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{{redirect|Enteric bacteria}}
[[File:E. coli Bacteria (7316101966).jpg|thumb|right|''[[Escherichia coli]]'', one of the many species of [[bacteria]] present in the human gut]]
'''Gut microbiota''', '''gut microbiome''', or '''gut flora''' are the [[microorganism]]s, including [[bacteria]], [[archaea]], [[fungi]], and [[viruses]], that live in the [[digestive tracts]] of [[animal]]s.<ref name="Moszak">{{Cite journal |last1=Moszak |first1=M |last2=Szulińska |first2=M |last3=Bogdański |first3=P |date=15 April 2020 |title=You Are What You Eat – The Relationship between Diet, Microbiota, and Metabolic Disorders-A Review. |journal=Nutrients |volume=12 |issue=4 |page=1096 |doi=10.3390/nu12041096 |pmc=7230850 |pmid=32326604 |doi-access=free
The microbial composition of the gut microbiota varies across regions of the digestive tract. The [[colon (anatomy)|colon]] contains the highest microbial density of any human-associated microbial community studied so far, representing between 300 and 1000 different [[species]].<ref name="Guarner and Malagelada 2003b" /> Bacteria are the largest and to date, best studied component and 99% of gut bacteria come from about 30 or 40 species.<ref name="Beaugerie L and Petit JC">{{Cite journal |last1=Beaugerie |first1=Laurent |last2=Petit |first2=Jean-Claude |year=2004 |title=Antibiotic-associated diarrhoea |journal=Best Practice & Research Clinical Gastroenterology |volume=18 |issue=2 |pages=337–352 |doi=10.1016/j.bpg.2003.10.002 |pmid=15123074}}</ref>
==Overview==
[[File:Composition and distribution of intestinal microflora.jpg|thumb|300px|Composition and distribution of gut microbiota in human body]]
In humans, the gut microbiota has the highest numbers and species of bacteria compared to other areas of the body.<ref name="Quigley2013rev">{{Cite journal |last1=Quigley |first1=E. M |year=2013 |title=Gut bacteria in health and disease |journal=Gastroenterology & Hepatology |volume=9 |issue=9 |pages=560–569 |pmc=3983973 |pmid=24729765}}</ref> The approximate number of bacteria composing the gut microbiota is about 10<sup>13</sup>–10<sup>14</sup> (10,000 to 100,000 billion).<ref>{{Cite journal |last1=Turnbaugh |first1=Peter J. |last2=Ley |first2=Ruth E. |last3=Hamady |first3=Micah |last4=Fraser-Liggett |first4=Claire M. |last5=Knight |first5=Rob |last6=Gordon |first6=Jeffrey I. |date=October 2007 |title=The Human Microbiome Project |url=|journal=Nature |volume=449 |issue=7164 |pages=804–810 |doi=10.1038/nature06244 |pmid=17943116 |pmc=3709439 |bibcode=2007Natur.449..804T
The relationship between some gut microbiota and humans is not merely [[commensalism|commensal]] (a non-harmful coexistence), but rather a [[Mutualism (biology)|mutualistic]] relationship.<ref name="Prescotts" />{{rp|700}} Some human gut microorganisms benefit the host by [[fermentation|fermenting]] [[dietary fiber]] into [[short-chain fatty acid]]s (SCFAs), such as [[acetic acid]] and [[butyric acid]], which are then absorbed by the host.<ref name=Quigley2013rev/><ref name=Clarke2014rev/> Intestinal [[bacteria]] also play a role in synthesizing certain [[
The composition of human gut microbiota changes over time, when the diet changes, and as overall health changes.<ref name=Quigley2013rev/><ref name=Shen2016rev/> A [[systematic review]] from 2016 examined the preclinical and small human trials that have been conducted with certain commercially available strains of probiotic bacteria and identified those that had the most potential to be useful for certain [[central nervous system disorder]]s.<ref name="CNS SystRev 2016" /> It should also be highlighted that the Mediterranean diet, rich in vegetables and fibers, stimulates the activity and growth of beneficial bacteria for the brain.<ref name="Microbiome summary">{{cite journal |last1=Salvadori |first1=M |title=Update on the gut microbiome in health and diseases |journal=World J Methodol |date=20 March 2024 |volume=14 |issue=1 |doi=10.5662/wjm.v14.i1.89196 |doi-access=free |pmid=38577200 |pmc=10989414 }}</ref>
== Classifications ==
The microbial composition of the gut microbiota varies across the digestive tract. In the [[stomach]] and [[small intestine]], relatively few species of bacteria are generally present.<ref name="Guarner and Malagelada 2003b">{{Cite journal |last1=Guarner |first1=F |last2=Malagelada |first2=J |year=2003 |title=Gut flora in health and disease |journal=The Lancet |volume=361 |issue=9356 |pages=512–519 |doi=10.1016/S0140-6736(03)12489-0 |pmid=12583961
[[File:Candida albicans.jpg|thumb|''[[Candida albicans]]'', a dimorphic fungus that grows as a yeast in the gut]]
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The four dominant [[bacterial phyla]] in the human gut are [[Bacillota]] (Firmicutes), [[Bacteroidota]], [[Actinomycetota]], and [[Pseudomonadota]].<ref name="pmid24388028">{{Cite journal |last1=Khanna |first1=Sahil |last2=Tosh |first2=Pritish K |year=2014 |title=A Clinician's Primer on the Role of the Microbiome in Human Health and Disease |journal=Mayo Clinic Proceedings |volume=89 |issue=1 |pages=107–114 |doi=10.1016/j.mayocp.2013.10.011 |pmid=24388028 |doi-access=}}</ref> Most bacteria belong to the genera ''[[Bacteroides]]'', ''[[Clostridium]]'', ''[[Faecalibacterium]]'',<ref name="Guarner and Malagelada 2003b" /><ref name="Beaugerie L and Petit JC" /> ''[[Eubacterium]]'', ''[[Ruminococcus]]'', ''[[Peptococcus]]'', ''[[Peptostreptococcus]]'', and ''[[Bifidobacterium]]''.<ref name="Guarner and Malagelada 2003b" /><ref name="Beaugerie L and Petit JC" /> Other genera, such as ''[[Escherichia]]'' and ''[[Lactobacillus]]'', are present to a lesser extent.<ref name="Guarner and Malagelada 2003b" /> Species from the genus ''Bacteroides'' alone constitute about 30% of all bacteria in the gut, suggesting that this genus is especially important in the functioning of the host.<ref name=Sears/>
Fungal genera that have been detected in the gut include ''[[Candida (genus)|Candida]]'', ''[[Saccharomyces]]'', ''[[Aspergillus]]'', ''[[Penicillium]]'', ''[[Rhodotorula]]'', ''[[Trametes]]'', ''[[Pleospora]]'', ''[[Sclerotinia]]'', ''[[Bullera]]'', and ''[[Galactomyces]]'', among others.<ref name="mycobiome">{{Cite journal |last1=Cui |first1=Lijia |last2=Morris |first2=Alison |last3=Ghedin |first3=Elodie |year=2013 |title=The human mycobiome in health and disease |journal=Genome Medicine |volume=5 |issue=7 |page=63 |doi=10.1186/gm467 |pmc=3978422 |pmid=23899327 |doi-access=free }}</ref><ref name="SIFO">{{Cite journal |last1=Erdogan |first1=Askin |last2=Rao |first2=Satish S. C |year=2015 |title=Small Intestinal Fungal Overgrowth |journal=Current Gastroenterology Reports |volume=17 |issue=4 |page=16 |doi=10.1007/s11894-015-0436-2 |pmid=25786900
Due to the prevalence of fungi in the natural environment, determining which genera and species are permanent members of the gut [[mycobiome]] is difficult.<ref>{{
[[Methanobrevibacter smithii|Archaea]] constitute another large class of gut flora which are important in the metabolism of the bacterial products of fermentation.
[[Industrialisation|Industrialization]] is associated with changes in the microbiota and the reduction of diversity could drive certain species to extinction; in 2018, researchers proposed a [[biobank]] repository of human microbiota.<ref>{{Cite journal |last1=Bello |first1=Maria G. Dominguez |last2=Knight |first2=Rob |last3=Gilbert |first3=Jack A. |last4=Blaser |first4=Martin J. |date=4 October 2018 |title=Preserving microbial diversity |journal=Science |volume=362 |issue=6410 |pages=33–34 |bibcode=2018Sci...362...33B |doi=10.1126/science.aau8816 |pmid=30287652
=== Enterotype ===
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The small intestine contains a trace amount of microorganisms due to the proximity and influence of the stomach. [[Gram-positive bacteria|Gram-positive]] [[coccus|cocci]] and [[Bacillus (shape)|rod-shaped bacteria]] are the predominant microorganisms found in the small intestine.<ref name="Prescotts" /> However, in the distal portion of the small intestine alkaline conditions support gram-negative bacteria of the ''Enterobacteriaceae''.<ref name="Prescotts" /> The bacterial flora of the small intestine aid in a wide range of intestinal functions. The bacterial flora provide regulatory signals that enable the development and utility of the gut. Overgrowth of bacteria in the small intestine can lead to intestinal failure.<ref name="quigley2006">{{Cite journal |last1=Quigley |first1=Eamonn M.M |last2=Quera |first2=Rodrigo |year=2006 |title=Small Intestinal Bacterial Overgrowth: Roles of Antibiotics, Prebiotics, and Probiotics |journal=Gastroenterology |volume=130 |issue=2 |pages=S78–90 |doi=10.1053/j.gastro.2005.11.046 |pmid=16473077
Bacteria make up most of the flora in the [[Colon (anatomy)|colon]]<ref name="University of Glasgow">{{Cite web|date=2004|title=The normal gut flora|url=http://www.gla.ac.uk/departments/humannutrition/students/resources/meden/Infection.pdf|access-date=2023-01-02|archive-url=https://web.archive.org/web/20040526195616/http://www.gla.ac.uk/departments/humannutrition/students/resources/meden/Infection.pdf |archive-date=2004-05-26| type= slideshow| via= University of Glasgow }}</ref> and accounts for 60% of [[fecal]] nitrogen.<ref name="Guarner and Malagelada 2003b" /> This fact makes feces an ideal source of gut flora for any tests and experiments by extracting the nucleic acid from fecal specimens, and bacterial 16S rRNA gene sequences are generated with bacterial primers. This form of testing is also often preferable to more invasive techniques, such as biopsies.
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Five [[phylum|phyla]] dominate the intestinal microbiota: [[Bacteroidota]], [[Bacillota]] (Firmicutes), [[Actinomycetota]], [[Pseudomonadota]], and [[Verrucomicrobiota]]{{snd}}with Bacteroidota and Bacillota constituting 90% of the composition.<ref name="pmid26963713">{{Cite journal |vauthors=Braune A, Blaut M |year=2016 |title=Bacterial species involved in the conversion of dietary flavonoids in the human gut |journal=[[Taylor & Francis|Gut Microbes]] |volume=7 |issue=3 |pages=216–234 |doi=10.1080/19490976.2016.1158395 |pmc=4939924 |pmid=26963713}}</ref> Somewhere between 300<ref name="Guarner and Malagelada 2003b" /> and 1000 different [[species]] live in the gut,<ref name="Sears" /> with most estimates at about 500.<ref name="Steinhoff">{{Cite journal |last1=Steinhoff |first1=U |year=2005 |title=Who controls the crowd? New findings and old questions about the intestinal microflora |journal=Immunology Letters |volume=99 |issue=1 |pages=12–16 |doi=10.1016/j.imlet.2004.12.013 |pmid=15894105}}</ref><ref name="gibson" /> However, it is probable that 99% of the bacteria come from about 30 or 40 species, with ''[[Faecalibacterium prausnitzii]]'' (phylum firmicutes) being the most common species in healthy adults.<ref name="Beaugerie L and Petit JC" /><ref>{{Cite journal |last1=Miquel |first1=S |last2=Martín |first2=R |last3=Rossi |first3=O |last4=Bermúdez-Humarán |first4=LG |last5=Chatel |first5=JM |last6=Sokol |first6=H |last7=Thomas |first7=M |last8=Wells |first8=JM |last9=Langella |first9=P |year=2013 |title=Faecalibacterium prausnitzii and human intestinal health |journal=Current Opinion in Microbiology |volume=16 |issue=3 |pages=255–261 |doi=10.1016/j.mib.2013.06.003 |pmid=23831042}}</ref>
Research suggests that the relationship between gut [[Flora (microbiology)|flora]] and humans is not merely [[Commensalism|commensal]] (a non-harmful coexistence), but rather is a [[Mutualism (biology)|mutualistic]], [[Symbiosis|symbiotic]] relationship.<ref name="Sears" /> Though people can survive with no gut flora,<ref name="Steinhoff" /> the microorganisms perform a host of useful functions, such as [[Fermentation (biochemistry)|fermenting]] unused energy substrates, training the [[immune system]] via end products of metabolism like [[propionate]] and [[acetate]], preventing growth of harmful species, regulating the development of the gut, producing vitamins for the host (such as [[biotin]] and [[vitamin K]]), and producing hormones to direct the host to store fats.<ref name="Prescotts" /> Extensive modification and imbalances of the gut microbiota and its microbiome or gene collection are associated with obesity.<ref>{{Cite journal |last1=Ley |first1=Ruth E |year=2010 |title=Obesity and the human microbiome |journal=Current Opinion in Gastroenterology |volume=26 |issue=1 |pages=5–11 |doi=10.1097/MOG.0b013e328333d751 |pmid=19901833
===Mycobiome===
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There are common patterns of microbiome composition evolution during life.<ref name="Gerritsen et al 2012">{{Cite journal |last1=Gerritsen |first1=Jacoline |last2=Smidt |first2=Hauke |last3=Rijkers |first3=Ger |last4=de Vos |first4=Willem |date=27 May 2011 |title=Intestinal microbiota in human health and disease: the impact of probiotics |journal=Genes & Nutrition |volume=6 |issue=3 |pages=209–240 |doi=10.1007/s12263-011-0229-7 |pmc=3145058 |pmid=21617937}}</ref> In general, the diversity of microbiota composition of fecal samples is significantly higher in adults than in children, although interpersonal differences are higher in children than in adults.<ref name="Tanya Yatsunenko 2012" /> Much of the maturation of microbiota into an adult-like configuration happens during the first three years of life.<ref name="Tanya Yatsunenko 2012">{{Cite journal |last1=Yatsunenko |first1=T. |last2=Rey |first2=F. E. |last3=Manary |first3=M. J. |last4=Trehan |first4=I. |last5=Dominguez-Bello |first5=M. G. |last6=Contreras |first6=M. |last7=Magris |first7=M. |last8=Hidalgo |first8=G. |last9=Baldassano |first9=R. N. |last10=Anokhin |first10=A. P. |last11=Heath |first11=A. C. |last12=Warner |first12=B. |last13=Reeder |first13=J. |last14=Kuczynski |first14=J. |last15=Caporaso |first15=J. G. |year=2012 |title=Human gut microbiome viewed across age and geography |journal=Nature |volume=486 |issue=7402 |pages=222–227 |bibcode=2012Natur.486..222Y |doi=10.1038/nature11053 |pmc=3376388 |pmid=22699611 |last16=Lozupone |first16=C. A. |last17=Lauber |first17=C. |last18=Clemente |first18=J. C. |last19=Knights |first19=D. |last20=Knight |first20=R. |last21=Gordon |first21=J. I.}}</ref>
As the microbiome composition changes, so does the composition of bacterial proteins produced in the gut. In adult microbiomes, a high prevalence of enzymes involved in [[fermentation]], [[methanogenesis]] and the metabolism of [[arginine]], [[glutamate]], [[aspartate]] and [[lysine]] have been found. In contrast, in infant microbiomes the dominant enzymes are involved in [[cysteine]] metabolism and fermentation pathways.<ref name="Tanya Yatsunenko 2012" />
=== Geography ===
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==== Malnourishment ====
[[Malnutrition|Malnourished]] children have less mature and less diverse gut microbiota than healthy children, and changes in the microbiome associated with nutrient scarcity can in turn be a pathophysiological cause of malnutrition.<ref name="Jonkers">{{Cite journal |last1=Jonkers |first1=Daisy M.A.E. |year=2016 |title=Microbial perturbations and modulation in conditions associated with malnutrition and malabsorption |journal=Best Practice & Research Clinical Gastroenterology |volume=30 |issue=2 |pages=161–172 |doi=10.1016/j.bpg.2016.02.006 |pmid=27086883}}</ref><ref name="Million">{{
===Race and ethnicity===
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===Socioeconomic status===
As of 2020, at least two studies have demonstrated a link between an individual's [[socioeconomic status]] (SES) and their gut microbiota. A study in [[Chicago]] found that individuals in higher SES neighborhoods had greater microbiota diversity. People from higher SES neighborhoods also had more abundant ''Bacteroides'' bacteria. Similarly, a study of [[twin]]s in the United Kingdom found that higher SES was also linked with a greater gut diversity.<ref name="Renson">{{Cite journal |last1=Renson |first1=Audrey |last2=Herd |first2=Pamela |last3=Dowd |first3=Jennifer B. |author-link3=Jennifer Dowd |year=2020 |title=Sick Individuals and Sick (Microbial) Populations: Challenges in Epidemiology and the Microbiome |journal=Annual Review of Public Health |volume=41 |pages=63–80 |doi=10.1146/annurev-publhealth-040119-094423 |pmid=31635533 |pmc=9713946 |doi-access=free}}</ref>
===Antibiotic Usage===
As of 2023, a study suggests that antibiotics, especially those used in the treatment of broad-spectrum bacterial infections, have negative effects on the gut microbiota.<ref>Colella, M., Charitos, I. A., Ballini, A., Cafiero, C., Topi, S., Palmirotta, R., & Santacroce, L. (2023). Microbiota revolution: How gut microbes regulate our lives. World journal of gastroenterology, 29(28), 4368–4383. https://doi.org/10.3748/wjg.v29.i28.4368</ref> The study also states that there are many experts on intestinal health concerned that antibody usage has reduced the diversity of the gut microbiota, many of the strains are lost, and if there is a re-emergence of the bacteria, is gradual and long-term. <ref>Colella, M., Charitos, I. A., Ballini, A., Cafiero, C., Topi, S., Palmirotta, R., & Santacroce, L. (2023). Microbiota revolution: How gut microbes regulate our lives. World journal of gastroenterology, 29(28), 4368–4383. https://doi.org/10.3748/wjg.v29.i28.4368</ref>
== Acquisition in human infants ==
The establishment of a gut flora is crucial to the health of an adult, as well as the functioning of the gastrointestinal tract.<ref>{{Cite journal |last1=Turroni |first1=Francesca |last2=Peano |first2=Clelia |last3=Pass |first3=Daniel A |last4=Foroni |first4=Elena |last5=Severgnini |first5=Marco |last6=Claesson |first6=Marcus J |last7=Kerr |first7=Colm |last8=Hourihane |first8=Jonathan |last9=Murray |first9=Deirdre |last10=Fuligni |first10=Fabio |last11=Gueimonde |first11=Miguel |last12=Margolles |first12=Abelardo |last13=De Bellis |first13=Gianluca |last14=o'Toole |first14=Paul W |last15=Van Sinderen |first15=Douwe |year=2012 |title=Diversity of Bifidobacteria within the Infant Gut Microbiota |journal=PLOS ONE |volume=7 |issue=5 |pages=e36957 |bibcode=2012PLoSO...736957T |doi=10.1371/journal.pone.0036957 |pmc=3350489 |pmid=22606315 |doi-access=free |last16=Marchesi |first16=Julian R |last17=Ventura |first17=Marco}}</ref> In humans, a gut flora similar to an adult's is formed within one to two years of birth as microbiota are acquired through parent-to-child transmission and transfer from food, water, and other environmental sources.<ref>{{
[[File:Illustration of the developmental colonization of gut bacteria.jpg|thumb|500px|Illustration showing the developmental colonization of gut microbiota]]
The traditional view of the [[gastrointestinal tract]] of a normal [[fetus]] is that it is sterile, although this view has been challenged in the past few years.{{clarify timeframe|date=May 2023}}<ref>{{Cite journal |last1=Perez-Muñoz |first1=Maria Elisa |last2=Arrieta |first2=Marie-Claire |last3=Ramer-Tait |first3=Amanda E |last4=Walter |first4=Jens |year=2017 |title=A critical assessment of the 'sterile womb' and 'in utero colonization' hypotheses: Implications for research on the pioneer infant microbiome |journal=Microbiome |volume=5 |issue=1 |page=48 |doi=10.1186/s40168-017-0268-4 |pmc=5410102 |pmid=28454555 |doi-access=free }}</ref> Multiple lines of evidence have begun to emerge that suggest there may be bacteria in the intrauterine environment. In humans, research has shown that microbial colonization may occur in the fetus<ref name="Matamoros2013">{{Cite journal |last1=Matamoros |first1=Sebastien |last2=Gras-Leguen |first2=Christele |last3=Le Vacon |first3=Françoise |last4=Potel |first4=Gilles |last5=de la Cochetiere |first5=Marie-France |year=2013 |title=Development of intestinal microbiota in infants and its impact on health |journal=Trends in Microbiology |volume=21 |issue=4 |pages=167–173 |doi=10.1016/j.tim.2012.12.001 |pmid=23332725}}</ref> with one study showing ''Lactobacillus'' and ''Bifidobacterium'' species were present in placental biopsies.<ref name="Mueller 109–117" /> Several [[animal testing on rodents|rodent studies]] have demonstrated the presence of bacteria in the amniotic fluid and placenta, as well as in the [[meconium]] of babies born by sterile cesarean section.<ref>{{Cite journal |last1=Jiménez |first1=Esther |last2=Fernández |first2=Leonides |last3=Marín |first3=María L |last4=Martín |first4=Rocío |last5=Odriozola |first5=Juan M |last6=Nueno-Palop |first6=Carmen |last7=Narbad |first7=Arjan |last8=Olivares |first8=Mónica |last9=Xaus |first9=Jordi |last10=Rodríguez |first10=Juan M |year=2005 |title=Isolation of Commensal Bacteria from Umbilical Cord Blood of Healthy Neonates Born by Cesarean Section |journal=Current Microbiology |volume=51 |issue=4 |pages=270–274 |doi=10.1007/s00284-005-0020-3 |pmid=16187156
During birth and rapidly thereafter, bacteria from the mother and the surrounding environment colonize the infant's gut.<ref name="Sommer2013rev" /> The exact sources of bacteria are not fully understood, but may include the birth canal, other people (parents, siblings, hospital workers), breastmilk, food, and the general environment with which the infant interacts.<ref>{{Cite journal |last1=Adlerberth |first1=I |last2=Wold |first2=AE |year=2009 |title=Establishment of the gut microbiota in Western infants |journal=Acta Paediatrica |volume=98 |issue=2 |pages=229–238 |doi=10.1111/j.1651-2227.2008.01060.x |pmid=19143664
During the first year of life, the composition of the gut flora is generally simple and changes a great deal with time and is not the same across individuals.<ref name="Sommer2013rev" /> The initial bacterial population are generally [[facultative anaerobic organism]]s; investigators believe that these initial colonizers decrease the oxygen concentration in the gut, which in turn allows obligately anaerobic bacteria like ''Bacteroidota'', ''Actinomycetota'', and ''Bacillota'' to become established and thrive.<ref name="Sommer2013rev" /> Breast-fed babies become dominated by [[bifidobacteria]], possibly due to the contents of [[Bifidus factor|bifidobacterial growth factors]] in breast milk, and by the fact that breast milk carries prebiotic components, allowing for healthy bacterial growth.<ref name="Mueller 109–117" /><ref>{{Cite journal |last1=Coppa |first1=G. V. |last2=Zampini |first2=L. |last3=Galeazzi |first3=T. |last4=Gabrielli |first4=O. |year=2006 |title=Prebiotics in human milk: A review |journal=Digestive and Liver Disease |volume=38 |pages=S291–294 |doi=10.1016/S1590-8658(07)60013-9 |pmid=17259094}}</ref> Breast milk also contains higher levels of Immunoglobulin A (IgA) to help with the tolerance and regulation of the baby's immune system.<ref>{{
Caesarean section, [[antibiotic]]s, and [[formula feeding]] may alter the gut microbiome composition.<ref name="Mueller 109–117" /> Children treated with antibiotics have less stable, and less diverse floral communities.<ref>{{Cite journal |last1=Yassour |first1=Moran |last2=Vatanen |first2=Tommi |last3=Siljander |first3=Heli |last4=Hämäläinen |first4=Anu-Maaria |last5=Härkönen |first5=Taina |last6=Ryhänen |first6=Samppa J |last7=Franzosa |first7=Eric A |last8=Vlamakis |first8=Hera |last9=Huttenhower |first9=Curtis |last10=Gevers |first10=Dirk |last11=Lander |first11=Eric S |last12=Knip |first12=Mikael |last13=Xavier |first13=Ramnik J |year=2016 |title=Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability |journal=Science Translational Medicine |volume=8 |issue=343 |pages=343ra81 |doi=10.1126/scitranslmed.aad0917 |pmc=5032909 |pmid=27306663}}</ref> Caesarean sections have been shown to be disruptive to mother-offspring transmission of bacteria, which impacts the overall health of the offspring by raising risks of disease such as [[celiac disease]], [[asthma]], and [[type 1 diabetes|type'' ''1 diabetes]].<ref name="Mueller 109–117" /> This further evidences the importance of a healthy gut microbiome. Various methods of microbiome restoration are being explored, typically involving exposing the infant to maternal vaginal contents, and oral probiotics.<ref name="Mueller 109–117" />
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=== Direct inhibition of pathogens ===
The gut flora community plays a direct role in defending against pathogens by fully colonising the space, making use of all available nutrients, and by secreting compounds known as [[cytokine]]s that kill or inhibit unwelcome organisms that would compete for nutrients with it.<ref name="Yoon2014rev">{{Cite journal |last1=Yoon |first1=My Young |last2=Lee |first2=Keehoon |last3=Yoon |first3=Sang Sun |year=2014 |title=Protective role of gut commensal microbes against intestinal infections |journal=Journal of Microbiology |volume=52 |issue=12 |pages=983–989 |doi=10.1007/s12275-014-4655-2 |pmid=25467115
===Development of enteric protection and immune system===
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In humans, a gut flora similar to an adult's is formed within one to two years of birth.<ref name=Sommer2013rev/> As the gut flora gets established, the lining of the intestines – the intestinal epithelium and the intestinal mucosal barrier that it secretes – develop as well, in a way that is tolerant to, and even supportive of, commensalistic microorganisms to a certain extent and also provides a barrier to pathogenic ones.<ref name=Sommer2013rev/> Specifically, [[goblet cell]]s that produce the mucosa proliferate, and the mucosa layer thickens, providing an outside mucosal layer in which "friendly" microorganisms can anchor and feed, and an inner layer that even these organisms cannot penetrate.<ref name=Sommer2013rev/><ref name=Faderl2015rev/> Additionally, the development of [[gut-associated lymphoid tissue]] (GALT), which forms part of the intestinal epithelium and which detects and reacts to pathogens, appears and develops during the time that the gut flora develops and established.<ref name=Sommer2013rev/> The GALT that develops is tolerant to gut flora species, but not to other microorganisms.<ref name=Sommer2013rev/> GALT also normally becomes tolerant to food to which the infant is exposed, as well as digestive products of food, and gut flora's [[metabolites]] (molecules formed from metabolism) produced from food.<ref name=Sommer2013rev/>
The human [[immune system]] creates [[cytokine]]s that can drive the immune system to produce inflammation in order to protect itself, and that can tamp down the immune response to maintain [[homeostasis]] and allow healing after insult or injury.<ref name=Sommer2013rev/> Different bacterial species that appear in gut flora have been shown to be able to drive the immune system to create cytokines selectively; for example ''[[Bacteroides fragilis]]'' and some ''[[Clostridia]]'' species appear to drive an anti-inflammatory response, while some [[segmented filamentous bacteria]] drive the production of inflammatory cytokines.<ref name=Sommer2013rev/><ref>{{Cite journal |last1=Reinoso Webb |first1=Cynthia |last2=Koboziev |first2=Iurii |last3=Furr |first3=Kathryn L |last4=Grisham |first4=Matthew B |year=2016 |title=Protective and pro-inflammatory roles of intestinal bacteria |journal=Pathophysiology |volume=23 |issue=2 |pages=67–80 |doi=10.1016/j.pathophys.2016.02.002 |pmc=4867289 |pmid=26947707}}</ref> Gut flora can also regulate the production of [[antibodies]] by the immune system.<ref name=Sommer2013rev/><ref>{{Cite journal |last1=Mantis |first1=N J |last2=Rol |first2=N |last3=Corthésy |first3=B |year=2011 |title=Secretory IgA's complex roles in immunity and mucosal homeostasis in the gut |journal=Mucosal Immunology |volume=4 |issue=6 |pages=603–611 |doi=10.1038/mi.2011.41 |pmc=3774538 |pmid=21975936}}</ref> One function of this regulation is to cause [[B cells]] to class switch to [[IgA]]. In most cases B cells need activation from [[T helper cells]] to induce [[class switching]]; however, in another pathway, gut flora cause [[NF-kB]] signaling by intestinal epithelial cells which results in further signaling molecules being secreted.<ref name="Peterson">{{Cite journal |last1=Peterson |first1=Lance W |last2=Artis |first2=David |year=2014 |title=Intestinal epithelial cells: Regulators of barrier function and immune homeostasis |journal=Nature Reviews Immunology |volume=14 |issue=3 |pages=141–153 |doi=10.1038/nri3608 |pmid=24566914
The immune system can also be altered due to the gut bacteria's ability to produce [[metabolites]] that can affect cells in the immune system. For example [[short-chain fatty acid]]s (SCFA) can be produced by some gut bacteria through [[fermentation]].<ref name="Levy">{{Cite journal |last1=Levy |first1=M. |last2=Thaiss |first2=C.A. |last3=Elinav |first3=E. |author-link3=Eran Elinav |date=2016 |title=Metabolites: messengers between the microbiota and the immune system |journal=Genes & Development |volume=30 |issue=14 |pages=1589–1597 |doi=10.1101/gad.284091.116 |pmc=4973288 |pmid=27474437}}</ref> SCFAs stimulate a rapid increase in the production of innate immune cells like [[neutrophils]], [[basophils]] and [[eosinophils]].<ref name=Levy/> These cells are part of the innate immune system that try to limit the spread of infection.
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Without gut flora, the human body would be unable to utilize some of the undigested [[carbohydrate]]s it consumes, because some types of gut flora have [[enzyme]]s that human cells lack for breaking down certain [[polysaccharide]]s.<ref name=Clarke2014rev/> Rodents raised in a [[Asepsis|sterile]] environment and lacking in gut flora need to eat 30% more [[calorie (food)|calories]] just to remain the same weight as their normal counterparts.<ref name=Clarke2014rev/> Carbohydrates that humans cannot [[digestion|digest]] without bacterial help include certain [[starch (food)|starches]], [[fiber (food)|fiber]], [[oligosaccharides]], and [[sugar]]s that the body failed to digest and absorb like [[lactose]] in the case of [[lactose intolerance]] and [[sugar alcohol]]s, [[mucus]] produced by the gut, and proteins.<ref name=Quigley2013rev/><ref name=Clarke2014rev/>
Bacteria turn carbohydrates they ferment into [[short-chain fatty acid]]s by a form of fermentation called [[saccharolytic fermentation]].<ref name=gibson/> Products include [[acetic acid]], [[propionic acid]] and [[butyric acid]].<ref name="Beaugerie L and Petit JC" /><ref name=gibson/> These materials can be used by host cells, providing a major source of energy and nutrients.<ref name=gibson/> Gases (which are involved in [[Gaseous signaling molecules|signaling]]<ref>{{
Gut flora also synthesize vitamins like [[biotin]] and [[folate]], and facilitate absorption of [[dietary minerals]], including magnesium, calcium, and iron.<ref name="Guarner and Malagelada 2003b" /><ref name="OHara06">{{Cite journal |last1=O'Hara |first1=Ann M |last2=Shanahan |first2=Fergus |year=2006 |title=The gut flora as a forgotten organ |journal=EMBO Reports |volume=7 |issue=7 |pages=688–693 |doi=10.1038/sj.embor.7400731 |pmc=1500832 |pmid=16819463}}</ref> ''[[Methanobrevibacter smithii]]'' is unique because it is not a species of bacteria, but rather a member of [[Domain (taxonomy)|domain]] ''[[Archaea]]'', and is the most abundant [[methane]]-producing archaeal species in the human gastrointestinal microbiota.<ref>{{Cite journal |last1=Rajilić-Stojanović |first1=Mirjana |last2=De Vos |first2=Willem M |year=2014 |title=The first 1000 cultured species of the human gastrointestinal microbiota |journal=FEMS Microbiology Reviews |volume=38 |issue=5 |pages=996–1047 |doi=10.1111/1574-6976.12075 |pmc=4262072 |pmid=24861948}}</ref>
Gut microbiota also serve as a source of vitamins K and B<sub>12</sub>, which are not produced by the body or produced in little amount.<ref>{{
==== Cellulose degradation ====
Bacteria that degrade cellulose (such as ''[[Ruminococcus]]'') are prevalent among [[Hominidae|great apes]], ancient human societies, [[hunter-gatherer]] communities, and even modern rural populations. However, they are rare in industrialized societies. Human-associated strains have acquired genes that can degrade specific plant fibers such as [[maize]], [[rice]], and [[wheat]]. Bacterial strains found in primates can also degrade [[chitin]], a polymer abundant in insects, which are part of the diet of many nonhuman [[Primate|primates]]. The decline of these bacteria in the human gut were likely influenced by the shift toward western lifestyles.<ref>{{
==== Pharmacomicrobiomics ====
The human [[metagenomics|metagenome]] (i.e., the genetic composition of an individual and all microorganisms that reside on or within the individual's body) varies considerably between individuals.<ref name="Pharmacomicrobiomics">{{Cite journal |vauthors=ElRakaiby M, Dutilh BE, Rizkallah MR, Boleij A, Cole JN, Aziz RK |date=July 2014 |title=Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics |journal=Omics |volume=18 |issue=7 |pages=402–414 |doi=10.1089/omi.2014.0018 |pmc=4086029 |pmid=24785449}}</ref><ref name="Human microbiome">{{cite journal | vauthors = Cho I, Blaser MJ | title = The human microbiome: at the interface of health and disease | journal = Nature Reviews. Genetics | volume = 13 | issue = 4 | pages = 260–270 | date = March 2012 | pmid = 22411464 | doi = 10.1038/nrg3182 | quote=The composition of the microbiome varies by anatomical site (Figure 1). The primary determinant of community composition is anatomical location: interpersonal variation is substantial<sup>23,24</sup> and is higher than the temporal variability seen at most sites in a single individual<sup>25</sup>.| pmc = 3418802 }}</ref> Since the total number of microbial cells in the human body (over 100 trillion) greatly outnumbers ''Homo sapiens'' cells (tens of trillions),{{#tag:ref|There is substantial variation in microbiome composition and microbial concentrations by anatomical site.<ref name="Pharmacomicrobiomics" /><ref name="Human microbiome" /> Fluid from the human colon – which contains the highest concentration of microbes of any anatomical site – contains approximately one trillion (10^12) bacterial cells/ml.<ref name="Pharmacomicrobiomics" />|group="note"}}<ref name="Pharmacomicrobiomics" /><ref name="Gut feeling">{{Cite journal |vauthors=Hutter T, Gimbert C, Bouchard F, Lapointe FJ |year=2015 |title=Being human is a gut feeling |journal=Microbiome |volume=3 |page=9 |doi=10.1186/s40168-015-0076-7 |pmc=4359430 |pmid=25774294|doi-access=free }}</ref> there is considerable potential for interactions between drugs and an individual's microbiome, including: drugs altering the composition of the [[human microbiome]], [[drug metabolism]] by microbial enzymes modifying the drug's [[pharmacokinetic]] profile, and microbial drug metabolism affecting a drug's clinical efficacy and [[toxicity]] profile.<ref name="Pharmacomicrobiomics" /><ref name="Human microbiome" /><ref name="Microbial amphetamine metabolism - E. coli">{{cite journal |
Apart from carbohydrates, gut microbiota can also metabolize other [[xenobiotic]]s such as drugs, [[phytochemical]]s, and food toxicants. More than 30 drugs have been shown to be metabolized by gut microbiota.<ref>{{Cite journal |last1=Sousa |first1=Tiago |last2=Paterson |first2=Ronnie |last3=Moore |first3=Vanessa |last4=Carlsson |first4=Anders |last5=Abrahamsson |first5=Bertil |last6=Basit |first6=Abdul W |year=2008 |title=The gastrointestinal microbiota as a site for the biotransformation of drugs |journal=International Journal of Pharmaceutics |volume=363 |issue=1–2 |pages=1–25 |doi=10.1016/j.ijpharm.2008.07.009 |pmid=18682282}}</ref> The microbial metabolism of drugs can sometimes inactivate the drug.<ref>{{Cite journal |last1=Haiser |first1=H. J |last2=Gootenberg |first2=D. B |last3=Chatman |first3=K |last4=Sirasani |first4=G |last5=Balskus |first5=E. P |last6=Turnbaugh |first6=P. J |year=2013 |title=Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta |journal=Science |volume=341 |issue=6143 |pages=295–298 |bibcode=2013Sci...341..295H |doi=10.1126/science.1235872 |pmc=3736355 |pmid=23869020}}</ref>
===== Contribution to drug metabolism =====
The gut microbiota is an enriched community that contains diverse genes with huge biochemical capabilities to modify drugs, especially those taken by mouth.<ref name=":8">{{
The human gut microbiota plays a crucial role in modulating the effect of the administered drugs on the human. Directly, gut microbiota can synthesize and release a series of enzymes with the capability to metabolize drugs such as microbial biotransformation of L-dopa by decarboxylase and dehydroxylase enzymes.<ref name="Maini Rekdal" /> On the contrary, gut microbiota may also alter the metabolism of the drugs by modulating the host drug metabolism. This mechanism can be mediated by microbial metabolites or by modifying host metabolites which in turn change the expression of host metabolizing enzymes.<ref name="Dempsey 481–490" />
A large number of studies have demonstrated the metabolism of over 50 drugs by the gut microbiota.<ref name=":9">{{
===== Secondary metabolites =====
This microbial community in the gut has a huge biochemical capability to produce distinct secondary metabolites that are sometimes produced from the metabolic conversion of dietary foods such as [[fiber]]s, endogenous biological compounds such as [[indole]] or [[bile acid]]s.<ref>{{Cite journal |last1=Koh |first1=Ara |last2=De Vadder |first2=Filipe |last3=Kovatcheva-Datchary |first3=Petia |last4=Bäckhed |first4=Fredrik |date=June 2016 |title=From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites |journal=Cell |volume=165 |issue=6 |pages=1332–1345 |doi=10.1016/j.cell.2016.05.041 |pmid=27259147
One of the most important bacterial metabolites produced by the gut microbiota is secondary bile acids (BAs).<ref name="
====Dysbiosis====
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<!--Please do not add new content here. Please add it to the body of [[Gut-brain axis]] and if it rises to the [[WP:LEAD]] of that article, update the lead, then copy that here. Per [[WP:SYNC]].-->
The gut microbiota contributes to digestion and immune modulation, as it plays a role in the gut-brain axis, where microbial metabolites such as short-chain fatty acids and neurotransmitters influence brain function and behavior. The gut–brain axis is the biochemical signaling that takes place between the [[gastrointestinal tract]] and the [[central nervous system]].<ref name="2014Wangrev" /> That term has been expanded to include the role of the gut flora in the interplay; the term "microbiome––brain axis" is sometimes used to describe paradigms explicitly including the gut flora.<ref name="2014Wangrev" /><ref name="Mayer2014rev">{{Cite journal |last1=Mayer |first1=E. A |last2=Knight |first2=R |last3=Mazmanian |first3=S. K |last4=Cryan |first4=J. F |last5=Tillisch |first5=K |year=2014 |title=Gut Microbes and the Brain: Paradigm Shift in Neuroscience |journal=Journal of Neuroscience |volume=34 |issue=46 |pages=15490–15496 |doi=10.1523/JNEUROSCI.3299-14.2014 |pmc=4228144 |pmid=25392516}}</ref><ref name="DinanandCryan2015">{{Cite journal |last1=Dinan |first1=Timothy G |last2=Cryan |first2=John F |year=2015 |title=The impact of gut microbiota on brain and behaviour |journal=Current Opinion in Clinical Nutrition and Metabolic Care |volume=18 |issue=6 |pages=552–558 |doi=10.1097/MCO.0000000000000221 |pmid=26372511
A [[systematic review]] from 2016 examined the preclinical and small human trials that have been conducted with certain commercially available strains of [[probiotic]] bacteria and found that among those tested, ''[[Bifidobacterium]]'' and ''Lactobacillus'' [[genera]] (''[[B. longum]]'', ''[[B. breve]]'', ''[[B. infantis]]'', ''[[L. helveticus]]'', ''[[L. rhamnosus]]'', ''[[Lactobacillus plantarum|L. plantarum]]'', and ''[[L. casei]]''), had the most potential to be useful for certain [[central nervous system disorder]]s.<ref name="CNS SystRev 2016">{{Cite journal |last1=Wang |first1=Huiying |last2=Lee |first2=In-Seon |last3=Braun |first3=Christoph |last4=Enck |first4=Paul |year=2016 |title=Effect of Probiotics on Central Nervous System Functions in Animals and Humans: A Systematic Review |journal=Journal of Neurogastroenterology and Motility |volume=22 |issue=4 |pages=589–605 |doi=10.5056/jnm16018 |pmc=5056568 |pmid=27413138}}</ref>
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Changing the numbers and species of gut microbiota can reduce the body's ability to ferment carbohydrates and metabolize [[bile]] acids and may cause [[diarrhea]]. Carbohydrates that are not broken down may absorb too much water and cause runny stools, or lack of SCFAs produced by gut microbiota could cause diarrhea.<ref name="Beaugerie L and Petit JC" />
A reduction in levels of native bacterial species also disrupts their ability to inhibit the growth of harmful species such as ''C. difficile'' and ''Salmonella'' Kedougou, and these species can get out of hand, though their overgrowth may be incidental and not be the true cause of diarrhea.<ref name="Guarner and Malagelada 2003b" /><ref name="Beaugerie L and Petit JC" /><ref name=Carman/> Emerging treatment protocols for C. difficile infections involve fecal microbiota transplantation of donor feces (see [[Fecal transplant]]).<ref>{{
The composition of the gut microbiome also changes in severe illnesses, due not only to antibiotic use but also to such factors as [[ischemia]] of the gut, failure to eat, and [[immune compromise]]. Negative effects from this have led to interest in [[selective digestive tract decontamination]], a treatment to kill only pathogenic bacteria and allow the re-establishment of healthy ones.<ref name="Knight">{{Cite journal |last1=Knight |first1=DJW |last2=Girling |first2=KJ |year=2003 |title=Gut flora in health and disease |journal=The Lancet |volume=361 |issue=9371 |pages=512–519 |doi=10.1016/S0140-6736(03)13438-1 |pmid=12781578
Antibiotics alter the population of the microbiota in the [[gastrointestinal tract]], and this may change the intra-community metabolic interactions, modify caloric intake by using carbohydrates, and globally
There is reasonable evidence that taking probiotics containing ''Lactobacillus'' species may help prevent antibiotic-associated diarrhea and that taking probiotics with ''Saccharomyces'' (e.g., ''[[Saccharomyces boulardii]] '') may help to prevent ''
=== Pregnancy ===
The gut microbiota of a woman changes as [[pregnancy]] advances, with the changes similar to those seen in [[metabolic syndromes]] such as diabetes. The change in gut microbiota causes no ill effects. The newborn's gut microbiota resemble the mother's first-trimester samples. The diversity of the microbiome decreases from the first to third trimester, as the numbers of certain species go up.<ref name="Mueller 109–117" /><ref>{{Cite journal |last1=Baker |first1=Monya |year=2012 |title=Pregnancy alters resident gut microbes |journal=Nature |doi=10.1038/nature.2012.11118
=== Probiotics, prebiotics, synbiotics, and pharmabiotics ===
[[Probiotics]]
With regard to gut microbiota, [[prebiotics]] are typically non-digestible, [[dietary fiber|fiber]] compounds that pass undigested through the upper part of the [[gastrointestinal tract]] and stimulate the growth or activity of advantageous gut flora by acting as [[substrate (biology)|substrate]] for them.<ref name="gibson">{{Cite journal |last1=Gibson |first1=Glenn R |year=2004 |title=Fibre and effects on probiotics (the prebiotic concept) |journal=Clinical Nutrition Supplements |volume=1 |issue=2 |pages=25–31 |doi=10.1016/j.clnu.2004.09.005}}</ref><ref name="2015defRev">{{Cite journal |last1=Hutkins |first1=Robert W |last2=Krumbeck |first2=Janina A |last3=Bindels |first3=Laure B |last4=Cani |first4=Patrice D |last5=Fahey |first5=George |last6=Goh |first6=Yong Jun |last7=Hamaker |first7=Bruce |last8=Martens |first8=Eric C |last9=Mills |first9=David A |last10=Rastal |first10=Robert A |last11=Vaughan |first11=Elaine |last12=Sanders |first12=Mary Ellen |year=2016 |title=Prebiotics: Why definitions matter |journal=Current Opinion in Biotechnology |volume=37 |pages=1–7 |doi=10.1016/j.copbio.2015.09.001 |pmc=4744122 |pmid=26431716}}</ref> [[Synbiotics]] refers to [[food ingredient]]s or [[dietary supplements]] combining probiotics and prebiotics in a form of [[Synergy|synergism]].<ref>{{Cite journal |last1=Pandey |first1=Kavita. R |last2=Naik |first2=Suresh. R |last3=Vakil |first3=Babu. V |year=2015 |title=Probiotics, prebiotics and synbiotics- a review |journal=Journal of Food Science and Technology |volume=52 |issue=12 |pages=7577–7587 |doi=10.1007/s13197-015-1921-1 |pmc=4648921 |pmid=26604335}}</ref>
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The term "pharmabiotics" is used in various ways, to mean: [[pharmaceutical formulation]]s (standardized manufacturing that can obtain regulatory approval as a drug) of probiotics, [[prebiotics]], or [[synbiotics]];<ref>{{Cite journal |last1=Broeckx |first1=Géraldine |last2=Vandenheuvel |first2=Dieter |last3=Claes |first3=Ingmar J.J |last4=Lebeer |first4=Sarah |last5=Kiekens |first5=Filip |year=2016 |title=Drying techniques of probiotic bacteria as an important step towards the development of novel pharmabiotics |url=https://repository.uantwerpen.be/docman/irua/9d9f03/132884.pdf |journal=International Journal of Pharmaceutics |volume=505 |issue=1–2 |pages=303–318 |doi=10.1016/j.ijpharm.2016.04.002 |pmid=27050865 |hdl-access=free |hdl=10067/1328840151162165141}}</ref> probiotics that have been genetically engineered or otherwise optimized for best performance (shelf life, survival in the digestive tract, etc.);<ref>{{Cite journal |last1=Sleator |first1=Roy D |last2=Hill |first2=Colin |year=2009 |title=Rational Design of Improved Pharmabiotics |journal=Journal of Biomedicine and Biotechnology |volume=2009 |page=275287 |doi=10.1155/2009/275287 |pmc=2742647 |pmid=19753318 |doi-access=free}}</ref> and the natural products of gut flora metabolism (vitamins, etc.).<ref>{{Cite journal |last1=Patterson |first1=Elaine |last2=Cryan |first2=John F |last3=Fitzgerald |first3=Gerald F |last4=Ross |first4=R. Paul |last5=Dinan |first5=Timothy G |last6=Stanton |first6=Catherine |year=2014 |title=Gut microbiota, the pharmabiotics they produce and host health |journal=Proceedings of the Nutrition Society |volume=73 |issue=4 |pages=477–489 |doi=10.1017/S0029665114001426 |pmid=25196939 |doi-access=free}}</ref>
There is some evidence that treatment with some probiotic strains of bacteria may be effective in [[irritable bowel syndrome]],<ref>{{cite web | url=https://www.gutmicrobiotaforhealth.com/non-prescription-therapeutics-for-ibs-where-are-we/ | title=Non-prescription therapeutics for IBS: Where are we? | date=30 January 2024 }}</ref><ref
* ''[[Bifidobacterium breve]]''
* ''[[Bifidobacterium infantis]]''
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* ''[[Saccharomyces boulardii]]''
* ''[[Escherichia coli Nissle 1917]]''
* ''[[Streptococcus thermophilus]]''<ref name="FordQuigley2014">{{cite journal |doi=10.1038/ajg.2014.202 |pmid=25070051 |title=Efficacy of Prebiotics, Probiotics and Synbiotics in Irritable Bowel Syndrome and Chronic Idiopathic Constipation: Systematic Review and Meta-analysis |journal=The American Journal of Gastroenterology |volume=109 |issue=10 |pages=1547–1561; quiz 1546, 1562 |year=2014 |last1=Ford |first1=Alexander C |last2=Quigley |first2=Eamonn M M |last3=Lacy |first3=Brian E |last4=Lembo |first4=Anthony J |last5=Saito |first5=Yuri A |last6=Schiller |first6=Lawrence R |last7=Soffer |first7=Edy E |last8=Spiegel |first8=Brennan M R |last9=Moayyedi |first9=Paul
=== Fecal floatation ===
Feces of about 10–15% of people consistently floats in toilet water ('floaters'), while the rest produce feces that sinks ('sinkers') and production of gas causes feces to float.<ref>{{
=== Research ===
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=== Ulcers ===
''[[Helicobacter pylori]]'' infection can initiate formation of stomach ulcers when the bacteria penetrate the stomach epithelial lining, then causing an [[phagocytosis|inflammatory phagocytotic response]].<ref name="kamboj">{{cite journal |
===Bowel perforation===
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==== Asthma ====
With asthma, two hypotheses have been posed to explain its rising prevalence in the developed world. The [[hygiene hypothesis]] posits that children in the developed world are not exposed to enough microbes and thus may contain lower prevalence of specific bacterial taxa that play protective roles.<ref name=":2">{{cite journal |doi=10.1126/scitranslmed.aab2271 |pmid=26424567 |title=Early infancy microbial and metabolic alterations affect risk of childhood asthma |journal=Science Translational Medicine |volume=7 |issue=307 |pages=307ra152 |year=2015 |last1=Arrieta |first1=Marie-Claire |last2=Stiemsma |first2=Leah T |last3=Dimitriu |first3=Pedro A |last4=Thorson |first4=Lisa |last5=Russell |first5=Shannon |last6=Yurist-Doutsch |first6=Sophie |last7=Kuzeljevic |first7=Boris |last8=Gold |first8=Matthew J |last9=Britton |first9=Heidi M |last10=Lefebvre |first10=Diana L |last11=Subbarao |first11=Padmaja |last12=Mandhane |first12=Piush |last13=Becker |first13=Allan |last14=McNagny |first14=Kelly M |last15=Sears |first15=Malcolm R |last16=Kollmann |first16=Tobias |last17=Mohn |first17=William W |last18=Turvey |first18=Stuart E |last19=Brett Finlay |first19=B
==== Diabetes mellitus type 1 ====
The connection between the gut microbiota and [[diabetes mellitus type 1|diabetes mellitus type 1]] has also been linked to SCFAs, such as [[butyrate]] and acetate. Diets yielding butyrate and acetate from bacterial fermentation show increased [[Regulatory T cell|T<sub>reg</sub>]] expression.<ref>{{
=== Obesity and metabolic syndrome ===
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== Other animals ==
The composition of the human gut microbiome is similar to that of the other great apes. However, humans' gut biota has decreased in diversity and changed in composition since our evolutionary split from ''Pan''.<ref name="ReferenceC">{{
In addition to humans and vertebrates, some insects also have complex and diverse gut microbiota that play key nutritional roles.<ref name="Engel">{{cite journal |last1=Engel |first1=P. |last2=Moran |first2=N. |year=2013 |title=The gut microbiota of insects–diversity in structure and function |journal=FEMS Microbiology Reviews |volume=37 |issue=5 |pages=699–735 |doi=10.1111/1574-6976.12025 |pmid=23692388|doi-access=free }}</ref> Microbial communities associated with [[termite]]s can constitute a majority of the weight of the individuals and perform important roles in the digestion of [[lignocellulose]] and [[nitrogen fixation]].<ref>{{cite journal |last1=Brune |first1=A. |year=2014 |title=Symbiotic digestion of lignocellulose in termite guts |journal=Nature Reviews Microbiology |volume=12 |issue=3 |pages=168–180 |doi=10.1038/nrmicro3182 |pmid=24487819 }}</ref> It is known that the disruption of gut microbiota of termites using agents like antibiotics<ref>{{cite journal |
For more than 51 years it has been known that the administration of low doses of antibacterial agents promotes the growth of farm animals to increase weight gain.<ref name=cho2012>{{cite journal |doi=10.1038/nature11400 |title=Antibiotics in early life alter the murine colonic microbiome and adiposity |year=2012 |last1=Cho |first1=I. |last2=Yamanishi |first2=S. |last3=Cox |first3=L. |last4=Methé |first4=B. A. |last5=Zavadil |first5=J. |last6=Li |first6=K. |last7=Gao |first7=Z. |last8=Mahana |first8=D. |last9=Raju |first9=K. |last10=Teitler |first10=I. |last11=Li |first11=H. |last12=Alekseyenko |first12=A. V. |last13=Blaser |first13=M. J. |journal=Nature |volume=488 |issue=7413 |pages=621–626 |pmid=22914093 |pmc=3553221|bibcode=2012Natur.488..621C }}</ref>
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