Suggestions & feedback for the wiki. More research links + book Feedback

[NiroZ]

Hi,
I was just looking through the wiki, and honestly it's a bit out of date. Not that I blame anyone, nobody can keep up with all the research on all the different conditions, but I thought I'd help by sharing what I've found.

Spoiler: To avoid a wall of text I've spoilered them

Ahmed, N., & Husain, M. M. (2023). Can probiotics reduce bipolar symptoms?: A systematic review. Personalized Medicine in Psychiatry, 39–40, 100098. https://doi.org/10.1016/j.pmip.2022.100098

Dai, W., Liu, J., Qiu, Y., Teng, Z., Li, S., Yuan, H., Huang, J., Xiang, H., Tang, H., Wang, B., Chen, J., & Wu, H. (2022). Gut Microbial Dysbiosis and Cognitive Impairment in Bipolar Disorder: Current Evidence. Frontiers in Pharmacology, 13. https://doi.org/10.3389/fphar.2022.893567

Kang, D.-W., Adams, J. B., Gregory, A. C., Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., Pollard, E. L., Roux, S., Sadowsky, M. J., Lipson, K. S., Sullivan, M. B., Caporaso, J. G., & Krajmalnik-Brown, R. (2017). Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: An open-label study. Microbiome, 5, 10. https://doi.org/10.1186/s40168-016-0225-7

Li, Y., Wang, Y., & Zhang, T. (2022). Fecal Microbiota Transplantation in Autism Spectrum Disorder. Neuropsychiatric Disease and Treatment, 18, 2905–2915. https://doi.org/10.2147/NDT.S382571

McGuinness, A. J., Loughman, A., Foster, J. A., & Jacka, F. (2024). Mood Disorders: The Gut Bacteriome and Beyond. Biological Psychiatry, 95(4), 319–328. https://doi.org/10.1016/j.biopsych.2023.08.020

Mörkl, S., Butler, M. I., & Lackner, S. (2023). Advances in the gut microbiome and mood disorders. Current Opinion in Psychiatry, 36(1), 1. https://doi.org/10.1097/YCO.0000000000000829

Parker, G., Spoelma, M. J., & Rhodes, N. (2022). Faecal microbiota transplantation for bipolar disorder: A detailed case study. Bipolar Disorders, 24(5), 559–563. https://doi.org/10.1111/bdi.13187

Retuerto, M., Al-Shakhshir, H., Herrada, J., McCormick, T. S., & Ghannoum, M. A. (2024). Analysis of Gut Bacterial and Fungal Microbiota in Children with Autism Spectrum Disorder and Their Non-Autistic Siblings. Nutrients, 16(17), Article 17. https://doi.org/10.3390/nu16173004

Rojo-Marticella, M., Arija, V., & Canals-Sans, J. (2025). Effect of Probiotics on the Symptomatology of Autism Spectrum Disorder and/or Attention Deficit/Hyperactivity Disorder in Children and Adolescents: Pilot Study. Research on Child and Adolescent Psychopathology, 53(2), 163–178. https://doi.org/10.1007/s10802-024-01278-7

Singh, J., Vanlallawmzuali, Singh, A., Biswal, S., Zomuansangi, R., Lalbiaktluangi, C., Singh, B. P., Singh, P. K., Vellingiri, B., Iyer, M., Ram, H., Udey, B., & Yadav, M. K. (2024). Microbiota-brain axis: Exploring the role of gut microbiota in psychiatric disorders - A comprehensive review. Asian Journal of Psychiatry, 97, 104068. https://doi.org/10.1016/j.ajp.2024.104068

Sublette, M. E., Cheung, S., Lieberman, E., Hu, S., Mann, J. J., Uhlemann, A.-C., & Miller, J. M. (2021). Bipolar disorder and the gut microbiome: A systematic review. Bipolar Disorders, 23(6), 544–564. https://doi.org/10.1111/bdi.13049

Wong, S. H., Ying, J., Xu, X., Zhou, R., Chung, A. C. K., Ng, S. K., Fan, X., & Subramaniam, M. (2025). Gut microbiota in young adults with high-functioning autism spectrum disorder and its performance as diagnostic biomarkers. Research Square. https://doi.org/10.21203/rs.3.rs-5753373/v1

I'd be curious to know what you make of this study and why you didn't discuss it in the diet section:

McDonald, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., DeRight Goldasich, L., Dorrestein, P. C., Dunn, R. R., Fahimipour, A. K., Gaffney, J., Gilbert, J. A., Gogul, G., Green, J. L., Hugenholtz, P., … Knight, R. (2018). American Gut: An Open Platform for Citizen Science Microbiome Research. mSystems, 3(3), 10.1128/msystems.00031-18. https://doi.org/10.1128/msystems.00031-18


Also, are you interested in studies that are related to the microbiome but don't explicitly make the link? For example:

Hamdani, N., Boukouaci, W., Hallouche, M. R., Charron, D., Krishnamoorthy, R., Leboyer, M., & Tamouza, R. (2015). Resolution of a manic episode treated with activated charcoal: Evidence for a brain–gut axis in bipolar disorder. Australian & New Zealand Journal of Psychiatry, 49(12), 1221–1223. https://doi.org/10.1177/0004867415595873

Huberts-Bosch, A., Bierens, M., Ly, V., van der Velde, J., de Boer, H., van Beek, G., Appelman, D., Visser, S., Bos, L. H. P., Reijmers, L., van der Meer, J., Kamphuis, N., Draaisma, J. M. T., Donders, R., van de Loo-Neus, G. H. H., Hoekstra, P. J., Bottelier, M., Arias-Vasquez, A., Klip, H., … Rommelse, N. N. (2024). Short-term effects of an elimination diet and healthy diet in children with attention-deficit/hyperactivity disorder: A randomized-controlled trial. European Child & Adolescent Psychiatry, 33(5), 1503–1516. https://doi.org/10.1007/s00787-023-02256-y

Pelsser, L. M., Frankena, K., Toorman, J., & Rodrigues Pereira, R. (2017). Diet and ADHD, Reviewing the Evidence: A Systematic Review of Meta-Analyses of Double-Blind Placebo-Controlled Trials Evaluating the Efficacy of Diet Interventions on the Behavior of Children with ADHD. PLoS ONE, 12(1), e0169277. https://doi.org/10.1371/journal.pone.0169277

Also curious to know if any of you are familiar with the books Eat More, Live well by Megan Rossi or Brain Changer by Felice Jacka. Both are diet books, Brain Changer doesn't fully grasp how pivotal the microbiome is to her findings, Eat More is explicitly based on the McDonald study above. I've been following the Eat more book primarily to reduce brain fog, tension headaches and constipation, with curiosity about how it'll affect my schizoaffective disorder and autism, and I've made a marked improvement over the last 3 weeks since I started it.

I'm also reading this book currently to try and get up to date with the state of knowledge on the microbiome as of 2021, because I contain multitudes and Missing microbes are a bit old now. It seems poorly edited in certain chapters, but otherwise interesting. Be curious if anyone else is familiar with it or knows of similar books.

 

[Michael Harrop]

I was just looking through the wiki, and honestly it's a bit out of date.

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I don't think "out of date" is the correct description. Rather, it doesn't include every study. Sometimes on purpose, other times because I never saw it.

Basically, I've been following the microbiome research daily for around 10 years and adding studies as I see them. I was largely relying on microbiomedigest.com but they've slowed to almost a full stop. I've switched to other sources, such as Pubmed and other websites that post daily science articles, but those miss a lot because I haven't tried to replace all the research alerts that microbiomedigest covered.

It would be great to have other people contributing, and thank you for your suggestions.

I'd be curious to know what you make of this study and why you didn't discuss it in the diet section

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My goal with the wiki is to allow someone to briefly scroll through a specific section and get a good overview of the status of the research.

The American Gut paper you reference doesn't really serve that purpose. It's more of something one would submit to the forum but not add to the wiki.

The bipolar probiotic one is a "maybe". If a paper is closed access I'm much less likely to add it to the wiki. The conclusions are also very mild ("a potentially effective treatment"), so again I'd tend to submit that kind of thing to the forum only.

For the newer 2022 bipolar review, it doesn't seem like a major update or that it adds much new/different information. Its conclusions also seem very mild.

Most of the other studies you listed fall under those same descriptions. But I'm open to arguments to the contrary.

The MTT autism one is in the wiki.

I added "Faecal microbiota transplantation for bipolar disorder: A detailed case study", thank you.

I contain multitudes and Missing microbes are a bit old now

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True, but I wouldn't say they're outdated, and they're both great & important.

I don't really read microbiome books anymore (I rely on the daily research) so I don't foresee adding more to the wiki.

are you interested in studies that are related to the microbiome but don't explicitly make the link?

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Those seem appropriate for the forum but not the wiki.

 

[NiroZ]

Ah, thanks for the detailed reply. Apologies for suggesting one that was already there, I usually check studies quickly by looking at the first author, which made checking difficult. I was more interested in making sure that you were aware of them, so if you don't think they're significant enough that's fine. But I feel like I should take a stand about the American diet study. Eating 30 or more plants over a week correlating with with significantly more alpha diversity and doing better on a variety of outcomes vs 10 or less is a finding that helps people understand a solid, practical thing they can try. I know correlation /= causation, but sticking to just what's in the literature and not making a personal commentary, it's something to try and worth following up on.

I'll try and get my hands on the bipolar probiotic paper for you. Researchers often understate their findings so that could be nothing.

The two diet books both talk about the SMILES study https://pubmed.ncbi.nlm.nih.gov/28137247/, which might be an alternative for people with depression that's safer and cheaper than FMT but could potentially achieve similar results for said condition, so worth noting as an alternative. One of them was the lead author.

I haven't finished Microbiome-Gut-Brain Axis: Implications on Health but there's a section on epilepsy which you could add to the brain section of the wiki:

Epilepsy is a chronic disease categorized by the abrupt abnormal discharge from cerebral neurons, leading to transient brain dysfunction. Genetic and environmental factors are associated with the person’s susceptibility to the disorder (Xie et al. 2017). Composition and distribution of gut microbiota in patients with intractable epilepsy are different from the healthy controls (Lum et al. 2020). From the studies, it was observed that intestinal Firmicutes/Bacteroides ratio and α-diversity (diversity in the number of species as well as levels) were considerably high in drug-resistant patients compared to drug-sensitive patients. The α-diversity was high in healthy individuals due to increase in rare bacterial genera (Peng et al. 2018). Reduction in seizures was observed by intake of ketogenic diet, increase in Lactobacillus and Bifidobacterium spp. was also observed (Dahlin and Prast-Nielsen 2019). Transplantation of ketogenic microbiota reduced the number of seizures in mice at a higher threshold. A probiotic strain shows positive results in patients suffering from epilepsy. Studies conducted on a 17-year-old patient suffering from epilepsy using FMT (feceal microbial transplant) observed that epileptic recurrence was reduced with treatment (He et al. 2017).

The increase number of evidences shows the gut microbiota involvement in the developmental and functional aspects of the nervous system including various acute and chronic diseases influenced by the gut microbiota. From various clinical models, it can be concluded that intestinal microbiota also plays an important role in not just assisting the pathogens but also in increasing the pathogenicity of a disease (Sampson et al. 2016).
(page 23)

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The book's findings on the infant's development of the microbiome is similar to what Missing Microbes says, but there are differences. I can look up the specifics if you're interested.

Also, just saw your other website. Have you considered looking in developed countries for donors? Chances are you'll find more donors there considering everything (diet, lack of antibiotics etc).

As for finding papers, you could just do occasional searches on google scholar from time to time (or if you could try google alerts if you're daring), which is how I found most of the studies. https://www.sciencealert.com/ and https://www.livescience.com/ and r/science sometimes post something relevant (although usually only tangentially relevant). Asking claude.ai about books is how I found Microbiome-Gut-Brain Axis. And contacting random people seems to be quite useful.

 

[Michael Harrop]

the American diet study [..] Eating 30 or more plants

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I just searched through the paper for all instances of "30". The problem is that they do not summarize their findings well. IE: they do not have one conclusion paragraph where they say "People who ate 30 or more different plants had higher diversity, lower antimicrobial resistance, and so on". They comment individually on some of the associations here and there and none of them stand out to me as "People should really know about this".

SMILES study

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Thanks, I added it to the Depression section.

Regarding the epilepsy quotes, "Peng et al. 2018" seems very useless to me. How are you using that to quickly find the study?

The book's findings on the infant's development of the microbiome is similar to what Missing Microbes says, but there are differences. I can look up the specifics if you're interested.

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Sure, but if it's covered on the Maternity page already it's probably not too useful to discuss.

Also, just saw your other website. Have you considered looking in developed countries for donors? Chances are you'll find more donors there considering everything (diet, lack of antibiotics etc).

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Yes. Humanmicrobes.org accepts donors from around the world. But chronic disease is now rampant in developing countries too. And antibiotic abuse is often even worse there due to the ability to get them OTC.

 

[NiroZ]

I just searched through the paper for all instances of "30". The problem is that they do not summarize their findings well. IE: they do not have one conclusion paragraph where they say "People who ate 30 or more different plants had higher diversity, lower antimicrobial resistance, and so on". They comment individually on some of the associations here and there and none of them stand out to me as "People should really know about this".

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You're right, they didn't explain themselves well. I'll go through and do my own summary in regards to that later today. But from memory the graphs are useful. But in the meantime I'm curious as to what you're strategy is for analysing papers.

Regarding the epilepsy quotes, "Peng et al. 2018" seems very useless to me. How are you using that to quickly find the study?

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If you want I can send you the pdf so you can grab the full reference. Epilepsy isn't a specific interest of mine so I'm not concerned with looking at it in detail (although the idea that keto might work at least partially through the microbiome is fascinating). I more quoted it to show that it has useful information. But if you want to look it up, try restricting the year in Google scholar, then author name + epilepsy.

Sure, but if it's covered on the Maternity page already it's probably not too useful to discuss.

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I said that more to make a point about Missing Microbes being dated.

Yes. Humanmicrobes.org accepts donors from around the world. But chronic disease is now rampant in developing countries too. And antibiotic abuse is often even worse there due to the ability to get them OTC.

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Maybe in India, not in PNG highlands or elsewhere. The developing world is a big place. Admittedly there are other issues like parasites and access though.

Also, this site is a bit temperamental when posting on mobile. The cursor keeps jumping around.

Oh, and forgot to mention, if you're read a lot of papers, figuring out which authors to follow and which journals publish good stuff can make your search more targeted. Researchgate lets you follow authors and journals will email you with new editions, sometimes even closed journals will offer papers for free for a few days after releases.

Ok, I've done the summary. I'll post it after you've responded in case there's anything else I need to add.

 

[Michael Harrop]

But if you want to look it up, try restricting the year in Google scholar, then author name + epilepsy.

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I'm generally not going to spend time doing that. If there are not links directly to the study, I'm generally going to ignore it.

I said that more to make a point about Missing Microbes being dated.

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Missing Microbes is quite an important book, so it's unlikely that I'm going to replace it any time soon. It's merely one of many citations in the wiki for people to review.

Also, this site is a bit temperamental when posting on mobile. The cursor keeps jumping around.

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I don't try to post on mobile, so I wouldn't know. But you could search https://xenforo.com/community/ to see if other people have experienced the same issue.

 

[NiroZ]

You seem to have switched your argument from "I don't need to read books because I'm already across the research" to "I'm just hosting a wiki/forum of interesting things, depending on the amount of time and effort I have available". The first line of argument is deeply concerning from someone who isn't trained in the field. Journal articles assume a level of knowledge and background experience that can mean you easily miss important things, and be fooled by poor or disingenuous studies. There's nothing wrong with the second argument except when I look at the wiki it's clear that you do consider yourself across to research, to the point of being able to make commentary and specific recommendations. Without an About Me page explaining your background and experience, or adding caveats to your claims, that's extremely dodgy. I'll freely admit that I haven't been trained in any form of biology, but I have been trained to read journal articles from studying social sciences.

Two specific issues I found browsing the wiki:

https://humanmicrobiome.info/faq/ has the claim

However, FMT (fecal microbiota transplant) is the only thing that will restore host-native microbes that were killed off by antibiotics, or are lost or missing for other reasons.

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Which you really need to back up.

https://humanmicrobiome.info/diet/#impacts-limitations references https://pmc.ncbi.nlm.nih.gov/articles/PMC3435786/ with this sentence:

One study showed that removing fiber from the diet improved all constipation symptoms and increased BM frequency[1]!

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Having no discussion of how it's a poor quality study. Interesting, but poor quality.

Given your time and effort is at a premium, I'd strongly suggest you make use of the various AI tools out there. They do hallucinate, but it's easy to double check their claims, and can save a lot of time and effort. I'm partial to claude.ai, but if you find you use up all your free allocation on that one, there's plenty of others you can turn to.

Anyway, as promised, here is the summary of that study, section by section:

Introduction
"As of May 2017, the AGP (the American gut project, which the paper is reporting on) included microbial sequence data from 15,096 samples from 11,336 human participants, totaling over 467 million (48,599 unique) 16S rRNA V4 gene fragments (abbreviated 16S)" It appears that they gathered samples (in 565 people it was more than 1) by mostly having people pay for information on their microbiome. They included the hunter gatherer Hadza people, who presumably didn't have to pay.

Fig 1
The US was poorer than the UK in alpha diversity. According to Text S1 supplementary .doc file, this was significant "(D) In a meta-analysis, the largely industrialized population that makes up American Gut exhibits significant differential abundances compared to nonindustrialized populations." In regards to D, over the entire sample the types of bacteria in hunter-gatherer and remote farmer communities compared to industrialised microbiomes was radically different.

Cohort characteristics
"AGP participants primarily reside in the United States (n = 7,860). However, interest in the AGP rapidly expanded beyond the United States to the United Kingdom (n = 2,518) and Australia (n = 321), with 42 other countries or territories also represented." Note that these are the numbers before people were excluded for reasons.

"General health status, disease history, and lifestyle data" was reported. All questions were optional and the median response per question was 70.9%. 14.8% of participants completed a validated picture-based food frequency questionnaire, and responses correlated well with general diet responses.

Removal of bacterial blooms
This section isn't relevant to us so I skipped it.

Novel taxa and microbiome configurations
This section is comparing the human microbiome to the environment, so I skipped it.

Temporal and spatial analyses
Looked at the 565 individuals with multiple samples, particular ones who had a bowel resection and were in the ICU. Not too interesting for what we're looking for, however, there were a few interesting things:

Fig 4
The most interesting thing here is that, from what I can make out, surgery for a bowel resection dropped diversity in the human gut from that of "marine sediment sample and a plant rhizosphere sample."

Dietary plant diversity
"The number of unique plant species that a subject consumes is associated with microbial diversity, rather than self-reported categories such as “vegan” or “omnivore”"

Fig 5
C, D and E are relevant.
" grouping by diets such as vegan, ... is consistent with differences in micronutrients and macronutrients ... however, these dietary differences do not explain relationships between the samples in 16S space (referring to the uniqueness of the bacteria)."

"(E) Differential abundances of sOTUs (showing the most specific taxon name per sOTU) between those who eat fewer than 10 plants per week and those who eat over 30 per week."

/Fig 5

"we identified several putative short-chain fatty acid (SCFA) fermenters associated with eating more than 30 types of plants ... the species Faecalibacterium prausnitzii and of the genus Oscillospira " "a diet containing various types of dietary fibers and resistant starches likely supports a more diverse microbial community. Studies suggest that these types of responses in the gut microbiome to a high-plant diet may be common across vertebrates."

"Individuals who consume more than 30 types of plants per week compared to those who consume 10 or fewer plants per week had significantly reduced abundance of antibiotic resistance genes" It's unclear what percentage of the >30 group were Hadza or non-industrialised, presumably the authors didn't think it noteworthy, but it'd be nice to know.

"[We studied those] eating <10 or >30 different types of plants per week. Several fecal metabolites differed between the two groups, with one key discriminating feature annotated as octadecadienoic acid ... [CLA] was significantly higher in individuals consuming >30 types of plants and those consuming more fruits and vegetables generally". "Several other putative octadecadienoic acid isomers were also detected ... some strongly correlated with plant consumption."

Molecular novelty in the human gut metabolome

Fig 6
D shows exactly what you're looking for, the difference in alpha and beta diversity in those who ate >30 and <10, with the >30 group showing greater.

/Fig 6

"we observe that, paradoxically, individuals who had taken antibiotics in the past month ... had significantly greater molecular diversity ... than those who had not taken antibiotics in the past year ... and differed in molecular beta-diversity ... suggesting that antibiotics promote unique metabolomes that result from differing chemical and microbial environments in the gut. ... the diversity relationships ... are not reflected in 16S diversity, where antibiotic use shows decreased diversity ... Within the dietary plant diversity cohort, we observed a significant increase ... in molecular alpha-diversity associated with a high diversity of plant consumption ... compared to low plant diversity ..., a relationship also observed in 16S diversity, where high dietary plant diversity increased 16S alpha-diversity." I'm assuming the high was >30 and low was <10, but it's unclear.

Citizen science aspects of the project
This is basically a limitations section + other stuff like a link to their course (https://www.coursera.org/learn/microbiome).

A living data set
Talks above finding differences between the mentally ill and matched controls. Doesn't go into details but you're invited to look at the supplementary materials yourself.

Discussion
More about the project and what they're doing generally. After this section there's technical detail on how they did the study and acknowledgements.

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[Michael Harrop]

Books are not peer-reviewed and thus often contain misinformation, even when they're written by highly regarded researchers. They are generally not the best sources of information.

You seem to have switched your argument from "I don't need to read books because I'm already across the research" to "I'm just hosting a wiki/forum of interesting things, depending on the amount of time and effort I have available".

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There's no switch; both are accurate, with the 2nd one a little less so.

Journal articles assume a level of knowledge and background experience that can mean you easily miss important things

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The authors have the option to summarize their findings for a broad audience. Most research studies do this in both the abstract and commentary sections. Many papers even use an additional "author summary" or "key findings" section now. Many studies are also accompanied by news articles that contain further commentary by the authors and salient points for laypeople.

as promised, here is the summary of that study, section by section

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If you want something in the wiki that isn't clearly specified in the study, you could look for reputable articles that have the text you desire. I searched the title of the study and found this article. I can add a quote from it to the Diet wiki page. I decided to submit it to the forum too.

Without an About Me page explaining your background and experience

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There is one under the "General" section. Please be more diligent before making accusations.

https://humanmicrobiome.info/faq/ has the claim

FMT (fecal microbiota transplant) is the only thing that will restore host-native microbes that were killed off by antibiotics, or are lost or missing for other reasons

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Which you really need to back up.

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Most of those FAQ sections have a "Forum discussion" link which would be a good place to ask that, but I left to DC before I could finish that one.

I try to keep those FAQs succinct, and that claim in particular seems self-evident as well as supported by the existing citations, such as the Diet, Probiotics, and Antibiotics pages.

Having no discussion of how it's a poor quality study.

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That belongs on the forum, not the wiki. I'll generally link directly to the forum posts instead of the study, when available, for this purpose. I see that study hasn't been submitted to the forum yet so you're welcome to submit it and offer your criticism, and I'll change the link in the wiki to the forum thread.

I'd strongly suggest you make use of the various AI tools out there. They do hallucinate, but it's easy to double check their claims, and can save a lot of time and effort

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That seems like a bad idea. Checking their claims doesn't seem any less time consuming than simply doing the work yourself in the first place.