Talk:Microbiota

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Opening[edit]

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)

Introduction[edit]

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)

Lederberg-microbiome connecting reference still missing[edit]

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)

Here is a citation to consult, as being the origin:
  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]

Science writer needed[edit]

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)

Microbbiome[edit]

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)

Move discussion in progress[edit]

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)

Transfer approaches[edit]

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]

Note that the above misspelled "pawnobes" => "pawnobiomes". Also, the Wikipedia doi servers don't seem to be working, so I expanded the references manually. Stigmatella aurantiaca (talk) 11:46, 10 July 2015 (UTC)

References

  1. ^ Ridaura, Vanessa K.; Faith, Jeremiah J.; Rey, Frederico E.; et al. (2013). "Cultured gut microbiota from twins discordant for obesity modulate adiposity and metabolic phenotypes in mice". Science. 341 (6150). doi:10.1126/science.1241214. PMID 24009397. Retrieved 10 July 2015. 
  2. ^ Finucane, Mariel M.; Sharpton, Thomas J.; Laurent, Timothy J.; Pollard, Katherine S. (2014). "A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter". PLoS ONE. 9 (1): e84689. doi:10.1371/journal.pone.0084689. Retrieved 10 July 2015. 
  3. ^ Voss, Jameson D.; Leon, Juan C.; Dhurandhar, Nikhil V.; Robb, Frank T. (2015). "Pawnobiome: Manipulation of the Hologenome Within One Host Generation and Beyond". Frontiers in Microbiology. 6 (00697). doi:10.3389/fmicb.2015.00697. Retrieved 10 July 2015. 

This article is wicked well written[edit]

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)

Ten to one: myth?[edit]

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)

first sentence anthropocentric: "our body space"[edit]

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)

PLoS One[edit]

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)

Maybe my memory is faulty, as I'd remembered P1 as having a bad rep over publishing dodgy stuff (#creatorgate ? or this[1]), but searching around now it doesn't seem so bad, if not stellar. Are you relaxed about it? Alexbrn (talk) 19:03, 16 June 2016 (UTC)
As the editor who added the citation: I admit I've seen some primary studies in P1 which looked less than reassuring (grammar mistakes, etc.), but Jytdog is right that it's indexed in Pubmed and MEDLINE, so it's a priori MEDRS-compliant. Furthermore, this material in particular is not controversial—I did a project involving microbiomics and malnutrition recently, and saw approximately equivalent statements in many reviews. Here are two probably better ones: [2][3] FourViolas (talk) 19:26, 16 June 2016 (UTC)
awesome, even more recent. Please feel free to restore. thx Jytdog (talk) 19:27, 16 June 2016 (UTC)
Cool, let's use those then. I would add that there's no such thing as an a priori MEDRS-compliant source - it's always a question of judgement which - sure - is informed by such things as MEDLINE-indexing, impact factor, history, etc. Alexbrn (talk) 19:29, 16 June 2016 (UTC)
You're right, I misspoke. Reliability is always relative to the claim in question. I probably meant ceteris paribus, and I really meant that if we're evaluating reliability at the journal level, it seems to be in the spirit of WP:RS to default to the opinion of respected index curation committees rather than indignant activist blogs (even if they're "on the right side"). Material restored after adjustment to new sources, PLoS kept to support the no-longer-cutting-edge non-gut info.

Size of human microbiome redux[edit]

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)

FourViolas: Your note shows a bias for the 1.3:1 ratio, perhaps because the 10:1 was challenged this year by one Nature News author's op-ed based on just two research groups contesting the 10:1 ratio. The source in Cell is the only peer-reviewed work supporting this concept, but we are unable to read the authors' reasoning (available only by subscription). By contrast, the HMP 10:1 statement is used in various NIH documents reviewed by dozens of the nation's top microbiome scientists. Someone would have challenged this number if it was out of order. MEDRS names NIH as one of the highest-quality sources; even if we don't have the original research deriving the number, my vote goes in support of 10:1 because it comes from NIH. --Zefr (talk) 03:49, 17 June 2016 (UTC)
The current NIH citation is to a 2012 press release (and language hasn't changed since); the first serious challenge to 10:1 seems to have been in 2014. Before then, it's entirely plausible that even stellar scientists would not have thought to hunt the original source for a factoid they'd heard hundreds of times (especially because experts "don’t think it will actually have any biological significance”), and in fact HMP "about us" literature never bothers to provide a source for it. A quick fair-use highlight reel of the Cell paper:
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.
As Alexbrn just reminded me, 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)
Or, to be fairer, one group's 45-year-old guesstimate vs. two groups' modern guesstimate. FourViolas (talk) 04:48, 17 June 2016 (UTC)
Thanks for the thorough review. I know the ratio is a rough guesstimate no matter who makes it, and deriving a satisfying rigorous number is unlikely to attract specific research. But let's keep in mind that we write the encyclopedia for all possible readers, most of whom are not scientists. Taking a generalist's view, I suggest the Cell guesstimate is a fringe number with undue weight until given more proof. The 10:1 ratio is what NIH/HMP is comfortable in communicating and so should we. Your note states: It has been widely reported that microbiota "outnumber human cells by 10 to 1"; however, more recent estimates suggest that the ratio, although variable, is closer to 1.3 to 1. I propose this statement be revised to say, "Experts estimate that microbiota outnumber human cells by 10 to 1,(HMP ref) although some scientists dispute this ratio as too large." --Zefr (talk) 13:29, 17 June 2016 (UTC)
FourViolas this is inappropriate use of sourcing. We don't source information about health in Wikipedia to press releases and unpublished (!) primary sources. We use reviews. This needs fixing here and at Human microbiome. Jytdog (talk) 15:16, 17 June 2016 (UTC)
I know we don't, and for good reason, but my point is that this isn't really health information at all; as multiple experts in the above-cited news stories noted, there no practical or clinical reason anyone would need to construct a one-to-one correspondence of microbiotic and somatic cells. That's precisely why 10:1 snuck into so many otherwise strictly checked sources. The only reason to check it is accuracy for accuracy's sake.
But WP:DUE is WP:DUE, so I guess Zefr's version is the right one to include (with a ref at the end to the Nature report). I appreciate the FRINGE concern, but I don't think it applies; 1.3:1 has been published as fact in a news story in Nature, and there's been no retraction. Anecdotally, my (respectable) university's entire Dept. of Molecular and Cellular Biology seems to have abandoned 10:1 due to this research, replacing it with the fact that the human gut metagenome is 150x larger than the human genome.[1][2] Sorry for all the fuss over trivia.

References

  1. ^ Greenblum, S.; Turnbaugh, P. J.; Borenstein, E. (2011). "Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease". Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. 109 (2): 594–599. doi:10.1073/pnas.1116053109. PMID 22184244. 
  2. ^ Sung, Jaeyun; Hale, Vanessa; Merkel, Annette C.; Kim, Pan-Jun; Chia, Nicholas (2016). "Metabolic modeling with Big Data and the gut microbiome". Applied & Translational Genomics. doi:10.1016/j.atg.2016.02.001. 
FourViolas (talk) 02:57, 18 June 2016 (UTC)
Two things:
The Nature News report was about an unpublished manuscript and has been noted indirectly, that paper has finally published in Cell and entered the literature; it is Sender R, Fuchs S, Milo R. Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans. Cell. 2016 Jan 28;164(3):337-40. PMID 26824647. They mention the Human microbiome article as typical badness (!). So what else. I found the 2014 commentary mentioned in the Nature News piece by Judah Rosner; Judah L. Rosner for Microbe Magazine, Feb 2014. Ten Times More Microbial Cells than Body Cells in Humans?. It makes note of, but doesn't cite, a "new American Academy of Microbiology report, “FAQ: Human Microbiome,”" that partly fixes the issue. That FAQ is: American Academy of Microbiology FAQ: Human Microbiome January 2014. The section on "how big" mentions the 10:1 ration, makes it clear the numbers are estimates, and says most recent estimates of human cells are much bigger, so the ratio is probably ~ 3:1. I am going to update the Human microbiome article with this stuff.
In this article, the section on humans should just be the lead of the Human microbiome article with a link to main, per WP:SYNC. There is content here that is not there. So after I update the the human microbiome article with the stuff about relative size, I am going to merge the content about human microbiome to that article, update the lead there if necessary, and then copy the lead of that article back over here. Jytdog (talk) 19:22, 18 June 2016 (UTC)

Lead too big, too detailed - remove second paragraph[edit]

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)

See the section directly above this one. That part of the LEAD used to be very brief, citing the incorrect meme that microbiota in/on a person outnumber human cells by some huge factor. That has been outdated for a long time. The real answer is not simple, so I had a dilemma on how to fix it. Omit that in the lead, or explain it. I figured omitting it would lead to people re-inserting the wrong info, so I went for the longer explanation. Folks at the time were OK with that. And hey we humans are pretty self-involved. But if you have a different notion about how to handle the problem I am all ears. Jytdog (talk) 07:20, 18 September 2016 (UTC)
Delete it and leave a comment that says to put any facts about human microbiota in the appropriate article. Richard-of-Earth (talk) 03:58, 19 September 2016 (UTC)
That makes sense to me. Since there are separate articles for human and general microbiota, the material should be split as cleanly as possible. (Wikipedia:Summary_style#Lead_section gives very little guidance.)
As a reader and science student in many areas of biology, I've noticed a general tendency for tightly-focused medical information to displace facts relevant to general background and basic research. Most of this article is a pleasant exception, staying at the generality of organisms, ecosystems, and general techniques and history; the lead should reflect this. FourViolas (talk) 04:26, 19 September 2016 (UTC)
Well, the 2nd paragraph has been removed. It is more concise now. Richard-of-Earth (talk) 18:49, 19 September 2016 (UTC)
FourViolas and Richard-of-Earth: true but the first sentence of the lede that has beeen there for I dunnow how long still irks me, because it is really no good definition, talking priestly about inhabiting "our body space" which this article isnt and hasnt been about, the human microbiome. It is from an inferior source and i am not sure it even quotes lederberg correctly. I ve tried to move the refs out to start the clean up, but alas, see below I was reverted by epipelagic. someone/anyone got a more neutral biologic definition?--Wuerzele (talk) 08:41, 20 February 2017 (UTC)

Awkward rewrite[edit]

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)

I'm not sure why you appended your comment to the thread above titled "Lead too big, too detailed", so I've taken the liberty of creating a separate title for a new thread. The reason I referred to your edits as an "awkward rewrite" was to do with the way you left microbiota defined in the lead using a quote, yet you withdrew the source for the quote. If you are going to make an extended quote at the start of an article, then you must source it on the spot. It's no good repeating the quote later in the article and providing a source there. In general, the article is well cited with 66 references. So why would you slap a global tag on the article claiming it is inadequately cited? I notice you subsequently made this absurd and pointy mess of one paragraph that could do with more citations. What would be constructive would be to do the work and supply the missing citations.--Epipelagic (talk) 09:05, 20 February 2017 (UTC)
Ahh...I'm not sure why you had to open a new section as my comment fit fine into the prior section, and editing other editors talk page edits is not exactly WP:netiquette. Your accusation of an awkward rewrite of mine remains moot, since if you took a careful look, I didnt rewrite anything but just left the (awkward) quote that had been there for ages, and its gotten mooter since. :-)
As far as me taking the liberty to attach (or as you call it pejoratively ¨slap¨ another unhappy term of yours) a refimprove to the article: consider that I may be looking more closely than you, and didint want to tag each unsourced sentence. its definitely not the number of refs that count. And reverting is for vandals, which i am not.
Lastly, your brazenness to suggest to me "what would be constructive" and not contribute yourself, puts the icing on the cake (or the pie that you throw, eh, slap in my face)! Oh, Epipelagic, behaving as if from the Hadopelagic, our nomen est omen and so i wish your dream may come true: may the sun truly shine on you! theres no need to reply here, as your reply above answered all questions I had. --Wuerzele (talk) 15:10, 20 February 2017 (UTC)
Yes, now we are ablaze in the light of your subsequent good works, a rescue from the hadopelagic has been achieved and the last sentence in my reply above has been exposed as idle pomposity. It was a delayed reaction to the behaviour of another editor, nothing to do with you, and a reminder to myself to not displace frustration. --Epipelagic (talk) 18:08, 20 February 2017 (UTC)
Epipelagic you dont ping, you mudsling, and now you are sarcastic because you have contributed nothing to the article in the last 3 years. please stay away. --Wuerzele (talk) 20:26, 20 February 2017 (UTC)