Microbiome

From MEpedia, a crowd-sourced encyclopedia of ME and CFS science and history

The microbiome is the community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment, especially the human body. [1]

Anatomical areas[edit | edit source]

The microorganisms live on the skin and genitals and in the nose, ears, mouth and gut. Dysbiosis or an imbalance in this community may play a role in the pathophysiology of chronic fatigue syndrome.[citation needed]

Gut flora[edit | edit source]

The gut microbiome is a complex community of trillions of microorganisms residing in the intestines. 99% of bacteria in the gut are anaerobes.

Skin flora[edit | edit source]

Nose flora[edit | edit source]

Oral flora[edit | edit source]

ME/CFS[edit | edit source]

A growing body of evidence suggests that an altered microbiome; mucosal barrier dysfunction;[2] the translocation or crossing of bacteria from the gut into the bloodstream; and subsequent immune response may pay a role in the pathophysiology of myalgic encephalomyelitis\chronic fatigue syndrome.

A 2021 study by Damiano and colleagues observed significant differences in several types of bacteria in the saliva and gut in CFS/ME patients compared to controls, but was unable to determine if the alteration of the microbiome is a cause or a consequence of the onset of CFS/ME and if the changes in the microbial composition are related to any of the several secondary symptoms.[3] The study showed that the intestinal microbial profile recorded in a group of ME/CFS patients was consistent with the reported for other autoimmune conditions, such as Crohn’s disease, ulcerative colitis and systemic lupus erythematous.[citation needed]

Immune response[edit | edit source]

A study of 128 ME/CFS patients found significantly increased IgA response to lipopolysaccharides from the cell walls of commensal bacteria. Increased IgA response was associated with increased serum 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.[4]

Dysbiosis[edit | edit source]

Main article: 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,[5] decreased levels of bifidobacteria,[6] and may suffer from small intestinal bacterial overgrowth (SIBO) at higher rates.[citation needed]

Exercise[edit | edit source]

A small study of ten CFS patients found significant changes in the composition of the microbiome and increased bacterial translocation (movement from the intestine into the bloodstream following exercise). In the blood, the study found increased Clostridium fifteen minutes after exercise and increased bacilli 48 hours later.[7][8][citation needed]

Sleep[edit | edit source]

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.[9]

Gender[edit | edit source]

A study of 274 ME/CFS patients found sex-specific interactions between Firmicutes (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.[10]

Factors affecting microbiome[edit | edit source]

Diet[edit | edit source]

The food we eat has a considerable effect on the composition of the intestinal microbiota.[11]

Viral infection[edit | edit source]

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.[12]

Pregnancy[edit | edit source]

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.[13]

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.[13] Overall bacterial load increases over the course of pregnancy.[14]

Nervous system[edit | edit source]

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

Stress[edit | edit source]

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 is introduced. Escherichia coli can activate the HPA.[15]

Stress also increases intestinal permeability.

Planned studies[edit | edit source]

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.[16]

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[edit | edit source]


Commercial testers[edit | edit source]

Academic projects[edit | edit source]

Learn more[edit | edit source]

See also[edit | edit source]

References[edit | edit source]

  1. ↑ "Definition of MICROBIOME". Merrian-Webster Medical Dictionary. Retrieved February 20, 2021.
  2. ↑ 2.0 2.1 Lakhan, Shaheen E; Kirchgessner, Annette (October 12, 2010), "Gut inflammation in chronic fatigue syndrome", Nutrition & Metabolism, 7: 79, doi:10.1186/1743-7075-7-79, ISSN 1743-7075, PMID 20939923, retrieved December 13, 2016
  3. ↑ 3.0 3.1 Lupo, Giuseppe Francesco Damiano; Rocchetti, Gabriele; Lucini, Luigi; Lorusso, Lorenzo; Manara, Elena; Bertelli, Matteo; Puglisi, Edoardo; Capelli, Enrica (March 2021). "Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME)". Scientific Reports. 11 (1): 7043. doi:10.1038/s41598-021-86425-6. ISSN 2045-2322. PMID 33782445.
  4. ↑ 4.0 4.1 Maes, Michael; Twisk, Frank N.M.; Kubera, Marta; Ringel, Karl; Leunis, Jean-Claude; Geffard, Michel (February 2012), "Increased IgA responses to the LPS of commensal bacteria is associated with inflammation and activation of cell-mediated immunity in chronic fatigue syndrome", Journal of Affective Disorders, 136 (3): 909–917, doi:10.1016/j.jad.2011.09.010, ISSN 1573-2517, PMID 21967891
  5. ↑ Sheedy, John R.; Wettenhall, Richard E. H.; Scanlon, Denis; Gooley, Paul R.; Lewis, Donald P.; McGregor, Neil; Stapleton, David I.; Butt, Henry L.; De Meirleir, Kenny L. (July 2009). "Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome". In Vivo (Athens, Greece). 23 (4): 621–628. ISSN 0258-851X. PMID 19567398.
  6. ↑ Logan, Alan C; Venket Rao, A; Irani, Dinaz (June 2003). "Chronic fatigue syndrome: lactic acid bacteria may be of therapeutic value". Medical Hypotheses. 60 (6): 915–923. doi:10.1016/S0306-9877(03)00096-3.
  7. ↑ 7.0 7.1 Shukla, Sanjay K.; Cook, Dane; Meyer, Jacob; Vernon, Suzanne D.; Le, Thao; Clevidence, Derek; Robertson, Charles E.; Schrodi, Steven J.; Yale, Steven; Frank, Daniel N. (December 18, 2015), "Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)", PLOS ONE, 10 (12): 0145453, doi:10.1371/journal.pone.0145453, ISSN 1932-6203, retrieved December 13, 2016
  8. ↑ Johnson, Cort (December 21, 2015), "Exercise Triggers Gut Changes in Chronic Fatigue Syndrome (ME/CFS)", HealthRising, Houston, retrieved December 12, 2016
  9. ↑ 9.0 9.1 Jackson, Melinda L; Butt, Henry L; Ball, Michelle; Lewis, Donald P; Bruck, Dorothy (October 23, 2015), "Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study", Sleep Science, 8 (3): 124–133, doi:10.1016/j.slsci.2015.10.001, PMID 26779319
  10. ↑ 10.0 10.1 Wallis, Amy; Butt, Henry L; Ball, Michelle; Lewis, Donald P; Bruck, Dorothy (January 13, 2016), "Support for the Microgenderome: Associations in a Human Clinical Population", Scientific Reports, doi:10.1038/srep19171, PMID 26757840
  11. ↑ Maslowski, Kendle M.; Mackay, Charles R. (January 2011), "Diet, gut microbiota and immune responses", Nature Immunology, 12 (1): 5–9, doi:10.1038/ni0111-5, ISSN 1529-2916, PMID 21169997
  12. ↑ Racaniello, Vincent (December 10, 2014), "How influenza virus infection might lead to gastrointestinal symptoms", Virology Blog, New York, retrieved December 12, 2016
  13. ↑ 13.0 13.1 Koren, Omry; Goodrich, Julia K.; Cullender, Tyler C.; Spor, Aymé; Laitinen, Kirsi; Bäckhed, Helene Kling; Gonzalez, Antonio; Werner, Jeffrey J.; Angenent, Largus T.; Knight, Rob; Bäckhed, Fredrik; Isolauri, Erika; Salminen, Seppo; Ley, Ruth E. (August 3, 2012), "Host remodeling of the gut microbiome and metabolic changes during pregnancy", Cell, 150 (3): 470–480, doi:10.1016/j.cell.2012.07.008, ISSN 1097-4172, PMID 22863002
  14. ↑ http://www.scopus.com/record/display.uri?eid=2-s2.0-53849104768&origin=inward&txGid=B73C4858FB9D5F216C9F222F22386A44.iqs8TDG0Wy6BURhzD3nFA%3a2
  15. ↑ Dinan, Timothy G.; Cryan, John F. (September 2012), "Regulation of the stress response by the gut microbiota: Implications for psychoneuroendocrinology", Psychoneuroendocrinology, 37 (9): 1369–1378, doi:10.1016/j.psyneuen.2012.03.007, ISSN 0306-4530, retrieved December 13, 2016
  16. ↑ Invest in ME – UK gut microbiota research
  17. ↑ Sheedy, John R.; Wettenhall, Richard E. H.; Scanlon, Denis; Gooley, Paul R.; Lewis, Donald P.; McGregor, Neil; Stapleton, David I.; Butt, Henry L.; De Meirleir, Kenny L. (July 2009). "Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome". In Vivo (Athens, Greece). 23 (4): 621–628. ISSN 0258-851X. PMID 19567398.
  18. ↑ Borody, Thomas J.; Nowak, Anna; Finlayson, Sarah (December 2012), "The GI microbiome and its role in Chronic Fatigue Syndrome: A summary of bacteriotherapy", Journal of the Australasian College of Nutritional and Environmental Medicine, 31 (3): 3, ISSN 1328-8040, retrieved December 13, 2016
  19. ↑ Frémont, Marc; Coomans, Danny; Massart, Sebastien; De Meirleir, Kenny (August 2013), "High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients", Anaerobe, 22: 50–56, doi:10.1016/j.anaerobe.2013.06.002, ISSN 1095-8274, PMID 23791918
  20. ↑ Morris, Gerwyn; Berk, Michael; Carvalho, A.F.; Caso, J.R.; Sanz, Y.; Maes, Michael (2016), "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.", Current Pharmaceutical Design, PMID 27634186
  21. ↑ Giloteaux, Ludovic; Goodrich, Julia K.; Walters, William A.; Levine, Susan M.; Ley, Ruth E.; Hanson, Maureen R. (December 2016). "Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome". Microbiome. 4 (1). doi:10.1186/s40168-016-0171-4. ISSN 2049-2618. PMC 4918027. PMID 27338587.
  22. ↑ Nagy-Szakal, Dorottya; Williams, Brent L.; Mishra, Nischay; Che, Xiaoyu; Lee, Bohyun; Bateman, Lucinda; Klimas, Nancy G.; Komaroff, Anthony L.; Levine, Susan; Montoya, Jose G.; Peterson, Daniel L.; Ramanan, Devi; Jain, Komal; Eddy, Meredith L.; Hornig, Mady; Lipkin, W. Ian (2017), "Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome", Microbiome, 5 (44), doi:10.1186/s40168-017-0261-y
  23. ↑ Newberry, F.; Hsieh, S.-Y.; Wileman, T.; Carding, S.R. (2018), "Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome?", Clinical Science, 132 (5): 523–542, doi:10.1042/CS20171330
  24. ↑ Wang, Taiwu; Yu, Lei; Xu, Cong; Pan, Keli; Mo, Minglu; Duan, Mingxiang; Zhang, Yao; Xiong, Hongyan (September 11, 2018). "Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function". PLOS ONE. 13 (9): e0203503. doi:10.1371/journal.pone.0203503. ISSN 1932-6203.
  25. ↑ Proal, Amy; Marshall, Trevor (November 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 immunity". Frontiers in Pediatrics. doi:10.3389/fped.2018.00373.
  26. ↑ Bakalar, Nicholas (July 7, 2016), "Gut Bacteria Are Different in People With Chronic Fatigue Syndrome", The New York Times, retrieved December 13, 2016
  27. ↑ Cha, Ariana Eunjung (June 30, 2016), "New study shows chronic fatigue syndrome may have to do with gut microbes", The Washington Post, retrieved December 13, 2016
  28. ↑ Ramanujan, Krishna (June 24, 2016), "Indicator of chronic fatigue syndrome found in gut bacteria", Cornell Chronicle, New York, retrieved December 13, 2016
  29. ↑ Johnson, Cort (February 21, 2016), "Gender Gut Wars: Australian ME/CFS Study Suggests Different Gut Treatment Protocols Needed For Men and Women", HealthRising, Houston, retrieved December 13, 2016

microbiome The full collection of microscopic organisms (especially bacteria and fungi) which are present in a particular environment, particularly inside the human body.

See ME/CFS.

The clear yellowish fluid that remains from blood plasma after clotting factors have been removed by clot formation. (Blood plasma is simply blood that has had its blood cells removed.)[1]

serum The clear yellowish fluid that remains from blood plasma after clotting factors have been removed by clot formation. (Blood plasma is simply blood that has had its blood cells removed.)

microbiome The full collection of microscopic organisms (especially bacteria and fungi) which are present in a particular environment, particularly inside the human body.

stress Stress can by either physical or psychological, or both. Stress is either 1) a state of emotional or psychological strain or 2) the physical stress (pressure or tension) that a physical object such the human body is placed under, e.g., a stress test is a medical test that monitors the cardiovascular system during strenuous exercise.

The human virome is the collection of all viruses that are found in or on humans.[2]

virome The human virome is the collection of all viruses that are found in or on humans.

myalgic encephalomyelitis (M.E.) - A disease often marked by neurological symptoms, but fatigue is sometimes a symptom as well. Some diagnostic criteria distinguish it from chronic fatigue syndrome, while other diagnostic criteria consider it to be a synonym for chronic fatigue syndrome. A defining characteristic of ME is post-exertional malaise (PEM), or post-exertional neuroimmune exhaustion (PENE), which is a notable exacerbation of symptoms brought on by small exertions. PEM can last for days or weeks. Symptoms can include cognitive impairments, muscle pain (myalgia), trouble remaining upright (orthostatic intolerance), sleep abnormalities, and gastro-intestinal impairments, among others. An estimated 25% of those suffering from ME are housebound or bedbound. The World Health Organization (WHO) classifies ME as a neurological disease.

microbiome The full collection of microscopic organisms (especially bacteria and fungi) which are present in a particular environment, particularly inside the human body.

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