Enterotype

An enterotype is a classification of living organisms based on the bacteriological composition of their gut microbiota. The discovery of three human enterotypes was announced in the April 2011 issue of Nature by Peer Bork and his associates.^[1] They found that enterotypes are not dictated by age, gender, body weight, or national divisions.^[2] There are indications that long-term diet influences enterotype.^[3] Type 1 is characterized by high levels of Bacteroides, type 2 has few Bacteroides but Prevotella are common, and type 3 has high levels of Ruminococcus.^[1]^[4]^[5]

The value of classifying by enterotype has been challenged.^[6]^[7]

In a study of gut bacteria of children in Burkina Faso (in Africa), Prevotella made up 53% of the gut bacteria, but were absent in age-matched European children.^[8]

Studies also indicate that long-term diet is strongly associated with the gut microbiome composition—those who eat plenty of protein and animal fats typical of Western diet have predominantly Bacteroides bacteria, while for those who consume more carbohydrates, especially fibre, the Prevotella species dominate.^[9]

Chimpanzees have enterotypes that are compositionally analogous to those found in humans. Using longitudinal samples, researchers found that the enterotype of individual chimpanzees varied over time.^[10]

References

^ ^a ^b Zimmer, Carl (20 April 2011). "Bacteria Divide People Into 3 Types, Scientists Say". The New York Times. Retrieved 21 April 2011. a group of scientists now report just three distinct ecosystems in the guts of people they have studied.
^ Arumugam M, Raes J, et al. (April 2011). "Enterotypes of the human gut microbiome". Nature. 473 (7346): 174–80. Bibcode:2011Natur.473..174.. doi:10.1038/nature09944. PMC 3728647. PMID 21508958. Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific.
^ Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, et al. (2011). "Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes". Science. 334 (6052): 105–108. Bibcode:2011Sci...334..105W. doi:10.1126/science.1208344. PMC 3368382. PMID 21885731.
^ Keim, Brandon (20 April 2011). "Gut-Bacteria Mapping Finds Three Global Varieties". Wired Magazine. Retrieved 21 April 2011.
^ Coghlan, Andy (20 April 2011). "Each human has one of only three gut ecosystems". New Scientist. Retrieved 21 April 2011.
^ Knights, Dan; Ward, Tonya; McKinlay, Christopher; Miller, Hannah; Gonzalez, Antonio; McDonald, Daniel; Knight, Rob (8 October 2014). "Rethinking "Enterotypes"". Cell Host & Microbe. 16 (4): 433–437. doi:10.1016/j.chom.2014.09.013. PMC 5558460. PMID 25299329.
^ Gorvitovskaia, Anastassia; Holmes, Susan P.; Huse, Susan M. (12 April 2016). "Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle". Microbiome. 15 (4): 15. doi:10.1186/s40168-016-0160-7. PMC 4828855. PMID 27068581.
^ De Filippo, C.; Cavalieri, D.; Di Paola, M.; Ramazzotti, M.; Poullet, J. B.; Massart, S.; Collini, S.; Pieraccini, G.; Lionetti, P. (2010). "Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa". Proceedings of the National Academy of Sciences. 107 (33): 14691–6. Bibcode:2010PNAS..10714691D. doi:10.1073/pnas.1005963107. PMC 2930426. PMID 20679230.
^ Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD (October 7, 2011). "Linking long-term dietary patterns with gut microbial enterotypes". Science. 334 (6052): 105–8. Bibcode:2011Sci...334..105W. doi:10.1126/science.1208344. PMC 3368382. PMID 21885731.
^ Andrew H. Moeller; Patrick H. Degnan; Anne E. Pusey; Michael L. Wilson; Beatrice H. Hahn; Howard Ochman (November 13, 2012). "Chimpanzees and humans harbour compositionally similar gut enterotypes". Nature Communications. 3 (1179): 1179. Bibcode:2012NatCo...3.1179M. doi:10.1038/ncomms2159. PMC 3520023. PMID 23149725.

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[NYT-1] Zimmer, Carl (20 April 2011). "Bacteria Divide People Into 3 Types, Scientists Say". The New York Times. Retrieved 21 April 2011. a group of scientists now report just three distinct ecosystems in the guts of people they have studied.

[Nature-2] Arumugam M, Raes J, et al. (April 2011). "Enterotypes of the human gut microbiome". Nature. 473 (7346): 174–80. Bibcode:2011Natur.473..174.. doi:10.1038/nature09944. PMC 3728647. PMID 21508958. Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific.

[Wu_et_al-3] Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, et al. (2011). "Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes". Science. 334 (6052): 105–108. Bibcode:2011Sci...334..105W. doi:10.1126/science.1208344. PMC 3368382. PMID 21885731.

[Wired-4] Keim, Brandon (20 April 2011). "Gut-Bacteria Mapping Finds Three Global Varieties". Wired Magazine. Retrieved 21 April 2011.

[NewScientist-5] Coghlan, Andy (20 April 2011). "Each human has one of only three gut ecosystems". New Scientist. Retrieved 21 April 2011.

[2014cellhostandmicrobentero-6] Knights, Dan; Ward, Tonya; McKinlay, Christopher; Miller, Hannah; Gonzalez, Antonio; McDonald, Daniel; Knight, Rob (8 October 2014). "Rethinking "Enterotypes"". Cell Host & Microbe. 16 (4): 433–437. doi:10.1016/j.chom.2014.09.013. PMC 5558460. PMID 25299329.

[2016microbiomejournalentero-7] Gorvitovskaia, Anastassia; Holmes, Susan P.; Huse, Susan M. (12 April 2016). "Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle". Microbiome. 15 (4): 15. doi:10.1186/s40168-016-0160-7. PMC 4828855. PMID 27068581.

[8] De Filippo, C.; Cavalieri, D.; Di Paola, M.; Ramazzotti, M.; Poullet, J. B.; Massart, S.; Collini, S.; Pieraccini, G.; Lionetti, P. (2010). "Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa". Proceedings of the National Academy of Sciences. 107 (33): 14691–6. Bibcode:2010PNAS..10714691D. doi:10.1073/pnas.1005963107. PMC 2930426. PMID 20679230.

[9] Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD (October 7, 2011). "Linking long-term dietary patterns with gut microbial enterotypes". Science. 334 (6052): 105–8. Bibcode:2011Sci...334..105W. doi:10.1126/science.1208344. PMC 3368382. PMID 21885731.

[10] Andrew H. Moeller; Patrick H. Degnan; Anne E. Pusey; Michael L. Wilson; Beatrice H. Hahn; Howard Ochman (November 13, 2012). "Chimpanzees and humans harbour compositionally similar gut enterotypes". Nature Communications. 3 (1179): 1179. Bibcode:2012NatCo...3.1179M. doi:10.1038/ncomms2159. PMC 3520023. PMID 23149725.

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