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Misleading opening: "A microbiome is "the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space." This is misleading, because one gets the impression that "microbiome" is limited to the human body. Better have this citation move further down when it comes to history of this term. Mosquito337 — Preceding unsigned comment added by 46.140.90.18 ( talk) 16:36, 3 September 2014 (UTC)
The last sentence in the "Introduction" section reads: "Indeed, an organism's complement of microbial inhabitants can be considered as a forgotten organ" (emphasis added). Besides needing a citation/source, was any microbiome ever really "forgotten"? If so, when was it last known? A better word is needed. -- Thorwald ( talk) 20:10, 23 July 2012 (UTC)
There is no mention of microbiome in the linked J Lederberg article, though the microbiome article credits him with coining the term without providing any citation other than this link. Per wiki policy, we need to cite something appropriate, or remove this statement. Prof D. — Preceding unsigned comment added by 67.175.245.235 ( talk) 23:18, 23 August 2012 (UTC)
J. Lederberg J & McCray AT (2001) ’Ome Sweet ’Omics—a genealogical treasury of words. Scientist 15:8.
This is cited by the following article, where the attribution of the term microbiome is made to Lederberg:
The NIH HMP Working Group, J. Peterson, S. Garges, et al. (2009) The NIH Human Microbiome Project, Genome Res. 19: 2317-2323.
[Prof D]
This is a terrific article, but could really use a rewrite for a general public audience. — Preceding unsigned comment added by 166.137.191.47 ( talk) 21:54, 31 December 2013 (UTC)
It would be useful if there was a discussion about colon fecal transplants and how disease has been cured by this procedure — Preceding unsigned comment added by 2601:3:9380:9AA:D58F:3480:9F62:84D ( talk) 01:48, 5 April 2014 (UTC)
There is a move discussion in progress on Talk:Microbiota (disambiguation) which affects this page. Please participate on that page and not in this talk page section. Thank you. — RMCD bot 20:15, 27 January 2015 (UTC)
An unregistered user added the content below today. It requires further consideration for content acceptance and editing . WP:NOTJOURNAL applies. -- Zefr ( talk) 01:50, 8 July 2015 (UTC)
The microbial source of some of the microbiome's effects are difficult to isolate regardless of sequencing technique. For instance, the obesity phenotype transfers from humans to mice with stool transplant. [1] However, the taxonomic signature of the gut microbiome is the same between those with and without obesity. [2] Thus, stool transfers allow identification of phenotypic effects even if the component(s) exerting the effects are unknown. Once a phenotype transfers to multiple hosts, continuing to select stool from the host with the strongest manifestation of phenotype could further select the causal component(s) with each transfer. With enough transfers this method would create microbial products of artificial selection known as "pawnobes." [3]
References
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I don't know which user is most responsible for writing this article, so I'm putting this here. This article is wicked well written. Good job, y'all! — Preceding unsigned comment added by 73.238.115.248 ( talk) 15:12, 3 October 2015 (UTC)
In 2010, the Small Things Considered blog challenged the reliability of the oft-repeated-in-supposedly-RS claim that "microbial cells outnumber human cells by 10 to 1". In 2014, microbiologist Judah Rosner wrote Microbe magazine arguing that the line, although catchy and very well-established in should-be-RS, is in fact an old myth dating back to one guy's rough estimate made in 1972. This Boston Globe story (non-MEDRS) agreed in 2014, and more recently this news report in Nature and this Atlantic article reported on a more careful new estimate of around 1.3:1. I'm going to BOLDly change the body text to something about "trillions of microbes" and describe the disagreement per WP:DUE in a footnote. FourViolas ( talk) 15:31, 9 February 2016 (UTC)
I really think the Joshua Lederberg sentence should not have this prominent position it currently has at the very front . The reason is it biases the site towards the human microbiome while the body of the article correctly shows otherwise.
I suggest using the more all encompassing NIH def for example, A microbiome is all of the genetic material found within an individual microbe such as a bacterium, fungal cell, or virus. It also may refer to the collection of genetic material found in a community of microbes that live together. by genome.gov. comments? -- Wuerzele ( talk) 00:05, 23 March 2016 (UTC)
User:Alexbrn I don't get this revert. that is a recent review indexed in Pubmed.. I am not aware of issues with PLoS One. Would you please explain? thx Jytdog ( talk) 18:40, 16 June 2016 (UTC)
While I have your attention, could either of you advise on the IRL citogenesis concern I raised two sections up? I'm not personally satisfied with the non-explanation currently in the article. It really does seem like a situation which doesn't fit standard MEDRS guidelines. Even though the statement has been cribbed back and forth through many otherwise impeccable sources, it's frankly a pretty meaningless statistic and is only used for gee-whiz value, and has therefore never been subjected to the rigorous scrutiny we expect from such sources. All the investigations I've found have concluded that the only apparent ultimate source is a very old study whose authors have explicitly stated that their work was insufficient to support this conclusion. So we don't have, as it appears at first glance, the NIH vs. a barely-cited primary source and preliminary news articles in Nature and Cell; we have a trivial dogma almost nobody has bothered to question vs. the few qualified people who have tried to fact-check or update it. My proposed alternative is to put something like the current Microbiota#cite_note-9 into the article. FourViolas ( talk) 02:49, 17 June 2016 (UTC)
Both the numerator (number of microbial cells) and the denominator (human cells) of this 10:1 ratio are based on crude assessments....We performed a thorough review of the literature and found a long chain of citations originating from one “back of the envelope” estimate....Almost all recent papers in the field of gut microbiota directly or indirectly rely on a single paper (Savage, 1977) discussing the overall number of bacteria in the gut. Interestingly, review of the original paper (Savage, 1977) demonstrates that it actually cites another paper for the estimate (Luckey, 1972)...an illuminating example of a back-of-the-envelope estimate, which was elegantly performed, yet was probably never meant to serve as the cornerstone reference number to be cited decades later. On top of this historical contingency, a recent report from the NIH stated that 1%–3% of body mass is composed of bacteria (with no reference ascribed)....[After detailed review of recent literature] we use 3.9 × 10^13 as our estimate for the number of bacteria in the “reference man”....[and based primarily on the assumptions that erythrocytes dominate human cells, there are 5L of blood in a reference man and 5 x 10^12 erythrocytes/L] 3.0 × 10^13 human cells in the 70 kg “reference man” with 2% uncertainty and 14% CV....we arrive at our updated estimate of B/H = 1.3, with an uncertainty of 25% and a variation of 53% over the population of standard 70 kg males.
there's no such thing as an a priori MEDRS-compliant source. Even the sources we trust most for substantive information need to be critically examined to see if a particular statement is actually based on empirical science or on hearsay. I agree the research is limited so far, but unless the Cell authors are lousy at literature reviews the empirical evidence has two research groups using modern knowledge and techniques vs. one group's 45-year-old guesstimate. FourViolas ( talk) 04:38, 17 June 2016 (UTC)
References
Per WP:LEAD the lead is suppose to introduce and summarize the article. The first paragraph seems fine. The second paragraph is a coatrack of items not in the article and is totally about humans when the article is about all living organisms that have microbiota. I was thinking of moving it to its own paragraph in the article, but I am leaning t word removing it completely. Richard-of-Earth ( talk) 05:38, 18 September 2016 (UTC)
In this edit, you accused me of an awkward rewrite, but only the refs were moved out of the lede into the body , Epipelagic, so your(pejorative) edit summary is incorrect. Also why did you remove the template calling for citations? -- Wuerzele ( talk) 08:13, 20 February 2017 (UTC)
@ Zefr: I am in favor of restoring recent improvements. Even though it's mostly based on primary research, it is well-written and improves the quality of the article. -- Vojtěch Dostál ( talk) 14:18, 5 February 2019 (UTC)
In 2019, microbiome field has several breakthroughs due to multidisciplinary research on host-microbiota interactions. A paper entitled “Hype or Hope?” published by Nature Reviews Microbiology, discussed the promising future of microbiome research which aims to promote human health. It is stated that some microbiome-based therapeutics such as probiotics and prebiotics are already on the market or in development thanks to the rapidly evolving microbiome research. Scientific evidence has shown associations between microbiome and metabolic diseases such as inflammatory bowel disease, fatty liver disease, cancer, and diabetes. [1] For example, a mouse study in 2015 shows that two commonly used dietary emulsifiers carboxymethylcellulose (CMC) and polysorbate 80 (P80) can potentially cause inflammatory bowel diseases, weight gain, and other metabolic syndromes. [2]
When investigating host-microbiota interactions, animal model organisms are taken into careful considerations. Even though mice are traditional experimental animals that have similar physiological characteristics to that of humans, Angela Douglas argues that simple animal models such as flies, worms, and zebrafish have unique advantages. With relatively short life spans, they are more time-efficient and cost-effective. This allows complex experiment designs and genetics screen. [3]
These findings have strong potential to be applied to human health by microbiota-based nutrition. Upon the realization that there may be no one-size-fits-all diet, a recent review paper stated that host-derived factors can influence diet-microbiota alterations in multiple ways. Thus, scientists still need to overcome the complexity of person-specific host, microbiota, and diet interactions. [4]
References
Lede says: "Microbiota are [...] microorganisms" found in and on all multicellular organisms[...]. Microbiota includes bacteria, archaea, protists, fungi and viruses." But microorganisms says "Viruses are generally regarded as not living and therefore not considered as microorganisms". So, which is it? Checking the refs, I can't find anywhere that explicitly states viruses are part of the microbiota or microbiome. -- DewiMorgan ( talk) 18:35, 5 April 2020 (UTC)
The lede claims these terms are synonymous. I suspect instead that microbiota is more likely to mean the group of things occupying the environmental niche called the microbiome. One can often be used as a synecdoche for the other, but that doesn't mean they're the same thing.
In the same way, the jungle is more than the sum of the "biota" (plants/animals/fungi/etc) that make it up - it's also things like weather systems, water tables and such that make up the whole jungle biome. But someone can say "the jungle" to refer just to the trees, or "the trees" to refer to the jungle. Doesn't mean they're synonymous, it's just a literary device. -- DewiMorgan ( talk) 18:40, 5 April 2020 (UTC)
Later in the page, it says "The human microbiome refers to their genomes" - which gives a different definition, which may or may not be correct, but calls out a clear distinction, saying that they are not synonymous. -- DewiMorgan ( talk) 18:54, 5 April 2020 (UTC)
![]() | This article is rated B-class on Wikipedia's
content assessment scale. It is of interest to the following WikiProjects: | ||||||||||
|
![]() | Ideal sources for Wikipedia's health content are defined in the guideline
Wikipedia:Identifying reliable sources (medicine) and are typically
review articles. Here are links to possibly useful sources of information about Microbiota.
|
![]() | Material from Microbiota was split to Earth Microbiome Project on 02:03, 5 March 2012. The former page's history now serves to provide attribution for that content in the latter page, and it must not be deleted so long as the latter page exists. Please leave this template in place to link the article histories and preserve this attribution. |
Misleading opening: "A microbiome is "the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space." This is misleading, because one gets the impression that "microbiome" is limited to the human body. Better have this citation move further down when it comes to history of this term. Mosquito337 — Preceding unsigned comment added by 46.140.90.18 ( talk) 16:36, 3 September 2014 (UTC)
The last sentence in the "Introduction" section reads: "Indeed, an organism's complement of microbial inhabitants can be considered as a forgotten organ" (emphasis added). Besides needing a citation/source, was any microbiome ever really "forgotten"? If so, when was it last known? A better word is needed. -- Thorwald ( talk) 20:10, 23 July 2012 (UTC)
There is no mention of microbiome in the linked J Lederberg article, though the microbiome article credits him with coining the term without providing any citation other than this link. Per wiki policy, we need to cite something appropriate, or remove this statement. Prof D. — Preceding unsigned comment added by 67.175.245.235 ( talk) 23:18, 23 August 2012 (UTC)
J. Lederberg J & McCray AT (2001) ’Ome Sweet ’Omics—a genealogical treasury of words. Scientist 15:8.
This is cited by the following article, where the attribution of the term microbiome is made to Lederberg:
The NIH HMP Working Group, J. Peterson, S. Garges, et al. (2009) The NIH Human Microbiome Project, Genome Res. 19: 2317-2323.
[Prof D]
This is a terrific article, but could really use a rewrite for a general public audience. — Preceding unsigned comment added by 166.137.191.47 ( talk) 21:54, 31 December 2013 (UTC)
It would be useful if there was a discussion about colon fecal transplants and how disease has been cured by this procedure — Preceding unsigned comment added by 2601:3:9380:9AA:D58F:3480:9F62:84D ( talk) 01:48, 5 April 2014 (UTC)
There is a move discussion in progress on Talk:Microbiota (disambiguation) which affects this page. Please participate on that page and not in this talk page section. Thank you. — RMCD bot 20:15, 27 January 2015 (UTC)
An unregistered user added the content below today. It requires further consideration for content acceptance and editing . WP:NOTJOURNAL applies. -- Zefr ( talk) 01:50, 8 July 2015 (UTC)
The microbial source of some of the microbiome's effects are difficult to isolate regardless of sequencing technique. For instance, the obesity phenotype transfers from humans to mice with stool transplant. [1] However, the taxonomic signature of the gut microbiome is the same between those with and without obesity. [2] Thus, stool transfers allow identification of phenotypic effects even if the component(s) exerting the effects are unknown. Once a phenotype transfers to multiple hosts, continuing to select stool from the host with the strongest manifestation of phenotype could further select the causal component(s) with each transfer. With enough transfers this method would create microbial products of artificial selection known as "pawnobes." [3]
References
{{
cite journal}}
: Explicit use of et al. in: |last4=
(
help)
{{
cite journal}}
: CS1 maint: unflagged free DOI (
link)
{{
cite journal}}
: CS1 maint: unflagged free DOI (
link)
I don't know which user is most responsible for writing this article, so I'm putting this here. This article is wicked well written. Good job, y'all! — Preceding unsigned comment added by 73.238.115.248 ( talk) 15:12, 3 October 2015 (UTC)
In 2010, the Small Things Considered blog challenged the reliability of the oft-repeated-in-supposedly-RS claim that "microbial cells outnumber human cells by 10 to 1". In 2014, microbiologist Judah Rosner wrote Microbe magazine arguing that the line, although catchy and very well-established in should-be-RS, is in fact an old myth dating back to one guy's rough estimate made in 1972. This Boston Globe story (non-MEDRS) agreed in 2014, and more recently this news report in Nature and this Atlantic article reported on a more careful new estimate of around 1.3:1. I'm going to BOLDly change the body text to something about "trillions of microbes" and describe the disagreement per WP:DUE in a footnote. FourViolas ( talk) 15:31, 9 February 2016 (UTC)
I really think the Joshua Lederberg sentence should not have this prominent position it currently has at the very front . The reason is it biases the site towards the human microbiome while the body of the article correctly shows otherwise.
I suggest using the more all encompassing NIH def for example, A microbiome is all of the genetic material found within an individual microbe such as a bacterium, fungal cell, or virus. It also may refer to the collection of genetic material found in a community of microbes that live together. by genome.gov. comments? -- Wuerzele ( talk) 00:05, 23 March 2016 (UTC)
User:Alexbrn I don't get this revert. that is a recent review indexed in Pubmed.. I am not aware of issues with PLoS One. Would you please explain? thx Jytdog ( talk) 18:40, 16 June 2016 (UTC)
While I have your attention, could either of you advise on the IRL citogenesis concern I raised two sections up? I'm not personally satisfied with the non-explanation currently in the article. It really does seem like a situation which doesn't fit standard MEDRS guidelines. Even though the statement has been cribbed back and forth through many otherwise impeccable sources, it's frankly a pretty meaningless statistic and is only used for gee-whiz value, and has therefore never been subjected to the rigorous scrutiny we expect from such sources. All the investigations I've found have concluded that the only apparent ultimate source is a very old study whose authors have explicitly stated that their work was insufficient to support this conclusion. So we don't have, as it appears at first glance, the NIH vs. a barely-cited primary source and preliminary news articles in Nature and Cell; we have a trivial dogma almost nobody has bothered to question vs. the few qualified people who have tried to fact-check or update it. My proposed alternative is to put something like the current Microbiota#cite_note-9 into the article. FourViolas ( talk) 02:49, 17 June 2016 (UTC)
Both the numerator (number of microbial cells) and the denominator (human cells) of this 10:1 ratio are based on crude assessments....We performed a thorough review of the literature and found a long chain of citations originating from one “back of the envelope” estimate....Almost all recent papers in the field of gut microbiota directly or indirectly rely on a single paper (Savage, 1977) discussing the overall number of bacteria in the gut. Interestingly, review of the original paper (Savage, 1977) demonstrates that it actually cites another paper for the estimate (Luckey, 1972)...an illuminating example of a back-of-the-envelope estimate, which was elegantly performed, yet was probably never meant to serve as the cornerstone reference number to be cited decades later. On top of this historical contingency, a recent report from the NIH stated that 1%–3% of body mass is composed of bacteria (with no reference ascribed)....[After detailed review of recent literature] we use 3.9 × 10^13 as our estimate for the number of bacteria in the “reference man”....[and based primarily on the assumptions that erythrocytes dominate human cells, there are 5L of blood in a reference man and 5 x 10^12 erythrocytes/L] 3.0 × 10^13 human cells in the 70 kg “reference man” with 2% uncertainty and 14% CV....we arrive at our updated estimate of B/H = 1.3, with an uncertainty of 25% and a variation of 53% over the population of standard 70 kg males.
there's no such thing as an a priori MEDRS-compliant source. Even the sources we trust most for substantive information need to be critically examined to see if a particular statement is actually based on empirical science or on hearsay. I agree the research is limited so far, but unless the Cell authors are lousy at literature reviews the empirical evidence has two research groups using modern knowledge and techniques vs. one group's 45-year-old guesstimate. FourViolas ( talk) 04:38, 17 June 2016 (UTC)
References
Per WP:LEAD the lead is suppose to introduce and summarize the article. The first paragraph seems fine. The second paragraph is a coatrack of items not in the article and is totally about humans when the article is about all living organisms that have microbiota. I was thinking of moving it to its own paragraph in the article, but I am leaning t word removing it completely. Richard-of-Earth ( talk) 05:38, 18 September 2016 (UTC)
In this edit, you accused me of an awkward rewrite, but only the refs were moved out of the lede into the body , Epipelagic, so your(pejorative) edit summary is incorrect. Also why did you remove the template calling for citations? -- Wuerzele ( talk) 08:13, 20 February 2017 (UTC)
@ Zefr: I am in favor of restoring recent improvements. Even though it's mostly based on primary research, it is well-written and improves the quality of the article. -- Vojtěch Dostál ( talk) 14:18, 5 February 2019 (UTC)
In 2019, microbiome field has several breakthroughs due to multidisciplinary research on host-microbiota interactions. A paper entitled “Hype or Hope?” published by Nature Reviews Microbiology, discussed the promising future of microbiome research which aims to promote human health. It is stated that some microbiome-based therapeutics such as probiotics and prebiotics are already on the market or in development thanks to the rapidly evolving microbiome research. Scientific evidence has shown associations between microbiome and metabolic diseases such as inflammatory bowel disease, fatty liver disease, cancer, and diabetes. [1] For example, a mouse study in 2015 shows that two commonly used dietary emulsifiers carboxymethylcellulose (CMC) and polysorbate 80 (P80) can potentially cause inflammatory bowel diseases, weight gain, and other metabolic syndromes. [2]
When investigating host-microbiota interactions, animal model organisms are taken into careful considerations. Even though mice are traditional experimental animals that have similar physiological characteristics to that of humans, Angela Douglas argues that simple animal models such as flies, worms, and zebrafish have unique advantages. With relatively short life spans, they are more time-efficient and cost-effective. This allows complex experiment designs and genetics screen. [3]
These findings have strong potential to be applied to human health by microbiota-based nutrition. Upon the realization that there may be no one-size-fits-all diet, a recent review paper stated that host-derived factors can influence diet-microbiota alterations in multiple ways. Thus, scientists still need to overcome the complexity of person-specific host, microbiota, and diet interactions. [4]
References
Lede says: "Microbiota are [...] microorganisms" found in and on all multicellular organisms[...]. Microbiota includes bacteria, archaea, protists, fungi and viruses." But microorganisms says "Viruses are generally regarded as not living and therefore not considered as microorganisms". So, which is it? Checking the refs, I can't find anywhere that explicitly states viruses are part of the microbiota or microbiome. -- DewiMorgan ( talk) 18:35, 5 April 2020 (UTC)
The lede claims these terms are synonymous. I suspect instead that microbiota is more likely to mean the group of things occupying the environmental niche called the microbiome. One can often be used as a synecdoche for the other, but that doesn't mean they're the same thing.
In the same way, the jungle is more than the sum of the "biota" (plants/animals/fungi/etc) that make it up - it's also things like weather systems, water tables and such that make up the whole jungle biome. But someone can say "the jungle" to refer just to the trees, or "the trees" to refer to the jungle. Doesn't mean they're synonymous, it's just a literary device. -- DewiMorgan ( talk) 18:40, 5 April 2020 (UTC)
Later in the page, it says "The human microbiome refers to their genomes" - which gives a different definition, which may or may not be correct, but calls out a clear distinction, saying that they are not synonymous. -- DewiMorgan ( talk) 18:54, 5 April 2020 (UTC)