• Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, et al, "Obesity alters gut microbial ecology," Proceedings of the National Academies of Science, August 2, 2005.
• Ley RE, Peterson DA, Gordon JI, "Ecological and evolutionary forces shaping microbial diversity in the human intestine," Cell, February 24, 2006.
• Ley RE, Turnbaugh PJ, Klein S, Gordon JI, "Microbial ecology: Human gut microbes associated with obesity," Nature, December 21, 2006.
• Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, et al, "An obesity-associated gut microbiome with increased capacity for energy harvest," Nature, December 21, 2006.
• Palmer C, Bik EM, Digiulio DB, Relman DA, Brown PO, "Development of the human infant intestinal microbiota," PLoS Biology, July 2007.
• Rajilic-Stojanovic M, Smidt H, de Vos WM, "Diversity of the human gastrointestinal tract microbiota revisited," Environ Microbiol, September 2007.
• Turnbaugh PJ, Backhed F, Fulton L, Gordon JI, "Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome," Cell Host & Microbe, April 17, 2008.
• Nam YD, Chang HW, Kim KH, Roh SW, Kim MS, et al, "Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people," J Microbiol, October 2008.
• Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, et al, "The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice," Science Translational Medicine, November 11, 2009.
• Peterson J, Garges S, Giovanni M. et al, "The NIH human microbiome project," Genome Research, December 2009.