Talk:Gut microbiota

Proposal to remove table of bacteria commonly found in the human colon

I suggest we remove the table titled “Bacteria commonly found in the human colon” which lists species like Bacteroides fragilis, E. coli, and others with fixed incidence percentages. The values provided are inaccurate, and don’t reflect current understanding of the gut microbiota. This data type is known to be sparse and highly variable across individuals. No species is universally present, so claiming 100% incidence for multiple organisms is misleading. The microbiota is also highly dynamic changing over lifespan which is not captured here.Decent swan (talk) 00:47, 4 April 2025 (UTC)

Section on development of enteric protection, immune system, and vaccine effect

Removal of content in Special:Diff/1283935295 was justified because the information was mostly based on sources from 9-12 years ago, such as the 2013 Sommer review, (WP:MEDDATE) and on conjecture from lab animal studies.

The review in NPJ Vaccines is not indexed for MEDLINE (i.e., insufficiently established to be reliable); the "review" is on a few preliminary human studies, but predominantly on lab animal research (WP:MEDANIMAL), which makes it an unreliable source, itself having a narrative that is highly speculative. Guidelines: WP:NOTTEXTBOOK #6,7 and WP:WFTWA. Zefr (talk) 16:34, 4 April 2025 (UTC)

Thanks again for the reply.

I’m keen to include the microbiota–vaccine response literature because it represents the strongest evidence we have that the microbiome modulates systemic immunity in humans. Vaccination is one of the only times we introduce a well-defined immune challenge in otherwise healthy individuals, and when paired with microbiome perturbations like antibiotics or probiotics, it allows for genuine causal inference in humans (as opposed to correlation). This is supported by germ-free and SPF animal studies, multiple human RCTs, meta-analyses, and retrospective analyses of health records. I honestly can’t imagine what stronger evidence would look like so I'm a little confused why it keeps getting removed?

"Strongest evidence" is not the same as a high-quality source, such as a meta-analysis of randomized controlled trials, which is the relative level of evidence certainty expected for the encyclopedia - see WP:MEDASSESS. It seems definition of the vaccine-microbiota-immune relationship is still evolving in the lab, and is not yet accepted across broad mainstream science. Zefr (talk) 03:43, 5 April 2025 (UTC)

This is a much higher quality of evidence than what’s available for topics like the gut-brain axis, which — for understandable reasons — is almost entirely based on animal work due to the difficulty of studying mechanistic effects in humans. So I would like us to apply a consistent standard for evidence. Perhaps the solution is to revise the section to focus more explicitly on this causal inference setting, which might clarify the rationale for including this vaccine-microbiome literature? I'm guessing you've some concern about health related claims from this? (Which is not my intention to make or discuss). Decent swan (talk) 23:34, 4 April 2025 (UTC)

See the pyramid information for levels of evidence and following discussion in WP:MEDASSESS, and also in WP:MEDANIMAL. Zefr (talk) 03:43, 5 April 2025 (UTC)

Thanks again. I’m keen to work collaboratively here, but I do want to flag that this article is badly in need of broader updates. Many of the current references are outdated — including some health-related claims still citing papers from over 20 years ago. There are also incomplete tables, scattered health statements without consistent sourcing standards, and a general lack of alignment with more recent systematic reviews and datasets.

I’m a bit confused by the very strict threshold being applied to this newer, peer-reviewed research, while much older and less robust citations remain untouched elsewhere in the article.

Rather than broadly invoking policy like MEDASSESS, I’d really appreciate a more specific discussion about which parts you see as problematic. Otherwise, I’ll proceed with drafting an updated section that stays within scope, avoids health claims, and clearly frames the strength and limitations of the evidence. Decent swan (talk) 03:58, 5 April 2025 (UTC)

Thanks. Your last sentence shows a constructive way forward for updating and improving the article. Zefr (talk) 21:19, 5 April 2025 (UTC)

Request to update opening definition based on current terminology

Hi all, I’d like to suggest revising the opening paragraph of the article to better reflect current usage of key terms like microbiota, microbiome, and flora. At the moment, the intro suggests these terms are interchangeable, but that’s not accurate based on current scientific consensus.

According to this highly cited commentary in Microbiome (2020) — https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00875-0 — the microbiota refers to the community of microorganisms, while the microbiome encompasses not just the organisms, but also their genes, metabolites, and environmental interactions. The term flora might be used colloquially in place of microbiota, although should probably be avoided in encyclopedic writing.

Figure 2 from that article does a great job of clarifying the distinction — I’d be keen to incorporate it here (under CC BY 4.0 licence)

Would others support a revision of the lead to reflect this more modern terminology? Decent swan (talk) 23:44, 4 April 2025 (UTC)

Figure 2 of the Berg review would be good to have presented in words. The current lede sources are outdated, and we should not use MDPI publications, such as this from Nutrients, which is suspected of being predatory. Zefr (talk) 03:52, 5 April 2025 (UTC)

Thanks. I will draft something on this. Decent swan (talk) 03:59, 5 April 2025 (UTC)

I would like to note that the view of MDPI is not so clear-cut - https://en.wikipedia.org/wiki/Wikipedia:Reliable_sources/Perennial_sources#MDPI Zemleroika11 (talk) 17:13, 5 April 2025 (UTC)