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Microbiome

2026-07-17T09:21:28Z

Tuxedocaspy:/* Gut flora */ reminder to cite a needed source

{{Cleanup/Citations needed | date = Mar 2021}}
The '''microbiome''' is the community of microorganisms (such as [[bacteria]], [[fungus|fungi]], and [[virus]]es) that inhabit a particular environment, especially the human body.
<ref>{{Cite web|website=Merrian-Webster Medical Dictionary|access-date=2021-02-20 | title = Definition of MICROBIOME|url=https://www.merriam-webster.com/dictionary/microbiome}}</ref>

==Anatomical areas==
The microorganisms live on the skin and genitals and in the [[nose microbiome|nose]], ears, [[oral microbiome|mouth]] and [[gut microbiome|gut]]. [[Dysbiosis]] or an imbalance in this community may play a role in the pathophysiology of [[chronic fatigue syndrome]].<ref>{{Cite journal|title=Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome|date=2017-04-26|url=https://pubmed.ncbi.nlm.nih.gov/28441964/|journal=Microbiome|volume=5|issue=1|pages=44|last=Nagy-Szakal|first=Dorottya|last2=Williams|first2=Brent L.|last3=Mishra|first3=Nischay|last4=Che|first4=Xiaoyu|last5=Lee|first5=Bohyun|last6=Bateman|first6=Lucinda|last7=Klimas|first7=Nancy G.|last8=Komaroff|first8=Anthony L.|last9=Levine|first9=Susan|last10=Montoya|first10=Jose G.|last11=Peterson|first11=Daniel L.|doi=10.1186/s40168-017-0261-y|pmc=5405467|pmid=28441964|issn=2049-2618}}</ref>

===Gut flora===

The [[gut microbiome]] is a complex community of trillions of microorganisms residing in the intestines. Around 99% of bacteria in the gut are [[Anaerobic bacteria|anaerobes]].<ref>{{Cite journal|title=Commensal Bacteria: An Emerging Player in Defense Against Respiratory Pathogens|date=October 2003|url=https://www.sciencedirect.com/science/article/abs/pii/S1369527403001176|journal=Current Opinion in Microbiology|volume=6|issue=5|pages=457-461|last=Vendantam|first=Gayatari|last2=Hecht|first2=David}}</ref>

An individual's gut microbiome begins as a sample from the maternal microbiome taken during childbirth. While proportions and specific diversities of bacteria vary between individuals, scientific evidence shows delivery method influences the founding population of intestinal bacteria. Vaginal births are seeded with bacteria found in the birth canal, including ''Bacteroides'', ''Actinobacteria, Lactobacillus, Bifidobacteria.'' Caesarean section births are taken from microbes found on the skin and in the environment, ranging from ''Staphylococcus, Enterococcus, Clostridium, Streptococcus''.<ref>Coelho GDP, Ayres LFA, Barreto DS, Henriques BD, Prado MRMC, Passos CMD. Acquisition of microbiota according to the type of birth: an integrative review. Rev Lat Am Enfermagem. 2021 Jul 19;29:e3446. doi: 10.1590/1518.8345.4466.3446. PMID: 34287544; PMCID: PMC8294792.</ref> Gut microbiomes founded by c-section births are less phylogenetically diverse and alter colonization of normal gut microbiota during early infancy,<ref>Nicholas A. Bokulich ''et al.'', Antibiotics, birth mode, and diet shape microbiome maturation during early life.''Sci. Transl. Med.'''''8''',343ra82-343ra82(2016).DOI:10.1126/scitranslmed.aad7121</ref> with studied links to immune disorders such as allergies.<ref>Zhang C, Li L, Jin B, Xu X, Zuo X, Li Y, Li Z. The Effects of Delivery Mode on the Gut Microbiota and Health: State of Art. Front Microbiol. 2021 Dec 23;12:724449. doi: 10.3389/fmicb.2021.724449. PMID: 35002992; PMCID: PMC8733716.</ref> Bacterial populations are known to stimulate immune development within infants during a period of plasticity, with certain metabolites priming immune cells during their maturation process, such as small-chain fatty acids promoting intestinal regulatory T-cells.<ref>Sanidad KZ, Zeng MY. Neonatal gut microbiome and immunity. Curr Opin Microbiol. 2020 Aug;56:30-37. doi: 10.1016/j.mib.2020.05.011. Epub 2020 Jul 4. PMID: 32634598; PMCID: PMC8729197.</ref> Furthermore, these initial, established populations serve to prevent colonization by pathogens.

Compositions change with an infant's dietary transition. At one year, the gut microbiome resembles an adult composition.{{Citation needed}}

A 2021 study by Damiano found significant differences in the composition of gut bacteria between CFS/ME patients and healthy controls. People with ME/CFS had:<ref name="Damiano2021" />

* Higher relative abundance of bacteria in the genus ''Bacteroides'' (phylum Bacteriodetes) and the genus ''Phascolarctobacterium'' (phylum Firmicutes)
* Lower relative abundance of bacteria in the genus ''Anaerostipes'' and genus ''Ruminococcus'' (both from phylum Firmicutes)

However, the study authors were unable to determine if the alteration of the microbiome is a cause or a consequence of the onset of CFS/ME, or if the changes in the microbial composition are related to any of the several secondary symptoms.<ref name="Damiano2021" />

Damiano et al. suggest the intestinal microbial profile recorded in their study is consistent with the profiles reported for other autoimmune conditions. For example, a 2021 review on pediatric [[inflammatory bowel disease]] found a reduced abundance of bacteria in genus ''Anaerostipes.''<ref>{{Cite journal|title=Gut Microbiota Profile in Pediatric Patients With Inflammatory Bowel Disease: A Systematic Review|date=2021-02-02|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884334/|journal=Frontiers in Pediatrics|volume=9|pages=626232|last=Zhuang|first=Xiaojun|last2=Liu|first2=Caiguang|last3=Zhan|first3=Shukai|last4=Tian|first4=Zhenyi|last5=Li|first5=Na|last6=Mao|first6=Ren|last7=Zeng|first7=Zhirong|last8=Chen|first8=Minhu|doi=10.3389/fped.2021.626232|pmc=7884334|pmid=33604319|issn=2296-2360}}</ref> A 2014 study found a higher abundance of the genus ''Bacteroides'' in people with [[systemic lupus erythematous]].<ref>{{Cite journal|title=Intestinal Dysbiosis Associated with Systemic Lupus Erythematosus|date=September 30, 2014|url=https://journals.asm.org/doi/10.1128/mbio.01548-14|journal=mBio|volume=5|issue=5|last=Hevia|first=Arancha|last2=Milani|first2=Christian|last3=Lopez|first3=Patricia|last4=Cuervo|first4=Adriana|last5=Arboleya|first5=Silvia|last6=Duranti|first6=Sabrina|last7=Turroni|first7=Francesca|last8=Suarez|first8=Ana|last9=Gueimonde|first9=Miguel|doi=10.1128/mbio.01548-14}}</ref>

===Oral flora===

The microbiome in the oral cavity (mouth and throat) is the second largest after the gut microbiome. The state of your oral microbiome can affect the rest of your body in two major ways<ref>{{Cite journal|title=Oral microbiota in human systematic diseases|date=2022-03-02|url=https://www.nature.com/articles/s41368-022-00163-7|journal=International Journal of Oral Science|volume=14|issue=1|pages=1–11|last=Peng|first=Xian|last2=Cheng|first2=Lei|last3=You|first3=Yong|last4=Tang|first4=Chengwei|last5=Ren|first5=Biao|last6=Li|first6=Yuqing|last7=Xu|first7=Xin|last8=Zhou|first8=Xuedong|language=en|doi=10.1038/s41368-022-00163-7|pmc=8891310|pmid=35236828|issn=2049-3169}}</ref>:

# Microorganisms in the mouth can travel "downstream" to the gut microbiome.
# An oral infection can cause bacteria and their metabolites (digestive byproducts) to enter the bloodstream. This can activate the immune system and cause widespread inflammation.

The 2021 Damiano study above also found differences in the composition of oral bacteria between CFS/ME patients and healthy controls. People with CFS/ME had higher relative abundance of bacteria in the genus ''Rothia'' (phylum Actinobacteria).<ref name="Damiano2021" />

==ME/CFS==

A growing body of evidence suggests that an [[dysbiosis|altered microbiome]]; [[intestinal permeability|mucosal barrier]] dysfunction;<ref name="Lakhan2010">{{Citation| doi = 10.1186/1743-7075-7-79| issn = 1743-7075| volume = 7|issue = | pages = 79| last1 = Lakhan | first1 = Shaheen E| last2 = Kirchgessner | first2 = Annette| title = Gut inflammation in chronic fatigue syndrome| journal = Nutrition & Metabolism| access-date = 2016-12-13 | date = 2010-10-12| url = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964729/| pmid = 20939923}}</ref> the translocation or crossing of bacteria from the gut into the [[blood|bloodstream]]; and subsequent immune response may pay a role in the pathophysiology of [[myalgic encephalomyelitis]]\[[chronic fatigue syndrome]].

===Immune response===

A study of 128 [[ME/CFS]] patients found significantly increased [[IgA]] response to [[lipopolysaccharide]]s from the cell walls of commensal bacteria. Increased IgA response was associated with increased serum [[interleukin 1|IL-1]], [[TNFα]], [[neopterin]] and [[elastase]]. The study concluded that increased translocation of commensal bacteria may be responsible for the disease activity in some ME/CFS patients.<ref name="Maes2012" />

===Dysbiosis===
:''{{main|page_name =Dysbiosis}}''

There is strong evidence that [[dysbiosis]] or an imbalance in the microbial ecology of the gut plays a role in the symptoms of [[ME/CFS]]. ME/CFS patients have higher levels of [[D-lactic acid]] bacteria,<ref>{{Cite journal | last = Sheedy | first = John R. | authorlink = | last2 = Wettenhall | first2 = Richard E. H. | authorlink2 = | last3 = Scanlon | first3 = Denis | authorlink3 = | last4 = Gooley | first4 = Paul R. | authorlink4 = Paul Gooley | last5 = Lewis | first5 = Donald P. | authorlink5 = Donald Lewis | last6 = McGregor | first6 = Neil | authorlink6 = Neil McGregor | last7 = Stapleton | first7 = David I. | last8 = Butt | first8 = Henry L. | authorlink8 = Henry Butt | last9 = De Meirleir | first9 = Kenny L. | authorlink9 = Kenny De Meirleir | date = Jul 2009 | title = Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome|url=https://pubmed.ncbi.nlm.nih.gov/19567398|journal=In Vivo (Athens, Greece)|volume=23|issue=4 | pages = 621–628|doi=|issn=0258-851X|pmc=|pmid=19567398|access-date=|quote=|via=}}</ref> decreased levels of [[bifidobacteria]],<ref>{{Cite journal | last = Logan | first = Alan C | authorlink = | last2 = Venket Rao | first2 = A | authorlink2 = | last3 = Irani | first3 = Dinaz | authorlink3 = | date = Jun 2003 | title = Chronic fatigue syndrome: lactic acid bacteria may be of therapeutic value|url=https://linkinghub.elsevier.com/retrieve/pii/S0306987703000963|journal=Medical Hypotheses|language=en|volume=60|issue=6 | pages = 915–923|doi=10.1016/S0306-9877(03)00096-3|pmc=|pmid=|access-date=|quote=|via=}}</ref> and may suffer from [[small intestinal bacterial overgrowth]] (SIBO) at higher rates.{{citation needed}}

===Exercise===

A small study of ten CFS patients found significant changes in the composition of the microbiome and increased bacterial translocation (movement from the [[gastrointestinal system|intestine]] into the [[blood|bloodstream]] following [[exercise]]). In the blood, the study found increased [[Clostridium]] fifteen minutes after exercise and increased [[bacilli]] 48 hours later.<ref name="Shukla2015" /><ref>{{citation | last = Johnson | first = Cort | date = December 21, 2015 | title = Exercise Triggers Gut Changes in Chronic Fatigue Syndrome (ME/CFS)|url= http://www.cortjohnson.org/blog/2015/12/21/exercise-gut-chronic-fatigue-syndrome-me-cfs/|newspaper= HealthRising|location= Houston|access-date= 2016-12-12}}</ref>{{citation needed | date = 2021 | reason=Add original research}}

===Sleep===

In a very small study, CFS patients treated with [[erythromycin]] who had clinical response (i.e., reduced [[streptococcus]]) had improved sleep. Higher [[lactobacillus]] was associated with poorer mood.<ref name="Jackson2015" />

===Gender===

A study of 274 [[ME/CFS]] patients found sex-specific interactions between [[Firmicute]]s ([[Clostridium]], [[Streptococcus]], [[Lactobacillus]] and [[Enterococcus]]) and ME/CFS symptoms (including neurological, immune and mood symptoms) and symptoms in spite of similar overall composition across sexes.<ref name="Wallis2016" />

==Factors affecting microbiome==

=== Diet ===

The food we eat has a considerable effect on the composition of the intestinal microbiota.<ref name="Maslowski2011" />

=== Viral infection ===

Viruses can cause shifts in the gut microbiome.

In mice, the influenza virus leads to injury of both the lungs (the primary site of infection) and the intestinal tract, even when there is no evidence of viral replication in the gut, and causes decreases [[Lactobacillus]] and [[Lactococcus]] species and increases in [[Enterobacteriaceae]].<ref>{{citation | last = Racaniello | first = Vincent | date = 10 December 2014 | title = How influenza virus infection might lead to gastrointestinal symptoms|url= http://www.virology.ws/2014/12/10/how-influenza-virus-infection-might-lead-to-gastrointestinal-symptoms/|newspaper= Virology Blog|location= New York|access-date= 2016-12-12}}</ref>

=== Pregnancy ===

Gut microbiota change dramatically from the first trimester to the third trimester of [[pregnancy]]. During the first trimester, there is an overrepresentation of 18 bacterial groups, mainly [[Faecalibacterium]], a [[butyrate]] producer that has been shown to improve symptoms of [[inflammatory bowel disease]].<ref name="koren2012" />

During the third trimester, populations of pro-inflammatory [[bacteria]] species such as [[proteobacteria]] and [[actinobacteria]] increase and there is a reduction in diversity. Populations of [[Faecalibacterium]] decrease.<ref name="koren2012" /> Overall bacterial load increases over the course of pregnancy.<ref>http://www.scopus.com/record/display.uri?eid=2-s2.0-53849104768&origin=inward&txGid=B73C4858FB9D5F216C9F222F22386A44.iqs8TDG0Wy6BURhzD3nFA%3a2</ref>

===Nervous system===

The intestinal microbiota play a major role in the [[gut-brain axis]] with consequences for both neurological development and host behavior.

=== Stress ===

There is growing evidence that the microbiome plays an important role in the [[stress]] response. Animals raised in a germ-free environment show an exaggerated [[HPA]] response to psychological stress which normalizes when [[Bifidobacterium infantis|''Bifidobacterium infantis'']] is introduced. [[Escherichia coli|''Escherichia coli'']] can activate the HPA.<ref name="Dinan2012" />

Stress also increases [[intestinal permeability]].

==Planned studies==
British patient charity [[Invest in ME]] is raising funds for a gut microbiome study at the University of East Anglia in the United Kingdom led by professor [[Simon Carding]].<ref>[http://www.investinme.org/LDR%20UK%20Gut%20Microbiota.htm Invest in ME – UK gut microbiota research]</ref>

Funds are being raised by patients (originally led by the late [[Vanessa Li]]) for [[Ian Lipkin]] and [[Mady Hornig]] of Columbia University in the United States to perform a study, called the [[ME/CFS Monster Study]], looking at many areas including the gut microbiome in [[ME/CFS]] patients. Fundraising efforts are led by the [[Microbe Discovery Project]].

==Notable studies==
*2009, Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome<ref>{{Cite journal | last = Sheedy | first = John R. | authorlink = | last2 = Wettenhall | first2 = Richard E. H. | authorlink2 = | last3 = Scanlon | first3 = Denis | authorlink3 = | last4 = Gooley | first4 = Paul R. | authorlink4 = Paul Gooley | last5 = Lewis | first5 = Donald P. | authorlink5 = Donald Lewis | last6 = McGregor | first6 = Neil | authorlink6 = Neil McGregor | last7 = Stapleton | first7 = David I. | last8 = Butt | first8 = Henry L. | authorlink8 = Henry Butt | last9 = De Meirleir | first9 = Kenny L. | authorlink9 = Kenny De Meirleir | date = Jul 2009 | title = Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome|url=https://pubmed.ncbi.nlm.nih.gov/19567398|journal=In Vivo (Athens, Greece)|volume=23|issue=4 | pages = 621–628|doi=|issn=0258-851X|pmc=|pmid=19567398|access-date=|quote=|via=}}</ref> - [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5843715/ (Full Text)]
*2010, [https://www.ncbi.nlm.nih.gov/pubmed/20939923 Gut inflammation in chronic fatigue syndrome]<ref name="Lakhan2010" />
*2012, [https://www.ncbi.nlm.nih.gov/pubmed/21967891 Increased IgA responses to the LPS of commensal bacteria is associated with inflammation and activation of cell-mediated immunity in chronic fatigue syndrome]<ref name="Maes2012" />
*2012, [http://www.cdd.com.au/pdf/publications/All%20Publications/2013%20-%20The%20GI%20microbiome%20and%20its%20role%20in%20CFS%20-%20ACNEM%20paper.pdf/ The GI Microbiome and its Role in Chronic Fatigue Syndrome: A Summary of Bacteriotherapy]<ref name="Borody2012" />
*2013, [https://www.ncbi.nlm.nih.gov/pubmed/23791918 High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients]<ref name="Fremont2013" />
*2015, [https://www.ncbi.nlm.nih.gov/pubmed/26779319 Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study]<ref name="Jackson2015" />
*2015, [https://www.ncbi.nlm.nih.gov/pubmed/26683192 Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)]<ref name="Shukla2015" />
*2016, [https://www.ncbi.nlm.nih.gov/pubmed/27634186 The role of microbiota and intestinal permeability in the pathophysiology of autoimmune and neuroimmune processes with an emphasis on Inflammatory Bowel Disease Type 1 Diabetes and Chronic Fatigue Syndrome]<ref name="Morris, 2016" />
*2016, [https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0171-4 Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome]<ref>{{Cite journal | last = Giloteaux | first = Ludovic | authorlink = Ludovic Giloteaux | last2 = Goodrich | first2 = Julia K. | authorlink2 = | last3 = Walters | first3 = William A. | authorlink3 = | last4 = Levine | first4 = Susan M. | authorlink4 = Susan Levine | last5 = Ley | first5 = Ruth E. | authorlink5 = | last6 = Hanson | first6 = Maureen R. | authorlink6 = Maureen Hanson | date = Dec 2016 | title = Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome|url=http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0171-4|journal=Microbiome|language=en|volume=4|issue=1|pages=|doi=10.1186/s40168-016-0171-4|issn=2049-2618|pmc=4918027|pmid=27338587|quote=|via=}}</ref>
*2016, [http://www.nature.com/articles/srep19171 Support for the Microgenderome: Associations in a Human Clinical Population]<ref name="Wallis2016" />
*2017, Fecal metagenomic profiles in subgroups of patients with [[ME/CFS|myalgic encephalomyelitis/chronic fatigue syndrome]]<ref name="Nagy-Szakal, 2017" /> [https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0261-y (Full Text)]
*2018, Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome?<ref name="Newberry, 2018" />
*2018, [[Chronic fatigue syndrome]] patients have alterations in their oral microbiome composition and function<ref>{{Cite journal | last = Wang | first = Taiwu | last2 = Yu | first2 = Lei | last3 = Xu | first3 = Cong | last4 = Pan | first4 = Keli | last5 = Mo | first5 = Minglu | last6 = Duan | first6 = Mingxiang | last7 = Zhang | first7 = Yao | last8 = Xiong | first8 = Hongyan | date = 2018-09-11 | title = Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function | url =https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203503|journal=PLOS ONE|language=en|volume=13|issue=9| pages = e0203503|doi=10.1371/journal.pone.0203503|issn=1932-6203}}</ref> [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203503 (Full Text)]
*2018, Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the era of the human microbiome: persistent pathogens drive chronic symptoms by interfering with host [[metabolism]], [[gene expression]] and [[Immune system|immunity]]<ref>{{Cite journal | last = Proal | first = Amy | authorlink = Amy Proal | last2 = Marshall | first2 = Trevor | authorlink2 = Trevor Marshall | date = Nov 2018 | title = Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the era of the human microbiome: persistent pathogens drive chronic symptoms by interfering with host metabolism, gene expression and immunity|url=https://www.frontiersin.org/articles/10.3389/fped.2018.00373/full|journal=Frontiers in Pediatrics|volume=|issue=|pages=|quote=|via=|doi=10.3389/fped.2018.00373}}</ref> [https://www.frontiersin.org/articles/10.3389/fped.2018.00373/full (Full text)]
* 2021, Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME)<ref name="Damiano2021">{{Cite journal | last = Lupo | first = Giuseppe Francesco Damiano | author-link = | last2 = Rocchetti | first2 = Gabriele | authorlink2 = | last3 = Lucini | first3 = Luigi | authorlink3 = | last4 = Lorusso | first4 = Lorenzo | authorlink4 = Lorenzo Lorusso | last5 = Manara | first5 = Elena | authorlink5 = | last6 = Bertelli | first6 = Matteo | authorlink6 = | last7 = Puglisi | first7 = Edoardo | last8 = Capelli | first8 = Enrica | authorlink8 = Enrica Capelli | date = March 2021 | title = Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME)|url=http://www.nature.com/articles/s41598-021-86425-6|journal=Scientific Reports|language=en|volume=11|issue=1 | pages = 7043|doi=10.1038/s41598-021-86425-6|issn=2045-2322|pmc=|pmid=33782445|access-date=|quote=|via=}}</ref> - [https://www.nature.com/articles/s41598-021-86425-6 (Full text)]

==Commercial testers==
*[[uBiome]]

==Academic projects==
*[[American Gut]]
*[[British Gut Project]]

==Learn more==
*[https://en.wikipedia.org/wiki/Microbiota Wikipedia - Microbiota]
*[[CFS Remission]] ([[Ken Lassesen]]'s blogs about experimental ME/CFS microbiome and probiotic treatments)
*2016, [https://cfsremission.wordpress.com/2016/08/09/what-should-be-in-the-ideal-microbiome-test-for-cfs/ What should be in the ideal microbiome test for CFS] ''[[CFS Remission]]''
*2016, [https://cfstreatment.blogspot.co.uk/2016/07/all-in-your-gut.html It's All in Your Gut] ''[[Onward Through the Fog]]''
*2016, [http://well.blogs.nytimes.com/2016/07/07/gut-bacteria-are-different-in-people-with-chronic-fatigue-syndrome/ Gut Bacteria Are Different in People With Chronic Fatigue Syndrome] ''The New York Times''<ref>{{citation | last = Bakalar | first = Nicholas | date = 7 July 2016 | title = Gut Bacteria Are Different in People With Chronic Fatigue Syndrome|url= http://well.blogs.nytimes.com/2016/07/07/gut-bacteria-are-different-in-people-with-chronic-fatigue-syndrome/|newspaper= The New York Times|location= |access-date= 2016-12-13}}</ref>
*2016, [https://www.washingtonpost.com/news/to-your-health/wp/2016/06/30/new-study-shows-chronic-fatigue-isnt-just-in-your-head-it-may-have-to-do-with-your-gut/ New study shows chronic fatigue syndrome may have to do with gut microbes] ''The Washington Post''<ref>{{citation | last = Cha | first = Ariana Eunjung | date = Jun 30, 2016 | title = New study shows chronic fatigue syndrome may have to do with gut microbes|url= https://www.washingtonpost.com/news/to-your-health/wp/2016/06/30/new-study-shows-chronic-fatigue-isnt-just-in-your-head-it-may-have-to-do-with-your-gut/|newspaper= The Washington Post|location= |access-date= 2016-12-13}}</ref>
*2016, [http://news.cornell.edu/stories/2016/06/indicator-chronic-fatigue-syndrome-found-gut-bacteria Indicator of chronic fatigue syndrome found in gut bacteria] ''Cornell Chronicle''<ref>{{citation | last = Ramanujan | first = Krishna | date = 24 June 2016 | title = Indicator of chronic fatigue syndrome found in gut bacteria|url= http://news.cornell.edu/stories/2016/06/indicator-chronic-fatigue-syndrome-found-gut-bacteria|newspaper= Cornell Chronicle|location= New York|access-date= 2016-12-13}}</ref>
*2016, [http://www.cortjohnson.org/blog/2016/02/21/gut-chronic-fatigue-syndrome-gender-differences/ Gender Gut Wars: Australian ME/CFS Study Suggests Different Gut Treatment Protocols Needed For Men and Women] ''[[Health Rising]]''<ref>{{citation | last = Johnson | first = Cort | date = 21 February 2016 | title = Gender Gut Wars: Australian ME/CFS Study Suggests Different Gut Treatment Protocols Needed For Men and Women | url = http://www.cortjohnson.org/blog/2016/02/21/gut-chronic-fatigue-syndrome-gender-differences/|newspaper= HealthRising|location= Houston|access-date= 2016-12-13}}</ref>
*[https://cfsremission.wordpress.com/2016/04/02/vitamin-d-and-the-microbiome/ Vitamin D and the Microbiome] ''[[CFS Remission]]''

==See also==
*[[Probiotics]]
*[[Gastrointestinal system]]
*[[Helminthic therapy]]
*[[Ken Lassesen's model]]
*[[Nasal microbiome]]
*[[Oral microbiome]]
*[[Indoor microbiome]]
*[[Dr Markov's chronic bacterial intoxication syndrome (CBIS) theory of ME/CFS]] (Dr Markov has evidence that ME/CFS is caused by a dysbiosis in the kidneys)

==References==
<references>
<ref name="Lakhan2010">{{Citation| doi = 10.1186/1743-7075-7-79| issn = 1743-7075| volume = 7|issue = | pages = 79| last1 = Lakhan | first1 = Shaheen E| last2 = Kirchgessner | first2 = Annette| title = Gut inflammation in chronic fatigue syndrome| journal = Nutrition & Metabolism| access-date = 2016-12-13 | date = 2010-10-12| url = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964729/| pmid = 20939923}}</ref>
<ref name="Maes2012">{{Citation| doi = 10.1016/j.jad.2011.09.010| issn = 1573-2517| volume = 136 | issue = 3| pages = 909–917| last1 = Maes | first1 = Michael | last2 = Twisk | first2 = Frank N.M. | last3 = Kubera | first3 = Marta | last4 = Ringel | first4 = Karl | last5 = Leunis | first5 = Jean-Claude | last6 = Geffard | first6 = Michel| title = Increased IgA responses to the LPS of commensal bacteria is associated with inflammation and activation of cell-mediated immunity in chronic fatigue syndrome| journal = Journal of Affective Disorders| date = February 2012 | pmid = 21967891}}</ref>
<ref name="Shukla2015">{{Citation| doi = 10.1371/journal.pone.0145453| issn = 1932-6203| volume = 10 | issue = 12| pages = 0145453| last1 = Shukla | first1 = Sanjay K. | last2 = Cook | first2 = Dane | last3 = Meyer | first3 = Jacob| last4 = Vernon | first4 = Suzanne D. | last5 = Le | first5 = Thao | last6 = Clevidence | first6 = Derek | last7 = Robertson | first7 = Charles E. | last8 = Schrodi | first8 = Steven J. | last9 = Yale | first9 = Steven | last10 = Frank | first10 = Daniel N.| title = Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)| journal = PLOS ONE| access-date = 2016-12-13 | date = 2015-12-18| url = http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145453}}</ref>
<ref name="Jackson2015">{{citation | last1 = Jackson | first1 = Melinda L | authorlink1 = Melinda Jackson | last2 = Butt | first2 = Henry L | authorlink2 = Henry Butt | last3 = Ball | first3 = Michelle | authorlink3 = Michelle Ball | last4 = Lewis | first4 = Donald P | authorlink4 = Donald Lewis | last5 = Bruck | first5 = Dorothy | authorlink5 = Dorothy Bruck | title = Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study | journal = Sleep Science | volume = 8 | issue = 3 | pages = 124-133 | date = 23 Oct 2015 | pmid = 26779319 | doi = 10.1016/j.slsci.2015.10.001 | url = http://www.sciencedirect.com/science/article/pii/S1984006315000632 }}</ref>
<ref name="Wallis2016">{{citation | last1 = Wallis | first1 = Amy| authorlink1 = Amy Wallis | last2 = Butt | first2 = Henry L | authorlink2 = Henry Butt | last3 = Ball | first3 = Michelle | authorlink3 = Michelle Ball | last4 = Lewis | first4 = Donald P | authorlink4 = Donald Lewis | last5 = Bruck | first5 = Dorothy | authorlink5 = Dorothy Bruck | title = Support for the Microgenderome: Associations in a Human Clinical Population | journal = Scientific Reports | volume = | pages = | date = 13 Jan 2016 |issue = | pmid = 26757840 | doi = 10.1038/srep19171 | url = http://www.nature.com/articles/srep19171 }}</ref>
<ref name="Maslowski2011">{{Citation| doi = 10.1038/ni0111-5| issn = 1529-2916| volume = 12 | issue = 1| pages = 5–9| last1 = Maslowski | first1 = Kendle M. | last2 = Mackay | first2 = Charles R.| title = Diet, gut microbiota and immune responses| journal = Nature Immunology | date = January 2011 | pmid = 21169997}}</ref>
<ref name="koren2012">{{Citation| doi = 10.1016/j.cell.2012.07.008| issn = 1097-4172| volume = 150 | issue = 3| pages = 470–480| last1 = Koren | first1 = Omry | last2 = Goodrich | first2 = Julia K. | last3 = Cullender | first3 = Tyler C. | last4 = Spor | first4 = Aymé| last5 = Laitinen | first5 = Kirsi | last6 = Bäckhed | first6 = Helene Kling | last7 = Gonzalez | first7 = Antonio | last8 = Werner | first8 = Jeffrey J. | last9 = Angenent | first9 = Largus T. | last10 = Knight | first10 = Rob| last11 = Bäckhed | first11 = Fredrik | last12 = Isolauri | first12 = Erika | last13 = Salminen | first13 = Seppo | last14 = Ley | first14 = Ruth E.| title = Host remodeling of the gut microbiome and metabolic changes during pregnancy| journal = Cell| date = 2012-08-03 | pmid = 22863002}}</ref>
<ref name="Dinan2012">{{Citation| doi = 10.1016/j.psyneuen.2012.03.007| issn = 0306-4530| volume = 37 | issue = 9| pages = 1369–1378| last1 = Dinan | first1 = Timothy G. | last2 = Cryan | first2 = John F.| title = Regulation of the stress response by the gut microbiota: Implications for psychoneuroendocrinology| journal = Psychoneuroendocrinology| access-date = 2016-12-13 | date = September 2012| url = http://www.sciencedirect.com/science/article/pii/S0306453012000935}}</ref>
<ref name="Fremont2013">{{Citation| doi = 10.1016/j.anaerobe.2013.06.002| issn = 1095-8274| volume = 22 | issue = | pages = 50–56| last1 = Frémont | first1 = Marc| last2 = Coomans | first2 = Danny | last3 = Massart | first3 = Sebastien | last4 = De Meirleir | first4 = Kenny| title = High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients| journal = Anaerobe | date = August 2013 | pmid = 23791918}}</ref>
<ref name="Borody2012">{{Citation| issn = 1328-8040| volume = 31 | issue = 3| pages = 3| last1 = Borody | first1 = Thomas J. | last2 = Nowak | first2 = Anna | last3 = Finlayson | first3 = Sarah| title = The GI microbiome and its role in Chronic Fatigue Syndrome: A summary of bacteriotherapy| journal = Journal of the Australasian College of Nutritional and Environmental Medicine| access-date = 2016-12-13 | date = December 2012| url = http://www.cdd.com.au/pdf/publications/All%20Publications/2013%20-%20The%20GI%20microbiome%20and%20its%20role%20in%20CFS%20-%20ACNEM%20paper.pdf/}}</ref>
<ref name="Morris, 2016">{{Citation | last1 = Morris | first1 = Gerwyn | authorlink1 = Gerwyn Morris | last2 = Berk | first2 = Michael | authorlink2 = Michael Berk | last3 = Carvalho | first3 = A.F. | authorlink3 = | last4 = Caso | first4 = J.R. | authorlink4 = | last5 = Sanz | first5 = Y. | authorlink5 = | last6 = Maes | first6 = Michael | authorlink6 = Michael Maes | title = The role of microbiota and intestinal permeability in the pathophysiology of autoimmune and neuroimmune processes with an emphasis on Inflammatory Bowel Disease Type 1 Diabetes and Chronic Fatigue Syndrome. | journal = Current Pharmaceutical Design | volume = | issue = | pages = | date = 2016 | pmid = 27634186 }}</ref>
<ref name="Nagy-Szakal, 2017">{{Citation | last1 = Nagy-Szakal | first1 = Dorottya | authorlink1 = Dorottya Nagy-Szakal | last2 = Williams | first2 = Brent L. | authorlink2 = | last3 = Mishra | first3 = Nischay | authorlink3 = | last4 = Che | first4 = Xiaoyu | authorlink4 = | last5 = Lee | first5 = Bohyun | authorlink5 = | last6 = Bateman | first6 = Lucinda | authorlink6 = Lucinda Bateman | last7 = Klimas | first7 = Nancy G. | authorlink7 = Nancy Klimas | last8 = Komaroff | first8 = Anthony L. | authorlink8 = Anthony Komaroff | last9 = Levine | first9 = Susan | authorlink9 = Susan Levine | last10 = Montoya | first10 = Jose G. | authorlink10 = Jose Montoya | last11 = Peterson | first11 = Daniel L. | authorlink11 = Daniel Peterson | last12 = Ramanan | first12 = Devi | authorlink12 = | last13 = Jain | first13 = Komal | authorlink13 = | last14 = Eddy | first14 = Meredith L. | authorlink14 = | last15 = Hornig | first15 = Mady | authorlink15 = Mady Hornig | last16 = Lipkin | first16 = W. Ian | authorlink16 = Ian Lipkin | title = Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome | journal = Microbiome | volume = 5 | issue = 44 | pages = | date = 2017 | pmid = | doi = 10.1186/s40168-017-0261-y }}</ref>
<ref name="Newberry, 2018">{{Citation | last1 = Newberry | first1 = F. | authorlink1 = | last2 = Hsieh | first2 = S.-Y. | authorlink2 = | last3 = Wileman | first3 = T. | authorlink3 = | last4 = Carding | first4 = S.R. | authorlink4 = Simon Carding | title = Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome? | journal = Clinical Science | volume = 132 | issue = 5 | pages = 523–542 | date = 2018 | pmid = | doi = 10.1042/CS20171330 }}</ref>
</references>

[[Category:Body systems]]
[[Category:Microbiome]]

Microbiome

2026-07-17T09:19:59Z

Tuxedocaspy:/* Gut flora */ Further updates to initial gut microbiota

{{Cleanup/Citations needed | date = Mar 2021}}
The '''microbiome''' is the community of microorganisms (such as [[bacteria]], [[fungus|fungi]], and [[virus]]es) that inhabit a particular environment, especially the human body.
<ref>{{Cite web|website=Merrian-Webster Medical Dictionary|access-date=2021-02-20 | title = Definition of MICROBIOME|url=https://www.merriam-webster.com/dictionary/microbiome}}</ref>

==Anatomical areas==
The microorganisms live on the skin and genitals and in the [[nose microbiome|nose]], ears, [[oral microbiome|mouth]] and [[gut microbiome|gut]]. [[Dysbiosis]] or an imbalance in this community may play a role in the pathophysiology of [[chronic fatigue syndrome]].<ref>{{Cite journal|title=Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome|date=2017-04-26|url=https://pubmed.ncbi.nlm.nih.gov/28441964/|journal=Microbiome|volume=5|issue=1|pages=44|last=Nagy-Szakal|first=Dorottya|last2=Williams|first2=Brent L.|last3=Mishra|first3=Nischay|last4=Che|first4=Xiaoyu|last5=Lee|first5=Bohyun|last6=Bateman|first6=Lucinda|last7=Klimas|first7=Nancy G.|last8=Komaroff|first8=Anthony L.|last9=Levine|first9=Susan|last10=Montoya|first10=Jose G.|last11=Peterson|first11=Daniel L.|doi=10.1186/s40168-017-0261-y|pmc=5405467|pmid=28441964|issn=2049-2618}}</ref>

===Gut flora===

The [[gut microbiome]] is a complex community of trillions of microorganisms residing in the intestines. Around 99% of bacteria in the gut are [[Anaerobic bacteria|anaerobes]].<ref>{{Cite journal|title=Commensal Bacteria: An Emerging Player in Defense Against Respiratory Pathogens|date=October 2003|url=https://www.sciencedirect.com/science/article/abs/pii/S1369527403001176|journal=Current Opinion in Microbiology|volume=6|issue=5|pages=457-461|last=Vendantam|first=Gayatari|last2=Hecht|first2=David}}</ref>

An individual's gut microbiome begins as a sample from the maternal microbiome taken during childbirth. While proportions and specific diversities of bacteria vary between individuals, scientific evidence shows delivery method influences the founding population of intestinal bacteria. Vaginal births are seeded with bacteria found in the birth canal, including ''Bacteroides'', ''Actinobacteria, Lactobacillus, Bifidobacteria.'' Caesarean section births are taken from microbes found on the skin and in the environment, ranging from ''Staphylococcus, Enterococcus, Clostridium, Streptococcus''.<ref>Coelho GDP, Ayres LFA, Barreto DS, Henriques BD, Prado MRMC, Passos CMD. Acquisition of microbiota according to the type of birth: an integrative review. Rev Lat Am Enfermagem. 2021 Jul 19;29:e3446. doi: 10.1590/1518.8345.4466.3446. PMID: 34287544; PMCID: PMC8294792.</ref> Gut microbiomes founded by c-section births are less phylogenetically diverse and alter colonization of normal gut microbiota during early infancy,<ref>Nicholas A. Bokulich ''et al.'', Antibiotics, birth mode, and diet shape microbiome maturation during early life.''Sci. Transl. Med.'''''8''',343ra82-343ra82(2016).DOI:10.1126/scitranslmed.aad7121</ref> with studied links to immune disorders such as allergies.<ref>Zhang C, Li L, Jin B, Xu X, Zuo X, Li Y, Li Z. The Effects of Delivery Mode on the Gut Microbiota and Health: State of Art. Front Microbiol. 2021 Dec 23;12:724449. doi: 10.3389/fmicb.2021.724449. PMID: 35002992; PMCID: PMC8733716.</ref> Bacterial populations are known to stimulate immune development within infants during a period of plasticity, with certain metabolites priming immune cells during their maturation process, such as small-chain fatty acids promoting intestinal regulatory T-cells.<ref>Sanidad KZ, Zeng MY. Neonatal gut microbiome and immunity. Curr Opin Microbiol. 2020 Aug;56:30-37. doi: 10.1016/j.mib.2020.05.011. Epub 2020 Jul 4. PMID: 32634598; PMCID: PMC8729197.</ref> Furthermore, these initial, established populations serve to prevent colonization by pathogens.

Compositions change with an infant's dietary transition. At one year, the gut microbiome resembles an adult composition.

A 2021 study by Damiano found significant differences in the composition of gut bacteria between CFS/ME patients and healthy controls. People with ME/CFS had:<ref name="Damiano2021" />

* Higher relative abundance of bacteria in the genus ''Bacteroides'' (phylum Bacteriodetes) and the genus ''Phascolarctobacterium'' (phylum Firmicutes)
* Lower relative abundance of bacteria in the genus ''Anaerostipes'' and genus ''Ruminococcus'' (both from phylum Firmicutes)

However, the study authors were unable to determine if the alteration of the microbiome is a cause or a consequence of the onset of CFS/ME, or if the changes in the microbial composition are related to any of the several secondary symptoms.<ref name="Damiano2021" />

Damiano et al. suggest the intestinal microbial profile recorded in their study is consistent with the profiles reported for other autoimmune conditions. For example, a 2021 review on pediatric [[inflammatory bowel disease]] found a reduced abundance of bacteria in genus ''Anaerostipes.''<ref>{{Cite journal|title=Gut Microbiota Profile in Pediatric Patients With Inflammatory Bowel Disease: A Systematic Review|date=2021-02-02|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884334/|journal=Frontiers in Pediatrics|volume=9|pages=626232|last=Zhuang|first=Xiaojun|last2=Liu|first2=Caiguang|last3=Zhan|first3=Shukai|last4=Tian|first4=Zhenyi|last5=Li|first5=Na|last6=Mao|first6=Ren|last7=Zeng|first7=Zhirong|last8=Chen|first8=Minhu|doi=10.3389/fped.2021.626232|pmc=7884334|pmid=33604319|issn=2296-2360}}</ref> A 2014 study found a higher abundance of the genus ''Bacteroides'' in people with [[systemic lupus erythematous]].<ref>{{Cite journal|title=Intestinal Dysbiosis Associated with Systemic Lupus Erythematosus|date=September 30, 2014|url=https://journals.asm.org/doi/10.1128/mbio.01548-14|journal=mBio|volume=5|issue=5|last=Hevia|first=Arancha|last2=Milani|first2=Christian|last3=Lopez|first3=Patricia|last4=Cuervo|first4=Adriana|last5=Arboleya|first5=Silvia|last6=Duranti|first6=Sabrina|last7=Turroni|first7=Francesca|last8=Suarez|first8=Ana|last9=Gueimonde|first9=Miguel|doi=10.1128/mbio.01548-14}}</ref>

===Oral flora===

The microbiome in the oral cavity (mouth and throat) is the second largest after the gut microbiome. The state of your oral microbiome can affect the rest of your body in two major ways<ref>{{Cite journal|title=Oral microbiota in human systematic diseases|date=2022-03-02|url=https://www.nature.com/articles/s41368-022-00163-7|journal=International Journal of Oral Science|volume=14|issue=1|pages=1–11|last=Peng|first=Xian|last2=Cheng|first2=Lei|last3=You|first3=Yong|last4=Tang|first4=Chengwei|last5=Ren|first5=Biao|last6=Li|first6=Yuqing|last7=Xu|first7=Xin|last8=Zhou|first8=Xuedong|language=en|doi=10.1038/s41368-022-00163-7|pmc=8891310|pmid=35236828|issn=2049-3169}}</ref>:

# Microorganisms in the mouth can travel "downstream" to the gut microbiome.
# An oral infection can cause bacteria and their metabolites (digestive byproducts) to enter the bloodstream. This can activate the immune system and cause widespread inflammation.

The 2021 Damiano study above also found differences in the composition of oral bacteria between CFS/ME patients and healthy controls. People with CFS/ME had higher relative abundance of bacteria in the genus ''Rothia'' (phylum Actinobacteria).<ref name="Damiano2021" />

==ME/CFS==

A growing body of evidence suggests that an [[dysbiosis|altered microbiome]]; [[intestinal permeability|mucosal barrier]] dysfunction;<ref name="Lakhan2010">{{Citation| doi = 10.1186/1743-7075-7-79| issn = 1743-7075| volume = 7|issue = | pages = 79| last1 = Lakhan | first1 = Shaheen E| last2 = Kirchgessner | first2 = Annette| title = Gut inflammation in chronic fatigue syndrome| journal = Nutrition & Metabolism| access-date = 2016-12-13 | date = 2010-10-12| url = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964729/| pmid = 20939923}}</ref> the translocation or crossing of bacteria from the gut into the [[blood|bloodstream]]; and subsequent immune response may pay a role in the pathophysiology of [[myalgic encephalomyelitis]]\[[chronic fatigue syndrome]].

===Immune response===

A study of 128 [[ME/CFS]] patients found significantly increased [[IgA]] response to [[lipopolysaccharide]]s from the cell walls of commensal bacteria. Increased IgA response was associated with increased serum [[interleukin 1|IL-1]], [[TNFα]], [[neopterin]] and [[elastase]]. The study concluded that increased translocation of commensal bacteria may be responsible for the disease activity in some ME/CFS patients.<ref name="Maes2012" />

===Dysbiosis===
:''{{main|page_name =Dysbiosis}}''

There is strong evidence that [[dysbiosis]] or an imbalance in the microbial ecology of the gut plays a role in the symptoms of [[ME/CFS]]. ME/CFS patients have higher levels of [[D-lactic acid]] bacteria,<ref>{{Cite journal | last = Sheedy | first = John R. | authorlink = | last2 = Wettenhall | first2 = Richard E. H. | authorlink2 = | last3 = Scanlon | first3 = Denis | authorlink3 = | last4 = Gooley | first4 = Paul R. | authorlink4 = Paul Gooley | last5 = Lewis | first5 = Donald P. | authorlink5 = Donald Lewis | last6 = McGregor | first6 = Neil | authorlink6 = Neil McGregor | last7 = Stapleton | first7 = David I. | last8 = Butt | first8 = Henry L. | authorlink8 = Henry Butt | last9 = De Meirleir | first9 = Kenny L. | authorlink9 = Kenny De Meirleir | date = Jul 2009 | title = Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome|url=https://pubmed.ncbi.nlm.nih.gov/19567398|journal=In Vivo (Athens, Greece)|volume=23|issue=4 | pages = 621–628|doi=|issn=0258-851X|pmc=|pmid=19567398|access-date=|quote=|via=}}</ref> decreased levels of [[bifidobacteria]],<ref>{{Cite journal | last = Logan | first = Alan C | authorlink = | last2 = Venket Rao | first2 = A | authorlink2 = | last3 = Irani | first3 = Dinaz | authorlink3 = | date = Jun 2003 | title = Chronic fatigue syndrome: lactic acid bacteria may be of therapeutic value|url=https://linkinghub.elsevier.com/retrieve/pii/S0306987703000963|journal=Medical Hypotheses|language=en|volume=60|issue=6 | pages = 915–923|doi=10.1016/S0306-9877(03)00096-3|pmc=|pmid=|access-date=|quote=|via=}}</ref> and may suffer from [[small intestinal bacterial overgrowth]] (SIBO) at higher rates.{{citation needed}}

===Exercise===

A small study of ten CFS patients found significant changes in the composition of the microbiome and increased bacterial translocation (movement from the [[gastrointestinal system|intestine]] into the [[blood|bloodstream]] following [[exercise]]). In the blood, the study found increased [[Clostridium]] fifteen minutes after exercise and increased [[bacilli]] 48 hours later.<ref name="Shukla2015" /><ref>{{citation | last = Johnson | first = Cort | date = December 21, 2015 | title = Exercise Triggers Gut Changes in Chronic Fatigue Syndrome (ME/CFS)|url= http://www.cortjohnson.org/blog/2015/12/21/exercise-gut-chronic-fatigue-syndrome-me-cfs/|newspaper= HealthRising|location= Houston|access-date= 2016-12-12}}</ref>{{citation needed | date = 2021 | reason=Add original research}}

===Sleep===

In a very small study, CFS patients treated with [[erythromycin]] who had clinical response (i.e., reduced [[streptococcus]]) had improved sleep. Higher [[lactobacillus]] was associated with poorer mood.<ref name="Jackson2015" />

===Gender===

A study of 274 [[ME/CFS]] patients found sex-specific interactions between [[Firmicute]]s ([[Clostridium]], [[Streptococcus]], [[Lactobacillus]] and [[Enterococcus]]) and ME/CFS symptoms (including neurological, immune and mood symptoms) and symptoms in spite of similar overall composition across sexes.<ref name="Wallis2016" />

==Factors affecting microbiome==

=== Diet ===

The food we eat has a considerable effect on the composition of the intestinal microbiota.<ref name="Maslowski2011" />

=== Viral infection ===

Viruses can cause shifts in the gut microbiome.

In mice, the influenza virus leads to injury of both the lungs (the primary site of infection) and the intestinal tract, even when there is no evidence of viral replication in the gut, and causes decreases [[Lactobacillus]] and [[Lactococcus]] species and increases in [[Enterobacteriaceae]].<ref>{{citation | last = Racaniello | first = Vincent | date = 10 December 2014 | title = How influenza virus infection might lead to gastrointestinal symptoms|url= http://www.virology.ws/2014/12/10/how-influenza-virus-infection-might-lead-to-gastrointestinal-symptoms/|newspaper= Virology Blog|location= New York|access-date= 2016-12-12}}</ref>

=== Pregnancy ===

Gut microbiota change dramatically from the first trimester to the third trimester of [[pregnancy]]. During the first trimester, there is an overrepresentation of 18 bacterial groups, mainly [[Faecalibacterium]], a [[butyrate]] producer that has been shown to improve symptoms of [[inflammatory bowel disease]].<ref name="koren2012" />

During the third trimester, populations of pro-inflammatory [[bacteria]] species such as [[proteobacteria]] and [[actinobacteria]] increase and there is a reduction in diversity. Populations of [[Faecalibacterium]] decrease.<ref name="koren2012" /> Overall bacterial load increases over the course of pregnancy.<ref>http://www.scopus.com/record/display.uri?eid=2-s2.0-53849104768&origin=inward&txGid=B73C4858FB9D5F216C9F222F22386A44.iqs8TDG0Wy6BURhzD3nFA%3a2</ref>

===Nervous system===

The intestinal microbiota play a major role in the [[gut-brain axis]] with consequences for both neurological development and host behavior.

=== Stress ===

There is growing evidence that the microbiome plays an important role in the [[stress]] response. Animals raised in a germ-free environment show an exaggerated [[HPA]] response to psychological stress which normalizes when [[Bifidobacterium infantis|''Bifidobacterium infantis'']] is introduced. [[Escherichia coli|''Escherichia coli'']] can activate the HPA.<ref name="Dinan2012" />

Stress also increases [[intestinal permeability]].

==Planned studies==
British patient charity [[Invest in ME]] is raising funds for a gut microbiome study at the University of East Anglia in the United Kingdom led by professor [[Simon Carding]].<ref>[http://www.investinme.org/LDR%20UK%20Gut%20Microbiota.htm Invest in ME – UK gut microbiota research]</ref>

Funds are being raised by patients (originally led by the late [[Vanessa Li]]) for [[Ian Lipkin]] and [[Mady Hornig]] of Columbia University in the United States to perform a study, called the [[ME/CFS Monster Study]], looking at many areas including the gut microbiome in [[ME/CFS]] patients. Fundraising efforts are led by the [[Microbe Discovery Project]].

==Notable studies==
*2009, Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome<ref>{{Cite journal | last = Sheedy | first = John R. | authorlink = | last2 = Wettenhall | first2 = Richard E. H. | authorlink2 = | last3 = Scanlon | first3 = Denis | authorlink3 = | last4 = Gooley | first4 = Paul R. | authorlink4 = Paul Gooley | last5 = Lewis | first5 = Donald P. | authorlink5 = Donald Lewis | last6 = McGregor | first6 = Neil | authorlink6 = Neil McGregor | last7 = Stapleton | first7 = David I. | last8 = Butt | first8 = Henry L. | authorlink8 = Henry Butt | last9 = De Meirleir | first9 = Kenny L. | authorlink9 = Kenny De Meirleir | date = Jul 2009 | title = Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome|url=https://pubmed.ncbi.nlm.nih.gov/19567398|journal=In Vivo (Athens, Greece)|volume=23|issue=4 | pages = 621–628|doi=|issn=0258-851X|pmc=|pmid=19567398|access-date=|quote=|via=}}</ref> - [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5843715/ (Full Text)]
*2010, [https://www.ncbi.nlm.nih.gov/pubmed/20939923 Gut inflammation in chronic fatigue syndrome]<ref name="Lakhan2010" />
*2012, [https://www.ncbi.nlm.nih.gov/pubmed/21967891 Increased IgA responses to the LPS of commensal bacteria is associated with inflammation and activation of cell-mediated immunity in chronic fatigue syndrome]<ref name="Maes2012" />
*2012, [http://www.cdd.com.au/pdf/publications/All%20Publications/2013%20-%20The%20GI%20microbiome%20and%20its%20role%20in%20CFS%20-%20ACNEM%20paper.pdf/ The GI Microbiome and its Role in Chronic Fatigue Syndrome: A Summary of Bacteriotherapy]<ref name="Borody2012" />
*2013, [https://www.ncbi.nlm.nih.gov/pubmed/23791918 High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients]<ref name="Fremont2013" />
*2015, [https://www.ncbi.nlm.nih.gov/pubmed/26779319 Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study]<ref name="Jackson2015" />
*2015, [https://www.ncbi.nlm.nih.gov/pubmed/26683192 Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)]<ref name="Shukla2015" />
*2016, [https://www.ncbi.nlm.nih.gov/pubmed/27634186 The role of microbiota and intestinal permeability in the pathophysiology of autoimmune and neuroimmune processes with an emphasis on Inflammatory Bowel Disease Type 1 Diabetes and Chronic Fatigue Syndrome]<ref name="Morris, 2016" />
*2016, [https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0171-4 Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome]<ref>{{Cite journal | last = Giloteaux | first = Ludovic | authorlink = Ludovic Giloteaux | last2 = Goodrich | first2 = Julia K. | authorlink2 = | last3 = Walters | first3 = William A. | authorlink3 = | last4 = Levine | first4 = Susan M. | authorlink4 = Susan Levine | last5 = Ley | first5 = Ruth E. | authorlink5 = | last6 = Hanson | first6 = Maureen R. | authorlink6 = Maureen Hanson | date = Dec 2016 | title = Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome|url=http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0171-4|journal=Microbiome|language=en|volume=4|issue=1|pages=|doi=10.1186/s40168-016-0171-4|issn=2049-2618|pmc=4918027|pmid=27338587|quote=|via=}}</ref>
*2016, [http://www.nature.com/articles/srep19171 Support for the Microgenderome: Associations in a Human Clinical Population]<ref name="Wallis2016" />
*2017, Fecal metagenomic profiles in subgroups of patients with [[ME/CFS|myalgic encephalomyelitis/chronic fatigue syndrome]]<ref name="Nagy-Szakal, 2017" /> [https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0261-y (Full Text)]
*2018, Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome?<ref name="Newberry, 2018" />
*2018, [[Chronic fatigue syndrome]] patients have alterations in their oral microbiome composition and function<ref>{{Cite journal | last = Wang | first = Taiwu | last2 = Yu | first2 = Lei | last3 = Xu | first3 = Cong | last4 = Pan | first4 = Keli | last5 = Mo | first5 = Minglu | last6 = Duan | first6 = Mingxiang | last7 = Zhang | first7 = Yao | last8 = Xiong | first8 = Hongyan | date = 2018-09-11 | title = Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function | url =https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203503|journal=PLOS ONE|language=en|volume=13|issue=9| pages = e0203503|doi=10.1371/journal.pone.0203503|issn=1932-6203}}</ref> [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203503 (Full Text)]
*2018, Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the era of the human microbiome: persistent pathogens drive chronic symptoms by interfering with host [[metabolism]], [[gene expression]] and [[Immune system|immunity]]<ref>{{Cite journal | last = Proal | first = Amy | authorlink = Amy Proal | last2 = Marshall | first2 = Trevor | authorlink2 = Trevor Marshall | date = Nov 2018 | title = Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the era of the human microbiome: persistent pathogens drive chronic symptoms by interfering with host metabolism, gene expression and immunity|url=https://www.frontiersin.org/articles/10.3389/fped.2018.00373/full|journal=Frontiers in Pediatrics|volume=|issue=|pages=|quote=|via=|doi=10.3389/fped.2018.00373}}</ref> [https://www.frontiersin.org/articles/10.3389/fped.2018.00373/full (Full text)]
* 2021, Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME)<ref name="Damiano2021">{{Cite journal | last = Lupo | first = Giuseppe Francesco Damiano | author-link = | last2 = Rocchetti | first2 = Gabriele | authorlink2 = | last3 = Lucini | first3 = Luigi | authorlink3 = | last4 = Lorusso | first4 = Lorenzo | authorlink4 = Lorenzo Lorusso | last5 = Manara | first5 = Elena | authorlink5 = | last6 = Bertelli | first6 = Matteo | authorlink6 = | last7 = Puglisi | first7 = Edoardo | last8 = Capelli | first8 = Enrica | authorlink8 = Enrica Capelli | date = March 2021 | title = Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME)|url=http://www.nature.com/articles/s41598-021-86425-6|journal=Scientific Reports|language=en|volume=11|issue=1 | pages = 7043|doi=10.1038/s41598-021-86425-6|issn=2045-2322|pmc=|pmid=33782445|access-date=|quote=|via=}}</ref> - [https://www.nature.com/articles/s41598-021-86425-6 (Full text)]

==Commercial testers==
*[[uBiome]]

==Academic projects==
*[[American Gut]]
*[[British Gut Project]]

==Learn more==
*[https://en.wikipedia.org/wiki/Microbiota Wikipedia - Microbiota]
*[[CFS Remission]] ([[Ken Lassesen]]'s blogs about experimental ME/CFS microbiome and probiotic treatments)
*2016, [https://cfsremission.wordpress.com/2016/08/09/what-should-be-in-the-ideal-microbiome-test-for-cfs/ What should be in the ideal microbiome test for CFS] ''[[CFS Remission]]''
*2016, [https://cfstreatment.blogspot.co.uk/2016/07/all-in-your-gut.html It's All in Your Gut] ''[[Onward Through the Fog]]''
*2016, [http://well.blogs.nytimes.com/2016/07/07/gut-bacteria-are-different-in-people-with-chronic-fatigue-syndrome/ Gut Bacteria Are Different in People With Chronic Fatigue Syndrome] ''The New York Times''<ref>{{citation | last = Bakalar | first = Nicholas | date = 7 July 2016 | title = Gut Bacteria Are Different in People With Chronic Fatigue Syndrome|url= http://well.blogs.nytimes.com/2016/07/07/gut-bacteria-are-different-in-people-with-chronic-fatigue-syndrome/|newspaper= The New York Times|location= |access-date= 2016-12-13}}</ref>
*2016, [https://www.washingtonpost.com/news/to-your-health/wp/2016/06/30/new-study-shows-chronic-fatigue-isnt-just-in-your-head-it-may-have-to-do-with-your-gut/ New study shows chronic fatigue syndrome may have to do with gut microbes] ''The Washington Post''<ref>{{citation | last = Cha | first = Ariana Eunjung | date = Jun 30, 2016 | title = New study shows chronic fatigue syndrome may have to do with gut microbes|url= https://www.washingtonpost.com/news/to-your-health/wp/2016/06/30/new-study-shows-chronic-fatigue-isnt-just-in-your-head-it-may-have-to-do-with-your-gut/|newspaper= The Washington Post|location= |access-date= 2016-12-13}}</ref>
*2016, [http://news.cornell.edu/stories/2016/06/indicator-chronic-fatigue-syndrome-found-gut-bacteria Indicator of chronic fatigue syndrome found in gut bacteria] ''Cornell Chronicle''<ref>{{citation | last = Ramanujan | first = Krishna | date = 24 June 2016 | title = Indicator of chronic fatigue syndrome found in gut bacteria|url= http://news.cornell.edu/stories/2016/06/indicator-chronic-fatigue-syndrome-found-gut-bacteria|newspaper= Cornell Chronicle|location= New York|access-date= 2016-12-13}}</ref>
*2016, [http://www.cortjohnson.org/blog/2016/02/21/gut-chronic-fatigue-syndrome-gender-differences/ Gender Gut Wars: Australian ME/CFS Study Suggests Different Gut Treatment Protocols Needed For Men and Women] ''[[Health Rising]]''<ref>{{citation | last = Johnson | first = Cort | date = 21 February 2016 | title = Gender Gut Wars: Australian ME/CFS Study Suggests Different Gut Treatment Protocols Needed For Men and Women | url = http://www.cortjohnson.org/blog/2016/02/21/gut-chronic-fatigue-syndrome-gender-differences/|newspaper= HealthRising|location= Houston|access-date= 2016-12-13}}</ref>
*[https://cfsremission.wordpress.com/2016/04/02/vitamin-d-and-the-microbiome/ Vitamin D and the Microbiome] ''[[CFS Remission]]''

==See also==
*[[Probiotics]]
*[[Gastrointestinal system]]
*[[Helminthic therapy]]
*[[Ken Lassesen's model]]
*[[Nasal microbiome]]
*[[Oral microbiome]]
*[[Indoor microbiome]]
*[[Dr Markov's chronic bacterial intoxication syndrome (CBIS) theory of ME/CFS]] (Dr Markov has evidence that ME/CFS is caused by a dysbiosis in the kidneys)

==References==
<references>
<ref name="Lakhan2010">{{Citation| doi = 10.1186/1743-7075-7-79| issn = 1743-7075| volume = 7|issue = | pages = 79| last1 = Lakhan | first1 = Shaheen E| last2 = Kirchgessner | first2 = Annette| title = Gut inflammation in chronic fatigue syndrome| journal = Nutrition & Metabolism| access-date = 2016-12-13 | date = 2010-10-12| url = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964729/| pmid = 20939923}}</ref>
<ref name="Maes2012">{{Citation| doi = 10.1016/j.jad.2011.09.010| issn = 1573-2517| volume = 136 | issue = 3| pages = 909–917| last1 = Maes | first1 = Michael | last2 = Twisk | first2 = Frank N.M. | last3 = Kubera | first3 = Marta | last4 = Ringel | first4 = Karl | last5 = Leunis | first5 = Jean-Claude | last6 = Geffard | first6 = Michel| title = Increased IgA responses to the LPS of commensal bacteria is associated with inflammation and activation of cell-mediated immunity in chronic fatigue syndrome| journal = Journal of Affective Disorders| date = February 2012 | pmid = 21967891}}</ref>
<ref name="Shukla2015">{{Citation| doi = 10.1371/journal.pone.0145453| issn = 1932-6203| volume = 10 | issue = 12| pages = 0145453| last1 = Shukla | first1 = Sanjay K. | last2 = Cook | first2 = Dane | last3 = Meyer | first3 = Jacob| last4 = Vernon | first4 = Suzanne D. | last5 = Le | first5 = Thao | last6 = Clevidence | first6 = Derek | last7 = Robertson | first7 = Charles E. | last8 = Schrodi | first8 = Steven J. | last9 = Yale | first9 = Steven | last10 = Frank | first10 = Daniel N.| title = Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)| journal = PLOS ONE| access-date = 2016-12-13 | date = 2015-12-18| url = http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145453}}</ref>
<ref name="Jackson2015">{{citation | last1 = Jackson | first1 = Melinda L | authorlink1 = Melinda Jackson | last2 = Butt | first2 = Henry L | authorlink2 = Henry Butt | last3 = Ball | first3 = Michelle | authorlink3 = Michelle Ball | last4 = Lewis | first4 = Donald P | authorlink4 = Donald Lewis | last5 = Bruck | first5 = Dorothy | authorlink5 = Dorothy Bruck | title = Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study | journal = Sleep Science | volume = 8 | issue = 3 | pages = 124-133 | date = 23 Oct 2015 | pmid = 26779319 | doi = 10.1016/j.slsci.2015.10.001 | url = http://www.sciencedirect.com/science/article/pii/S1984006315000632 }}</ref>
<ref name="Wallis2016">{{citation | last1 = Wallis | first1 = Amy| authorlink1 = Amy Wallis | last2 = Butt | first2 = Henry L | authorlink2 = Henry Butt | last3 = Ball | first3 = Michelle | authorlink3 = Michelle Ball | last4 = Lewis | first4 = Donald P | authorlink4 = Donald Lewis | last5 = Bruck | first5 = Dorothy | authorlink5 = Dorothy Bruck | title = Support for the Microgenderome: Associations in a Human Clinical Population | journal = Scientific Reports | volume = | pages = | date = 13 Jan 2016 |issue = | pmid = 26757840 | doi = 10.1038/srep19171 | url = http://www.nature.com/articles/srep19171 }}</ref>
<ref name="Maslowski2011">{{Citation| doi = 10.1038/ni0111-5| issn = 1529-2916| volume = 12 | issue = 1| pages = 5–9| last1 = Maslowski | first1 = Kendle M. | last2 = Mackay | first2 = Charles R.| title = Diet, gut microbiota and immune responses| journal = Nature Immunology | date = January 2011 | pmid = 21169997}}</ref>
<ref name="koren2012">{{Citation| doi = 10.1016/j.cell.2012.07.008| issn = 1097-4172| volume = 150 | issue = 3| pages = 470–480| last1 = Koren | first1 = Omry | last2 = Goodrich | first2 = Julia K. | last3 = Cullender | first3 = Tyler C. | last4 = Spor | first4 = Aymé| last5 = Laitinen | first5 = Kirsi | last6 = Bäckhed | first6 = Helene Kling | last7 = Gonzalez | first7 = Antonio | last8 = Werner | first8 = Jeffrey J. | last9 = Angenent | first9 = Largus T. | last10 = Knight | first10 = Rob| last11 = Bäckhed | first11 = Fredrik | last12 = Isolauri | first12 = Erika | last13 = Salminen | first13 = Seppo | last14 = Ley | first14 = Ruth E.| title = Host remodeling of the gut microbiome and metabolic changes during pregnancy| journal = Cell| date = 2012-08-03 | pmid = 22863002}}</ref>
<ref name="Dinan2012">{{Citation| doi = 10.1016/j.psyneuen.2012.03.007| issn = 0306-4530| volume = 37 | issue = 9| pages = 1369–1378| last1 = Dinan | first1 = Timothy G. | last2 = Cryan | first2 = John F.| title = Regulation of the stress response by the gut microbiota: Implications for psychoneuroendocrinology| journal = Psychoneuroendocrinology| access-date = 2016-12-13 | date = September 2012| url = http://www.sciencedirect.com/science/article/pii/S0306453012000935}}</ref>
<ref name="Fremont2013">{{Citation| doi = 10.1016/j.anaerobe.2013.06.002| issn = 1095-8274| volume = 22 | issue = | pages = 50–56| last1 = Frémont | first1 = Marc| last2 = Coomans | first2 = Danny | last3 = Massart | first3 = Sebastien | last4 = De Meirleir | first4 = Kenny| title = High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients| journal = Anaerobe | date = August 2013 | pmid = 23791918}}</ref>
<ref name="Borody2012">{{Citation| issn = 1328-8040| volume = 31 | issue = 3| pages = 3| last1 = Borody | first1 = Thomas J. | last2 = Nowak | first2 = Anna | last3 = Finlayson | first3 = Sarah| title = The GI microbiome and its role in Chronic Fatigue Syndrome: A summary of bacteriotherapy| journal = Journal of the Australasian College of Nutritional and Environmental Medicine| access-date = 2016-12-13 | date = December 2012| url = http://www.cdd.com.au/pdf/publications/All%20Publications/2013%20-%20The%20GI%20microbiome%20and%20its%20role%20in%20CFS%20-%20ACNEM%20paper.pdf/}}</ref>
<ref name="Morris, 2016">{{Citation | last1 = Morris | first1 = Gerwyn | authorlink1 = Gerwyn Morris | last2 = Berk | first2 = Michael | authorlink2 = Michael Berk | last3 = Carvalho | first3 = A.F. | authorlink3 = | last4 = Caso | first4 = J.R. | authorlink4 = | last5 = Sanz | first5 = Y. | authorlink5 = | last6 = Maes | first6 = Michael | authorlink6 = Michael Maes | title = The role of microbiota and intestinal permeability in the pathophysiology of autoimmune and neuroimmune processes with an emphasis on Inflammatory Bowel Disease Type 1 Diabetes and Chronic Fatigue Syndrome. | journal = Current Pharmaceutical Design | volume = | issue = | pages = | date = 2016 | pmid = 27634186 }}</ref>
<ref name="Nagy-Szakal, 2017">{{Citation | last1 = Nagy-Szakal | first1 = Dorottya | authorlink1 = Dorottya Nagy-Szakal | last2 = Williams | first2 = Brent L. | authorlink2 = | last3 = Mishra | first3 = Nischay | authorlink3 = | last4 = Che | first4 = Xiaoyu | authorlink4 = | last5 = Lee | first5 = Bohyun | authorlink5 = | last6 = Bateman | first6 = Lucinda | authorlink6 = Lucinda Bateman | last7 = Klimas | first7 = Nancy G. | authorlink7 = Nancy Klimas | last8 = Komaroff | first8 = Anthony L. | authorlink8 = Anthony Komaroff | last9 = Levine | first9 = Susan | authorlink9 = Susan Levine | last10 = Montoya | first10 = Jose G. | authorlink10 = Jose Montoya | last11 = Peterson | first11 = Daniel L. | authorlink11 = Daniel Peterson | last12 = Ramanan | first12 = Devi | authorlink12 = | last13 = Jain | first13 = Komal | authorlink13 = | last14 = Eddy | first14 = Meredith L. | authorlink14 = | last15 = Hornig | first15 = Mady | authorlink15 = Mady Hornig | last16 = Lipkin | first16 = W. Ian | authorlink16 = Ian Lipkin | title = Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome | journal = Microbiome | volume = 5 | issue = 44 | pages = | date = 2017 | pmid = | doi = 10.1186/s40168-017-0261-y }}</ref>
<ref name="Newberry, 2018">{{Citation | last1 = Newberry | first1 = F. | authorlink1 = | last2 = Hsieh | first2 = S.-Y. | authorlink2 = | last3 = Wileman | first3 = T. | authorlink3 = | last4 = Carding | first4 = S.R. | authorlink4 = Simon Carding | title = Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome? | journal = Clinical Science | volume = 132 | issue = 5 | pages = 523–542 | date = 2018 | pmid = | doi = 10.1042/CS20171330 }}</ref>
</references>

[[Category:Body systems]]
[[Category:Microbiome]]

Microbiome

2026-07-17T08:59:09Z

Tuxedocaspy:/* Gut flora */ Expanding on establishment of gut microbiota

{{Cleanup/Citations needed | date = Mar 2021}}
The '''microbiome''' is the community of microorganisms (such as [[bacteria]], [[fungus|fungi]], and [[virus]]es) that inhabit a particular environment, especially the human body.
<ref>{{Cite web|website=Merrian-Webster Medical Dictionary|access-date=2021-02-20 | title = Definition of MICROBIOME|url=https://www.merriam-webster.com/dictionary/microbiome}}</ref>

==Anatomical areas==
The microorganisms live on the skin and genitals and in the [[nose microbiome|nose]], ears, [[oral microbiome|mouth]] and [[gut microbiome|gut]]. [[Dysbiosis]] or an imbalance in this community may play a role in the pathophysiology of [[chronic fatigue syndrome]].<ref>{{Cite journal|title=Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome|date=2017-04-26|url=https://pubmed.ncbi.nlm.nih.gov/28441964/|journal=Microbiome|volume=5|issue=1|pages=44|last=Nagy-Szakal|first=Dorottya|last2=Williams|first2=Brent L.|last3=Mishra|first3=Nischay|last4=Che|first4=Xiaoyu|last5=Lee|first5=Bohyun|last6=Bateman|first6=Lucinda|last7=Klimas|first7=Nancy G.|last8=Komaroff|first8=Anthony L.|last9=Levine|first9=Susan|last10=Montoya|first10=Jose G.|last11=Peterson|first11=Daniel L.|doi=10.1186/s40168-017-0261-y|pmc=5405467|pmid=28441964|issn=2049-2618}}</ref>

===Gut flora===

The [[gut microbiome]] is a complex community of trillions of microorganisms residing in the intestines. Around 99% of bacteria in the gut are [[Anaerobic bacteria|anaerobes]].<ref>{{Cite journal|title=Commensal Bacteria: An Emerging Player in Defense Against Respiratory Pathogens|date=October 2003|url=https://www.sciencedirect.com/science/article/abs/pii/S1369527403001176|journal=Current Opinion in Microbiology|volume=6|issue=5|pages=457-461|last=Vendantam|first=Gayatari|last2=Hecht|first2=David}}</ref>

An individual's gut microbiome begins as a sample from the maternal microbiome taken during childbirth. While proportions and specific diversities of bacteria vary between individuals, scientific evidence shows delivery method influences the founding population of intestinal bacteria. Vaginal births are seeded with bacteria found in the birth canal, including ''Bacteroides'', ''Actinobacteria, Lactobacillus, Bifidobacteria.'' Caesarean section births are taken from microbes found on the skin and in the environment, ranging from ''Staphylococcus, Enterococcus, Clostridium, Streptococcus''.<ref>Coelho GDP, Ayres LFA, Barreto DS, Henriques BD, Prado MRMC, Passos CMD. Acquisition of microbiota according to the type of birth: an integrative review. Rev Lat Am Enfermagem. 2021 Jul 19;29:e3446. doi: 10.1590/1518.8345.4466.3446. PMID: 34287544; PMCID: PMC8294792.</ref> Gut microbiomes founded by c-section births are less phylogenetically diverse and alter colonization of normal gut microbiota during early infancy.

A 2021 study by Damiano found significant differences in the composition of gut bacteria between CFS/ME patients and healthy controls. People with ME/CFS had:<ref name="Damiano2021" />

* Higher relative abundance of bacteria in the genus ''Bacteroides'' (phylum Bacteriodetes) and the genus ''Phascolarctobacterium'' (phylum Firmicutes)
* Lower relative abundance of bacteria in the genus ''Anaerostipes'' and genus ''Ruminococcus'' (both from phylum Firmicutes)

However, the study authors were unable to determine if the alteration of the microbiome is a cause or a consequence of the onset of CFS/ME, or if the changes in the microbial composition are related to any of the several secondary symptoms.<ref name="Damiano2021" />

Damiano et al. suggest the intestinal microbial profile recorded in their study is consistent with the profiles reported for other autoimmune conditions. For example, a 2021 review on pediatric [[inflammatory bowel disease]] found a reduced abundance of bacteria in genus ''Anaerostipes.''<ref>{{Cite journal|title=Gut Microbiota Profile in Pediatric Patients With Inflammatory Bowel Disease: A Systematic Review|date=2021-02-02|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884334/|journal=Frontiers in Pediatrics|volume=9|pages=626232|last=Zhuang|first=Xiaojun|last2=Liu|first2=Caiguang|last3=Zhan|first3=Shukai|last4=Tian|first4=Zhenyi|last5=Li|first5=Na|last6=Mao|first6=Ren|last7=Zeng|first7=Zhirong|last8=Chen|first8=Minhu|doi=10.3389/fped.2021.626232|pmc=7884334|pmid=33604319|issn=2296-2360}}</ref> A 2014 study found a higher abundance of the genus ''Bacteroides'' in people with [[systemic lupus erythematous]].<ref>{{Cite journal|title=Intestinal Dysbiosis Associated with Systemic Lupus Erythematosus|date=September 30, 2014|url=https://journals.asm.org/doi/10.1128/mbio.01548-14|journal=mBio|volume=5|issue=5|last=Hevia|first=Arancha|last2=Milani|first2=Christian|last3=Lopez|first3=Patricia|last4=Cuervo|first4=Adriana|last5=Arboleya|first5=Silvia|last6=Duranti|first6=Sabrina|last7=Turroni|first7=Francesca|last8=Suarez|first8=Ana|last9=Gueimonde|first9=Miguel|doi=10.1128/mbio.01548-14}}</ref>

===Oral flora===

The microbiome in the oral cavity (mouth and throat) is the second largest after the gut microbiome. The state of your oral microbiome can affect the rest of your body in two major ways<ref>{{Cite journal|title=Oral microbiota in human systematic diseases|date=2022-03-02|url=https://www.nature.com/articles/s41368-022-00163-7|journal=International Journal of Oral Science|volume=14|issue=1|pages=1–11|last=Peng|first=Xian|last2=Cheng|first2=Lei|last3=You|first3=Yong|last4=Tang|first4=Chengwei|last5=Ren|first5=Biao|last6=Li|first6=Yuqing|last7=Xu|first7=Xin|last8=Zhou|first8=Xuedong|language=en|doi=10.1038/s41368-022-00163-7|pmc=8891310|pmid=35236828|issn=2049-3169}}</ref>:

# Microorganisms in the mouth can travel "downstream" to the gut microbiome.
# An oral infection can cause bacteria and their metabolites (digestive byproducts) to enter the bloodstream. This can activate the immune system and cause widespread inflammation.

The 2021 Damiano study above also found differences in the composition of oral bacteria between CFS/ME patients and healthy controls. People with CFS/ME had higher relative abundance of bacteria in the genus ''Rothia'' (phylum Actinobacteria).<ref name="Damiano2021" />

==ME/CFS==

A growing body of evidence suggests that an [[dysbiosis|altered microbiome]]; [[intestinal permeability|mucosal barrier]] dysfunction;<ref name="Lakhan2010">{{Citation| doi = 10.1186/1743-7075-7-79| issn = 1743-7075| volume = 7|issue = | pages = 79| last1 = Lakhan | first1 = Shaheen E| last2 = Kirchgessner | first2 = Annette| title = Gut inflammation in chronic fatigue syndrome| journal = Nutrition & Metabolism| access-date = 2016-12-13 | date = 2010-10-12| url = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964729/| pmid = 20939923}}</ref> the translocation or crossing of bacteria from the gut into the [[blood|bloodstream]]; and subsequent immune response may pay a role in the pathophysiology of [[myalgic encephalomyelitis]]\[[chronic fatigue syndrome]].

===Immune response===

A study of 128 [[ME/CFS]] patients found significantly increased [[IgA]] response to [[lipopolysaccharide]]s from the cell walls of commensal bacteria. Increased IgA response was associated with increased serum [[interleukin 1|IL-1]], [[TNFα]], [[neopterin]] and [[elastase]]. The study concluded that increased translocation of commensal bacteria may be responsible for the disease activity in some ME/CFS patients.<ref name="Maes2012" />

===Dysbiosis===
:''{{main|page_name =Dysbiosis}}''

There is strong evidence that [[dysbiosis]] or an imbalance in the microbial ecology of the gut plays a role in the symptoms of [[ME/CFS]]. ME/CFS patients have higher levels of [[D-lactic acid]] bacteria,<ref>{{Cite journal | last = Sheedy | first = John R. | authorlink = | last2 = Wettenhall | first2 = Richard E. H. | authorlink2 = | last3 = Scanlon | first3 = Denis | authorlink3 = | last4 = Gooley | first4 = Paul R. | authorlink4 = Paul Gooley | last5 = Lewis | first5 = Donald P. | authorlink5 = Donald Lewis | last6 = McGregor | first6 = Neil | authorlink6 = Neil McGregor | last7 = Stapleton | first7 = David I. | last8 = Butt | first8 = Henry L. | authorlink8 = Henry Butt | last9 = De Meirleir | first9 = Kenny L. | authorlink9 = Kenny De Meirleir | date = Jul 2009 | title = Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome|url=https://pubmed.ncbi.nlm.nih.gov/19567398|journal=In Vivo (Athens, Greece)|volume=23|issue=4 | pages = 621–628|doi=|issn=0258-851X|pmc=|pmid=19567398|access-date=|quote=|via=}}</ref> decreased levels of [[bifidobacteria]],<ref>{{Cite journal | last = Logan | first = Alan C | authorlink = | last2 = Venket Rao | first2 = A | authorlink2 = | last3 = Irani | first3 = Dinaz | authorlink3 = | date = Jun 2003 | title = Chronic fatigue syndrome: lactic acid bacteria may be of therapeutic value|url=https://linkinghub.elsevier.com/retrieve/pii/S0306987703000963|journal=Medical Hypotheses|language=en|volume=60|issue=6 | pages = 915–923|doi=10.1016/S0306-9877(03)00096-3|pmc=|pmid=|access-date=|quote=|via=}}</ref> and may suffer from [[small intestinal bacterial overgrowth]] (SIBO) at higher rates.{{citation needed}}

===Exercise===

A small study of ten CFS patients found significant changes in the composition of the microbiome and increased bacterial translocation (movement from the [[gastrointestinal system|intestine]] into the [[blood|bloodstream]] following [[exercise]]). In the blood, the study found increased [[Clostridium]] fifteen minutes after exercise and increased [[bacilli]] 48 hours later.<ref name="Shukla2015" /><ref>{{citation | last = Johnson | first = Cort | date = December 21, 2015 | title = Exercise Triggers Gut Changes in Chronic Fatigue Syndrome (ME/CFS)|url= http://www.cortjohnson.org/blog/2015/12/21/exercise-gut-chronic-fatigue-syndrome-me-cfs/|newspaper= HealthRising|location= Houston|access-date= 2016-12-12}}</ref>{{citation needed | date = 2021 | reason=Add original research}}

===Sleep===

In a very small study, CFS patients treated with [[erythromycin]] who had clinical response (i.e., reduced [[streptococcus]]) had improved sleep. Higher [[lactobacillus]] was associated with poorer mood.<ref name="Jackson2015" />

===Gender===

A study of 274 [[ME/CFS]] patients found sex-specific interactions between [[Firmicute]]s ([[Clostridium]], [[Streptococcus]], [[Lactobacillus]] and [[Enterococcus]]) and ME/CFS symptoms (including neurological, immune and mood symptoms) and symptoms in spite of similar overall composition across sexes.<ref name="Wallis2016" />

==Factors affecting microbiome==

=== Diet ===

The food we eat has a considerable effect on the composition of the intestinal microbiota.<ref name="Maslowski2011" />

=== Viral infection ===

Viruses can cause shifts in the gut microbiome.

In mice, the influenza virus leads to injury of both the lungs (the primary site of infection) and the intestinal tract, even when there is no evidence of viral replication in the gut, and causes decreases [[Lactobacillus]] and [[Lactococcus]] species and increases in [[Enterobacteriaceae]].<ref>{{citation | last = Racaniello | first = Vincent | date = 10 December 2014 | title = How influenza virus infection might lead to gastrointestinal symptoms|url= http://www.virology.ws/2014/12/10/how-influenza-virus-infection-might-lead-to-gastrointestinal-symptoms/|newspaper= Virology Blog|location= New York|access-date= 2016-12-12}}</ref>

=== Pregnancy ===

Gut microbiota change dramatically from the first trimester to the third trimester of [[pregnancy]]. During the first trimester, there is an overrepresentation of 18 bacterial groups, mainly [[Faecalibacterium]], a [[butyrate]] producer that has been shown to improve symptoms of [[inflammatory bowel disease]].<ref name="koren2012" />

During the third trimester, populations of pro-inflammatory [[bacteria]] species such as [[proteobacteria]] and [[actinobacteria]] increase and there is a reduction in diversity. Populations of [[Faecalibacterium]] decrease.<ref name="koren2012" /> Overall bacterial load increases over the course of pregnancy.<ref>http://www.scopus.com/record/display.uri?eid=2-s2.0-53849104768&origin=inward&txGid=B73C4858FB9D5F216C9F222F22386A44.iqs8TDG0Wy6BURhzD3nFA%3a2</ref>

===Nervous system===

The intestinal microbiota play a major role in the [[gut-brain axis]] with consequences for both neurological development and host behavior.

=== Stress ===

There is growing evidence that the microbiome plays an important role in the [[stress]] response. Animals raised in a germ-free environment show an exaggerated [[HPA]] response to psychological stress which normalizes when [[Bifidobacterium infantis|''Bifidobacterium infantis'']] is introduced. [[Escherichia coli|''Escherichia coli'']] can activate the HPA.<ref name="Dinan2012" />

Stress also increases [[intestinal permeability]].

==Planned studies==
British patient charity [[Invest in ME]] is raising funds for a gut microbiome study at the University of East Anglia in the United Kingdom led by professor [[Simon Carding]].<ref>[http://www.investinme.org/LDR%20UK%20Gut%20Microbiota.htm Invest in ME – UK gut microbiota research]</ref>

Funds are being raised by patients (originally led by the late [[Vanessa Li]]) for [[Ian Lipkin]] and [[Mady Hornig]] of Columbia University in the United States to perform a study, called the [[ME/CFS Monster Study]], looking at many areas including the gut microbiome in [[ME/CFS]] patients. Fundraising efforts are led by the [[Microbe Discovery Project]].

==Notable studies==
*2009, Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome<ref>{{Cite journal | last = Sheedy | first = John R. | authorlink = | last2 = Wettenhall | first2 = Richard E. H. | authorlink2 = | last3 = Scanlon | first3 = Denis | authorlink3 = | last4 = Gooley | first4 = Paul R. | authorlink4 = Paul Gooley | last5 = Lewis | first5 = Donald P. | authorlink5 = Donald Lewis | last6 = McGregor | first6 = Neil | authorlink6 = Neil McGregor | last7 = Stapleton | first7 = David I. | last8 = Butt | first8 = Henry L. | authorlink8 = Henry Butt | last9 = De Meirleir | first9 = Kenny L. | authorlink9 = Kenny De Meirleir | date = Jul 2009 | title = Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome|url=https://pubmed.ncbi.nlm.nih.gov/19567398|journal=In Vivo (Athens, Greece)|volume=23|issue=4 | pages = 621–628|doi=|issn=0258-851X|pmc=|pmid=19567398|access-date=|quote=|via=}}</ref> - [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5843715/ (Full Text)]
*2010, [https://www.ncbi.nlm.nih.gov/pubmed/20939923 Gut inflammation in chronic fatigue syndrome]<ref name="Lakhan2010" />
*2012, [https://www.ncbi.nlm.nih.gov/pubmed/21967891 Increased IgA responses to the LPS of commensal bacteria is associated with inflammation and activation of cell-mediated immunity in chronic fatigue syndrome]<ref name="Maes2012" />
*2012, [http://www.cdd.com.au/pdf/publications/All%20Publications/2013%20-%20The%20GI%20microbiome%20and%20its%20role%20in%20CFS%20-%20ACNEM%20paper.pdf/ The GI Microbiome and its Role in Chronic Fatigue Syndrome: A Summary of Bacteriotherapy]<ref name="Borody2012" />
*2013, [https://www.ncbi.nlm.nih.gov/pubmed/23791918 High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients]<ref name="Fremont2013" />
*2015, [https://www.ncbi.nlm.nih.gov/pubmed/26779319 Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study]<ref name="Jackson2015" />
*2015, [https://www.ncbi.nlm.nih.gov/pubmed/26683192 Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)]<ref name="Shukla2015" />
*2016, [https://www.ncbi.nlm.nih.gov/pubmed/27634186 The role of microbiota and intestinal permeability in the pathophysiology of autoimmune and neuroimmune processes with an emphasis on Inflammatory Bowel Disease Type 1 Diabetes and Chronic Fatigue Syndrome]<ref name="Morris, 2016" />
*2016, [https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0171-4 Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome]<ref>{{Cite journal | last = Giloteaux | first = Ludovic | authorlink = Ludovic Giloteaux | last2 = Goodrich | first2 = Julia K. | authorlink2 = | last3 = Walters | first3 = William A. | authorlink3 = | last4 = Levine | first4 = Susan M. | authorlink4 = Susan Levine | last5 = Ley | first5 = Ruth E. | authorlink5 = | last6 = Hanson | first6 = Maureen R. | authorlink6 = Maureen Hanson | date = Dec 2016 | title = Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome|url=http://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0171-4|journal=Microbiome|language=en|volume=4|issue=1|pages=|doi=10.1186/s40168-016-0171-4|issn=2049-2618|pmc=4918027|pmid=27338587|quote=|via=}}</ref>
*2016, [http://www.nature.com/articles/srep19171 Support for the Microgenderome: Associations in a Human Clinical Population]<ref name="Wallis2016" />
*2017, Fecal metagenomic profiles in subgroups of patients with [[ME/CFS|myalgic encephalomyelitis/chronic fatigue syndrome]]<ref name="Nagy-Szakal, 2017" /> [https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0261-y (Full Text)]
*2018, Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome?<ref name="Newberry, 2018" />
*2018, [[Chronic fatigue syndrome]] patients have alterations in their oral microbiome composition and function<ref>{{Cite journal | last = Wang | first = Taiwu | last2 = Yu | first2 = Lei | last3 = Xu | first3 = Cong | last4 = Pan | first4 = Keli | last5 = Mo | first5 = Minglu | last6 = Duan | first6 = Mingxiang | last7 = Zhang | first7 = Yao | last8 = Xiong | first8 = Hongyan | date = 2018-09-11 | title = Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function | url =https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203503|journal=PLOS ONE|language=en|volume=13|issue=9| pages = e0203503|doi=10.1371/journal.pone.0203503|issn=1932-6203}}</ref> [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203503 (Full Text)]
*2018, Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the era of the human microbiome: persistent pathogens drive chronic symptoms by interfering with host [[metabolism]], [[gene expression]] and [[Immune system|immunity]]<ref>{{Cite journal | last = Proal | first = Amy | authorlink = Amy Proal | last2 = Marshall | first2 = Trevor | authorlink2 = Trevor Marshall | date = Nov 2018 | title = Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the era of the human microbiome: persistent pathogens drive chronic symptoms by interfering with host metabolism, gene expression and immunity|url=https://www.frontiersin.org/articles/10.3389/fped.2018.00373/full|journal=Frontiers in Pediatrics|volume=|issue=|pages=|quote=|via=|doi=10.3389/fped.2018.00373}}</ref> [https://www.frontiersin.org/articles/10.3389/fped.2018.00373/full (Full text)]
* 2021, Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME)<ref name="Damiano2021">{{Cite journal | last = Lupo | first = Giuseppe Francesco Damiano | author-link = | last2 = Rocchetti | first2 = Gabriele | authorlink2 = | last3 = Lucini | first3 = Luigi | authorlink3 = | last4 = Lorusso | first4 = Lorenzo | authorlink4 = Lorenzo Lorusso | last5 = Manara | first5 = Elena | authorlink5 = | last6 = Bertelli | first6 = Matteo | authorlink6 = | last7 = Puglisi | first7 = Edoardo | last8 = Capelli | first8 = Enrica | authorlink8 = Enrica Capelli | date = March 2021 | title = Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME)|url=http://www.nature.com/articles/s41598-021-86425-6|journal=Scientific Reports|language=en|volume=11|issue=1 | pages = 7043|doi=10.1038/s41598-021-86425-6|issn=2045-2322|pmc=|pmid=33782445|access-date=|quote=|via=}}</ref> - [https://www.nature.com/articles/s41598-021-86425-6 (Full text)]

==Commercial testers==
*[[uBiome]]

==Academic projects==
*[[American Gut]]
*[[British Gut Project]]

==Learn more==
*[https://en.wikipedia.org/wiki/Microbiota Wikipedia - Microbiota]
*[[CFS Remission]] ([[Ken Lassesen]]'s blogs about experimental ME/CFS microbiome and probiotic treatments)
*2016, [https://cfsremission.wordpress.com/2016/08/09/what-should-be-in-the-ideal-microbiome-test-for-cfs/ What should be in the ideal microbiome test for CFS] ''[[CFS Remission]]''
*2016, [https://cfstreatment.blogspot.co.uk/2016/07/all-in-your-gut.html It's All in Your Gut] ''[[Onward Through the Fog]]''
*2016, [http://well.blogs.nytimes.com/2016/07/07/gut-bacteria-are-different-in-people-with-chronic-fatigue-syndrome/ Gut Bacteria Are Different in People With Chronic Fatigue Syndrome] ''The New York Times''<ref>{{citation | last = Bakalar | first = Nicholas | date = 7 July 2016 | title = Gut Bacteria Are Different in People With Chronic Fatigue Syndrome|url= http://well.blogs.nytimes.com/2016/07/07/gut-bacteria-are-different-in-people-with-chronic-fatigue-syndrome/|newspaper= The New York Times|location= |access-date= 2016-12-13}}</ref>
*2016, [https://www.washingtonpost.com/news/to-your-health/wp/2016/06/30/new-study-shows-chronic-fatigue-isnt-just-in-your-head-it-may-have-to-do-with-your-gut/ New study shows chronic fatigue syndrome may have to do with gut microbes] ''The Washington Post''<ref>{{citation | last = Cha | first = Ariana Eunjung | date = Jun 30, 2016 | title = New study shows chronic fatigue syndrome may have to do with gut microbes|url= https://www.washingtonpost.com/news/to-your-health/wp/2016/06/30/new-study-shows-chronic-fatigue-isnt-just-in-your-head-it-may-have-to-do-with-your-gut/|newspaper= The Washington Post|location= |access-date= 2016-12-13}}</ref>
*2016, [http://news.cornell.edu/stories/2016/06/indicator-chronic-fatigue-syndrome-found-gut-bacteria Indicator of chronic fatigue syndrome found in gut bacteria] ''Cornell Chronicle''<ref>{{citation | last = Ramanujan | first = Krishna | date = 24 June 2016 | title = Indicator of chronic fatigue syndrome found in gut bacteria|url= http://news.cornell.edu/stories/2016/06/indicator-chronic-fatigue-syndrome-found-gut-bacteria|newspaper= Cornell Chronicle|location= New York|access-date= 2016-12-13}}</ref>
*2016, [http://www.cortjohnson.org/blog/2016/02/21/gut-chronic-fatigue-syndrome-gender-differences/ Gender Gut Wars: Australian ME/CFS Study Suggests Different Gut Treatment Protocols Needed For Men and Women] ''[[Health Rising]]''<ref>{{citation | last = Johnson | first = Cort | date = 21 February 2016 | title = Gender Gut Wars: Australian ME/CFS Study Suggests Different Gut Treatment Protocols Needed For Men and Women | url = http://www.cortjohnson.org/blog/2016/02/21/gut-chronic-fatigue-syndrome-gender-differences/|newspaper= HealthRising|location= Houston|access-date= 2016-12-13}}</ref>
*[https://cfsremission.wordpress.com/2016/04/02/vitamin-d-and-the-microbiome/ Vitamin D and the Microbiome] ''[[CFS Remission]]''

==See also==
*[[Probiotics]]
*[[Gastrointestinal system]]
*[[Helminthic therapy]]
*[[Ken Lassesen's model]]
*[[Nasal microbiome]]
*[[Oral microbiome]]
*[[Indoor microbiome]]
*[[Dr Markov's chronic bacterial intoxication syndrome (CBIS) theory of ME/CFS]] (Dr Markov has evidence that ME/CFS is caused by a dysbiosis in the kidneys)

==References==
<references>
<ref name="Lakhan2010">{{Citation| doi = 10.1186/1743-7075-7-79| issn = 1743-7075| volume = 7|issue = | pages = 79| last1 = Lakhan | first1 = Shaheen E| last2 = Kirchgessner | first2 = Annette| title = Gut inflammation in chronic fatigue syndrome| journal = Nutrition & Metabolism| access-date = 2016-12-13 | date = 2010-10-12| url = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964729/| pmid = 20939923}}</ref>
<ref name="Maes2012">{{Citation| doi = 10.1016/j.jad.2011.09.010| issn = 1573-2517| volume = 136 | issue = 3| pages = 909–917| last1 = Maes | first1 = Michael | last2 = Twisk | first2 = Frank N.M. | last3 = Kubera | first3 = Marta | last4 = Ringel | first4 = Karl | last5 = Leunis | first5 = Jean-Claude | last6 = Geffard | first6 = Michel| title = Increased IgA responses to the LPS of commensal bacteria is associated with inflammation and activation of cell-mediated immunity in chronic fatigue syndrome| journal = Journal of Affective Disorders| date = February 2012 | pmid = 21967891}}</ref>
<ref name="Shukla2015">{{Citation| doi = 10.1371/journal.pone.0145453| issn = 1932-6203| volume = 10 | issue = 12| pages = 0145453| last1 = Shukla | first1 = Sanjay K. | last2 = Cook | first2 = Dane | last3 = Meyer | first3 = Jacob| last4 = Vernon | first4 = Suzanne D. | last5 = Le | first5 = Thao | last6 = Clevidence | first6 = Derek | last7 = Robertson | first7 = Charles E. | last8 = Schrodi | first8 = Steven J. | last9 = Yale | first9 = Steven | last10 = Frank | first10 = Daniel N.| title = Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)| journal = PLOS ONE| access-date = 2016-12-13 | date = 2015-12-18| url = http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145453}}</ref>
<ref name="Jackson2015">{{citation | last1 = Jackson | first1 = Melinda L | authorlink1 = Melinda Jackson | last2 = Butt | first2 = Henry L | authorlink2 = Henry Butt | last3 = Ball | first3 = Michelle | authorlink3 = Michelle Ball | last4 = Lewis | first4 = Donald P | authorlink4 = Donald Lewis | last5 = Bruck | first5 = Dorothy | authorlink5 = Dorothy Bruck | title = Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study | journal = Sleep Science | volume = 8 | issue = 3 | pages = 124-133 | date = 23 Oct 2015 | pmid = 26779319 | doi = 10.1016/j.slsci.2015.10.001 | url = http://www.sciencedirect.com/science/article/pii/S1984006315000632 }}</ref>
<ref name="Wallis2016">{{citation | last1 = Wallis | first1 = Amy| authorlink1 = Amy Wallis | last2 = Butt | first2 = Henry L | authorlink2 = Henry Butt | last3 = Ball | first3 = Michelle | authorlink3 = Michelle Ball | last4 = Lewis | first4 = Donald P | authorlink4 = Donald Lewis | last5 = Bruck | first5 = Dorothy | authorlink5 = Dorothy Bruck | title = Support for the Microgenderome: Associations in a Human Clinical Population | journal = Scientific Reports | volume = | pages = | date = 13 Jan 2016 |issue = | pmid = 26757840 | doi = 10.1038/srep19171 | url = http://www.nature.com/articles/srep19171 }}</ref>
<ref name="Maslowski2011">{{Citation| doi = 10.1038/ni0111-5| issn = 1529-2916| volume = 12 | issue = 1| pages = 5–9| last1 = Maslowski | first1 = Kendle M. | last2 = Mackay | first2 = Charles R.| title = Diet, gut microbiota and immune responses| journal = Nature Immunology | date = January 2011 | pmid = 21169997}}</ref>
<ref name="koren2012">{{Citation| doi = 10.1016/j.cell.2012.07.008| issn = 1097-4172| volume = 150 | issue = 3| pages = 470–480| last1 = Koren | first1 = Omry | last2 = Goodrich | first2 = Julia K. | last3 = Cullender | first3 = Tyler C. | last4 = Spor | first4 = Aymé| last5 = Laitinen | first5 = Kirsi | last6 = Bäckhed | first6 = Helene Kling | last7 = Gonzalez | first7 = Antonio | last8 = Werner | first8 = Jeffrey J. | last9 = Angenent | first9 = Largus T. | last10 = Knight | first10 = Rob| last11 = Bäckhed | first11 = Fredrik | last12 = Isolauri | first12 = Erika | last13 = Salminen | first13 = Seppo | last14 = Ley | first14 = Ruth E.| title = Host remodeling of the gut microbiome and metabolic changes during pregnancy| journal = Cell| date = 2012-08-03 | pmid = 22863002}}</ref>
<ref name="Dinan2012">{{Citation| doi = 10.1016/j.psyneuen.2012.03.007| issn = 0306-4530| volume = 37 | issue = 9| pages = 1369–1378| last1 = Dinan | first1 = Timothy G. | last2 = Cryan | first2 = John F.| title = Regulation of the stress response by the gut microbiota: Implications for psychoneuroendocrinology| journal = Psychoneuroendocrinology| access-date = 2016-12-13 | date = September 2012| url = http://www.sciencedirect.com/science/article/pii/S0306453012000935}}</ref>
<ref name="Fremont2013">{{Citation| doi = 10.1016/j.anaerobe.2013.06.002| issn = 1095-8274| volume = 22 | issue = | pages = 50–56| last1 = Frémont | first1 = Marc| last2 = Coomans | first2 = Danny | last3 = Massart | first3 = Sebastien | last4 = De Meirleir | first4 = Kenny| title = High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients| journal = Anaerobe | date = August 2013 | pmid = 23791918}}</ref>
<ref name="Borody2012">{{Citation| issn = 1328-8040| volume = 31 | issue = 3| pages = 3| last1 = Borody | first1 = Thomas J. | last2 = Nowak | first2 = Anna | last3 = Finlayson | first3 = Sarah| title = The GI microbiome and its role in Chronic Fatigue Syndrome: A summary of bacteriotherapy| journal = Journal of the Australasian College of Nutritional and Environmental Medicine| access-date = 2016-12-13 | date = December 2012| url = http://www.cdd.com.au/pdf/publications/All%20Publications/2013%20-%20The%20GI%20microbiome%20and%20its%20role%20in%20CFS%20-%20ACNEM%20paper.pdf/}}</ref>
<ref name="Morris, 2016">{{Citation | last1 = Morris | first1 = Gerwyn | authorlink1 = Gerwyn Morris | last2 = Berk | first2 = Michael | authorlink2 = Michael Berk | last3 = Carvalho | first3 = A.F. | authorlink3 = | last4 = Caso | first4 = J.R. | authorlink4 = | last5 = Sanz | first5 = Y. | authorlink5 = | last6 = Maes | first6 = Michael | authorlink6 = Michael Maes | title = The role of microbiota and intestinal permeability in the pathophysiology of autoimmune and neuroimmune processes with an emphasis on Inflammatory Bowel Disease Type 1 Diabetes and Chronic Fatigue Syndrome. | journal = Current Pharmaceutical Design | volume = | issue = | pages = | date = 2016 | pmid = 27634186 }}</ref>
<ref name="Nagy-Szakal, 2017">{{Citation | last1 = Nagy-Szakal | first1 = Dorottya | authorlink1 = Dorottya Nagy-Szakal | last2 = Williams | first2 = Brent L. | authorlink2 = | last3 = Mishra | first3 = Nischay | authorlink3 = | last4 = Che | first4 = Xiaoyu | authorlink4 = | last5 = Lee | first5 = Bohyun | authorlink5 = | last6 = Bateman | first6 = Lucinda | authorlink6 = Lucinda Bateman | last7 = Klimas | first7 = Nancy G. | authorlink7 = Nancy Klimas | last8 = Komaroff | first8 = Anthony L. | authorlink8 = Anthony Komaroff | last9 = Levine | first9 = Susan | authorlink9 = Susan Levine | last10 = Montoya | first10 = Jose G. | authorlink10 = Jose Montoya | last11 = Peterson | first11 = Daniel L. | authorlink11 = Daniel Peterson | last12 = Ramanan | first12 = Devi | authorlink12 = | last13 = Jain | first13 = Komal | authorlink13 = | last14 = Eddy | first14 = Meredith L. | authorlink14 = | last15 = Hornig | first15 = Mady | authorlink15 = Mady Hornig | last16 = Lipkin | first16 = W. Ian | authorlink16 = Ian Lipkin | title = Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome | journal = Microbiome | volume = 5 | issue = 44 | pages = | date = 2017 | pmid = | doi = 10.1186/s40168-017-0261-y }}</ref>
<ref name="Newberry, 2018">{{Citation | last1 = Newberry | first1 = F. | authorlink1 = | last2 = Hsieh | first2 = S.-Y. | authorlink2 = | last3 = Wileman | first3 = T. | authorlink3 = | last4 = Carding | first4 = S.R. | authorlink4 = Simon Carding | title = Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome? | journal = Clinical Science | volume = 132 | issue = 5 | pages = 523–542 | date = 2018 | pmid = | doi = 10.1042/CS20171330 }}</ref>
</references>

[[Category:Body systems]]
[[Category:Microbiome]]

MEpedia:Sample page

2026-07-17T06:23:13Z

Tuxedocaspy:Editing practice

Welcome to the '''sample page'''! This page has been created for anyone who wants to practice some edits on the site. Have a go, play around. Leave your edits behind for the next person who comes along to see.

=='''Introduction'''==111111111
this is new to me\

Hello world

== New Editor Questions ==

==Generic questions:==

===What is your favourite movie?===
Harold and Maude{{Citation needed|reason=We need documentation supporting this statement about a cat. | date=2018}}

===What is something that always makes you laugh?===

John Waters{{Citation needed|reason=We need documentation supporting this statement about a cat. | date=2018}}

===What is the weather currently like where you are?===

* previous editor: Early winter in drought-stricken California; 5-15 degrees Celsius and often-cloudy in daytime, 3-10 degrees at night, occasional drizzle/rain when we should be getting frequent rain, with occasionally drenching rainstorms.
* ChaiTea: The sky is green.{{Citation needed|date=28 October 2025}}

===Where in the world are you right now, and where would you most like to be?===
In California. Would love to be in New Zealand, Norway, Switzerland, or the Czech Republic.

===What are a few of your favorite things?===

* previous editor: Music, Fredo, crickets at night, autumn, my husband, being in water, water skiing
* L.Berlin: Funny cat videos, especially Siberian cats; laughing babies; any effective attack on Russia's war infrastructure, by Ukraine's home-grown missiles
* ChaiTea: Autumn, cats, logic puzzles

=== What are your favourite books? ===

* L.Berlin: Asimov's Treasury of Humor<ref>{{Cite book|title=Asimov's Treasury of Humor|date=1991|publisher=Houghton Mifflin|last=Asimov|first=Isaac|quote=A lifetime collection of favorite jokes, anecdotes, and limericks with copious notes on how to tell them and why}}</ref>
* next editor:

==An inspiring blog post==

* previous editor: My new blog.
* ChaiTea: A few posts by [[Whitney Dafoe]].

==Notable studies==

==Online resources==
All [[Welcome to MEpedia|MEpedia]] [[Special:AllPages|pages here!]]

== See also ==
* [[MEpedia:Article outlines|MEpedia article outlines]]
* [[MEpedia:Help desk|Help desk]]
* [[Help:Tutorial|Help Tutorial]]

==References==
<ref>{{Citation | last1 = Mendelson | first1 = Scott| authorlink1 = Scott Mendelson | last2 = Smith | first2 = Scott
| display-authors = 1 | title = Star Wars: The Force Awakens: A Look at Its Record-Breaking Box Office Run
}}
</ref>
<references />
[[Category:MEpedia documentation]]