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Library of Research on the Human Microbiome

Understanding the influence of the gut microbiome on our well-being, and of the environment on our microbiome.

Detailing all the ways our microbiomes impact our health, function, and development. Providing answers on how we can maintain or achieve a healthy, eubiotic microbiome, and how to prevent and correct dysbiosis.

For feedback, edits, contributions, suggestions, etc., feel free to make a post on the forum.

If you're curious about a condition not listed here, do a web, pubmed, or google scholar search for "condition microbiome" or "condition dysbiosis".

Research in the area of the microbiome is growing rapidly in recent years due to advances in detection/sequencing techniques:
Microbiome instances graph
(image from microbiomedigest.com)

This means that many long standing positions are being debunked, and even much of what you read (here or elsewhere) can become quickly outdated.

See the Testing page for examples of current status/limitations of detecting & identifying human microbes.

Notable pages:

General:

Researcher Elisabeth Bik's list of other sources of microbiome info: https://microbiomedigest.com/microbiome-papers-collection/microbiome-blogs-tweeps-and-books/

Some of 2016's most discussed research papers: https://microbiomedigest.com/2016/12/21/vote-for-the-best-microbiome-papers-of-2016/
Same for 2017: https://microbiomedigest.com/2017/12/26/vote-for-the-best-microbiome-papers-of-2017/ - https://microbiomedigest.com/2018/01/02/the-best-microbiome-papers-of-2017/

Use PubPeer's browser addon to see peer discussions of academic publications: https://pubpeer.com/static/faq#29

Blog: Understanding Microbiome Research: https://microbiomethod.blogspot.co.uk/

Things that can harm our microbiome:

Acid suppression medicines [1][2][2].

Advanced glycation end products (AGEs) [1].

Air Pollution [1][2][3][4][6].

Alcohol: Generally [1]. Chronic vapour alcohol exposure [1]. Acute-on-chronic alcohol [1]. Detrimental to mouth microbiome [1]. Alcohol induced alterations of the microbiome may explain reward-seeking behaviors as well as anxiety, depression, and craving in withdrawal and increase the risk of developing psychiatric disorders [1]. Increases susceptibility to pneumococcal pneumonia in a humanized murine HIV model mediated by intestinal dysbiosis [1]. Aug 2019 systematic review and meta-analysis.

Antibiotics (see abx section below).

Artificial sweeteners [1][2][3].

Cadmium [1].

Cocaine [1].

Diet soda [1][2].

Dirt [1].

Food additives [1][2]. Emulsifiers [1][2][3][4][5][6][7]. Soy lecithin [1]. Sulfites [1]. Glycerol Monolaurate [1]. Trehalose (sugar additive) [1]. Carrageenan and carboxymethylcellulose (CMC) [1][2]. CMC and polysorbate 80 (P80) [1][2][3]. Titanium dioxide [1].

Hygiene Hypothesis [1][2][3][4][5][5]. The more accurate alternative hypothesis is Missing Microbes.

Insecticides: aldicarb [1].

Lead [1][2].

Mercury: Acute oral methylmercury, Jan 2020, rats.

PCBs [1].

Perfluorooctane sulfonate (PFOS): Jan 2020, mice.

Pesticides: Organophosphates [1][2][3]. Glyphosate [1][2,3]. Subchronic low-dose 2,4-D. Penconazole and its enantiomers.

Plastic: Polystyrene microplastics [1][2]. BPA [1][2][3].

Poor diet (which compounds over generations) [1][2][3].

Stress [1].

Tobacco: Smoking dokha [1].

Trans fats [1].

Tributyltin (TBT) [1].

Antimicrobial peptides:

Peptides are created by gut bacteria, as well as by eukaryotic hosts during symbiotic interactions with bacteria.

AMPs are involved in aging: https://humanmicrobiome.info/aging#peptides

Antimicrobial Peptides Vs. Antibiotics: http://biorxiv.org/content/early/2017/05/23/138107

Spider peptides battle superbugs and cancer - Gomesin, an antimicrobial peptide (AMP) from a spider, can function as an antibiotic, and it also has anticancer activity. Australian scientists synthesized new versions that were 10 times better at killing most bacteria than previously reported: https://www.acs.org/content/acs/en/pressroom/presspacs/2017/acs-presspac-august-9-2017/spider-peptides-battle-superbugs-and-cancer.html

Review, 2018: Role of antimicrobial peptides in controlling symbiotic bacterial populations: https://sci-hub.tw/http://pubs.rsc.org/en/Content/ArticleLanding/2018/NP/C7NP00056A#!divAbstract

Diet:

Moved to: https://humanmicrobiome.info/diet

Fungi:

Contribution of fungal microbiome to intestinal physiology, early-life immune development and mucosal inflammation in mice (Oct 2019) https://www.biorxiv.org/content/10.1101/819979v1.abstract "Our results demonstrate a dominant ecological and physiological role of bacteria in gut microbiomes, but highlight fungi as an ecological factor shaping the assembly of the bacterial community and a direct capacity to impact immune system and modulate disease susceptibility"

Probiotic yeast may offer an effective treatment for drug-resistant fungal infections. Study shows that yeasts derived from food are effective in preventing infections and reducing the virulence of several Candida species https://www.eurekalert.org/pub_releases/2019-12/wpi-pym121019.php. Probiotic Yeasts Inhibit Virulence of Non-albicans Candida Species (Oct 2019).

More at: https://web.archive.org/web/20230722183020/https://old.reddit.com/r/humanmicrobiome/search?q=flair%3A%27Fungi%27&sort=new&restrict_sr=on

Candida:

Moved to: https://humanmicrobiome.info/candida

Testing:

Moved to: https://humanmicrobiome.info/testing

Viruses:

The Intestinal Virome and Immunity (2018): https://doi.org/10.4049/jimmunol.1800631

Bacteriophages (phages):

Review, 2018: Beyond Bacteria: Bacteriophage-Eukaryotic Host Interactions Reveal Emerging Paradigms of Health and Disease https://www.frontiersin.org/articles/10.3389/fmicb.2018.01394/full - "Phages may be naturally internalized into eukaryotic cells. As phages are significant reservoirs of genetic diversity and considering phages are capable of entering eukaryotic cells, this raises questions about the possibility of bidirectional trans-kingdom gene exchange between phages and their animal hosts."

Potential for harm: Review, 2018: Bacteriophages as New Human Viral Pathogens: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027513/ "We suggest that bacterial viruses have different ways to directly and indirectly interact with eukaryotic cells and proteins, leading to human diseases"

Review, June 2019: What is (not) known about the dynamics of the human gut virome in health and disease https://www.sciencedirect.com/science/article/pii/S1879625719300173

Review, June 2019: Phage Therapy in the Twenty-First Century: Facing the Decline of The Antibiotic Era; Is it Finally Time for The Age of the Phage? https://www.annualreviews.org/doi/10.1146/annurev-micro-090817-062535

Healthy human gut phageome identified (2016), (2019 comparison with IBD patients).

Review, 2017: Phages in the Human Body: http://journal.frontiersin.org/article/10.3389/fmicb.2017.00566/full

Review, 2017: Bacteriophages in the human gut: our fellow travelers throughout life and potential biomarkers of heath or disease. Phages are the largest part of the human microbiome: http://www.sciencedirect.com/science/article/pii/S0168170217302149

Review, 2017: The human intestinal virome in health and disease: http://onlinelibrary.wiley.com/doi/10.1111/apt.14280/full

Review, 2017: Bacteriophages in the gastrointestinal tract and their implications: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5553654/

Source of phages doesn't seem to matter. Phages obtained from sewer have beneficial effects.

Phages vs antibiotics: "The upside and downside to using phage therapy is that the viruses are extremely specific. The upside is that phage will only kill a very specific type of bacterium, whereas antibiotics lay waste to many different bacteria, including friendly ones. The downside is that the phage are too specific."

Addressing superbug resistance with phage therapy. "The study is significant because it is the first time bacteriophage therapy has been used in the USA to treat a patient who had an antibiotic-resistant, blood stream infection." (Aug 2017) https://medicalxpress.com/news/2017-08-superbug-resistance-phage-therapy.html

Great article on the current (Nov 2017) status in the US of the use of phages for fighting an infectious disease: http://www.cidrap.umn.edu/news-perspective/2017/11/save-life-doctors-turn-bacteria-killing-viruses | Another from Nov 2017 about a separate occurrence: https://www.statnews.com/2017/11/28/phage-therapy-mallory-smith/ | Another from Dec 2017: https://motherboard.vice.com/en_us/article/9kdbqa/bacteriophages-phage-therapy-antibiotic-resistant-bacteria (the video on the page has even more).

Phages are an important component of FMT success [2016].

Transferring just the bacteriophage was sufficient to reduce resting metabolic rate and cause weight gain in control mice (2015): https://www.sciencedaily.com/releases/2015/12/151214130811.htm

The Virus That Could Cure Alzheimer’s, Parkinson’s, and More: http://www.pbs.org/wgbh/nova/next/body/phage-alzheimers-cure/

Phage therapy via clinics ($1k-4k) or supplements ($30-200) - link.

Phage supplements in the US: https://archive.fo/hF4y8#selection-789.0-789.1

More info on phages:

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