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Introduction to the Human Microbiome

Table of Contents:

General articles:

Fantastic microbiome 101 podcast by Yale: || Other parts of series (not as good/accurate):

Excellent 2018 PBS NOVA documentary: NOVA Wonders What's Living in You?

Kurzgesagt – How Bacteria Rule Over Your Body – The Microbiome - A good, simple intro, but some things might be wrong/outdated.

Missing Microbes with Dr Martin Blaser (American Society for Microbiology, 2016)

Ed Yong's 2016 "I contain multitudes" book is excellent.

And Martin Blaser's (2014) "Missing Microbes". Discussion, interviews, summary.

"It is now clear that the gut microbiota contributes significantly to the traits of humans as much as our genes, especially in the case of atherosclerosis, hypertension, obesity, diabetes, metabolic syndrome, inflammatory bowel disease (IBD), gastrointestinal tract malignancies, hepatic encephalopathy, allergies, behavior, intelligence, autism, neurological diseases, and psychological diseases. It has also been found that alteration of the composition of the gut microbiota in its host affects the behavior, intelligence, mood, autism, psychology, and migraines of its host through the gut-brain axis." (2018):

How the Western Diet (and antimicrobials) Has Derailed Our Evolution (2015):

Is a Disrupted Gut Microbiome at the Root of Modern Disease? (2016)

Meet Your Second Brain: The Gut (2015)

How the Gut's "Second Brain" Influences Mood and Well-Being. The emerging and surprising view of how the enteric nervous system in our bellies goes far beyond just processing the food we eat (2010):

Documentary: In Defense of Food, 1:25:00 talks about study in twins where one is malnurished and one isn't. Bacteria transplant tests. Also testing gut microbes in Hadza tribe. || Also talked about during the 2016 whitehouse microbiome event:

A group of scientists have found that a single molecule from a bacterial cell wall component can lead to the unusual behaviour of 100 million clotting molecules in blood, which may be a major contributor to many diseases including Alzheimer's, Parkinson's, diabetes, rheumatoid arthritis, & strokes: || Related: The dormant blood microbiome in chronic, inflammatory diseases (2015):

How gut bacteria affects your health: What we know, what we don't (2015):

11 overlooked factors that affect the bacteria on your body and help determine your health (2015):

9 fascinating facts about the microbiome (2015) (birthing section is wrong on sterility):

Slightly more advanced course provided for free by University of Colorado Boulder & University of California San Diego:
Gut Check: Exploring Your Microbiome

Fantastic site for keeping up with the latest literature; run by Stanford researcher:


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Brain function:

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Obesity & diet:

Gut flora manipulate (through the vagus nerve) their host's eating patterns & cravings, behavior & mood, taste receptors, and more (Aug 2014):

Recent data show a link between the diversity and richness of gut microbiota and the way we store fat, how we regulate digestion hormones and blood glucose levels, and even what types of food we prefer (Aug 2017):

Review, 2012: Impact of the Gut Microbiota on the Development of Obesity: Current Concepts:

Review, 2016: Treating Obesity and Metabolic Syndrome with Fecal Microbiota Transplantation

Review, 2017: Fecal microbiota transplantation in metabolic syndrome: History, present and future

Review, 2018: Gut Microbes and Health: A Focus on the Mechanisms Linking Microbes, Obesity, and Related Disorders:

Review, 2018: Insights into the role of gut microbiota in obesity: pathogenesis, mechanisms, and therapeutic perspectives:

Review, 2018: Importance of gut microbiota in obesity "the increase in fat mass is not only due to a more efficient harvest of energy, but also the microbiota participates in changes in endotoxemia, bowel permeability, insulin resistance, hormonal environment, expression of genes regulating lipogenesis, interaction with bile acids, as well as changes in the proportion of brown adipose tissue, and effects associated with the use of drugs such as metformin"

Host Genetic Background and Gut Microbiota Contribute to Differential Metabolic Responses to High Fructose Consumption in Mice (2018):

A single genetic change in gut bacteria alters host metabolism via microbial enzymes impacting bile metabolism (2018):

Immune system defects seem to contribute to obesity in mice. T cell–mediated regulation of the microbiota protects against obesity (July 2019) "healthy mice have plenty of Clostridia—a class of 20 to 30 bacteria—but those with an impaired immune system lose these microbes from their gut as they age. Even when fed a healthy diet, the mice inevitably become obese. Giving this class of microbes back to these animals allowed them to stay slim"

The gut microbiota regulates white adipose tissue inflammation and obesity via a family of microRNAs expressed in adipocytes (fat cells) (June 2019) - How a Disturbed Gut Microbiome May Dysregulate Fat Tissue in Obesity (2 of 2) (image)

Gut intraepithelial T cells calibrate metabolism and accelerate cardiovascular disease (Jan 2019): "Integrin β7− mice that lack natural IELs are metabolically hyperactive and, when fed a high-fat and high-sugar diet, are resistant to obesity, hypercholesterolaemia, hypertension, diabetes and atherosclerosis"

Study suggests bacteria in the gut has a greater influence on body fat compared to diet. Dissecting the role of the gut microbiota and diet on visceral fat mass accumulation (Jul 2019, 1760 female twins)

Human gut microbiota after bariatric surgery alters intestinal morphology and glucose absorption in mice independently of obesity (Aug 2022)

Adenovirus 36 and Obesity: An Overview (2015):

The Inhibitory Innate Immune Sensor NLRP12 Maintains a Threshold against Obesity by Regulating Gut Microbiota Homeostasis (2018):

Host genotype affects the abundance of taxa associated with metabolic disease. Gut microbiota affects susceptibility to diet-induced metabolic disease. The gut microbiome modulates insulin secretion (Feb 2017):

Long term but not short term exposure to obesity related microbiota promotes host insulin resistance (Nov 2018):

Study Links BMI, Lipid Levels to Gut Microbes (Sep 2015). || Including fungal mycobiota (Oct 2015):

Fat and thin people have different gut bacteria: (Oct 2018) - (Sep 2016)

Heritable components of the human fecal microbiome are associated with visceral fat (Sep 2016): | Maternal prepregnancy obesity may imprint a selective gut microbial composition during late infancy with distinct functional performances (Aug 2017):

Gut bacteria can help to predict how the body will respond to fatty foods. Chemical signatures from gut bacteria which show up in urine can be used to predict how the body will respond to a 'junk' diet. (July 2017)

Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study (May 2022, 2224 adults)

Doctors call for fecal transplant regulation after seeing unexpected results (obesity transfer in people) (Feb 2015): -

Transfer of Obesity via the Gut Microbiome is Mediated Specifically through Suppression of Non-Aerobic Resting Metabolism (Apr 2015): || Researchers find it's not just the bacteria that could produce this effect. Transferring just the bacteriophage was sufficient to reduce resting metabolic rate and cause weight gain in control mice (Nov 2015):

When researchers in China took a strain of E. cloacae (B29) from the gut of a volunteer who weighed in at 385 pounds and transplanted it into germ-free mice, the rodents themselves then became obese compared to similar mice fed an identical diet, but without the E. cloacae (Dec 2012): -

Dysosmobacter welbionis is a newly isolated human commensal bacterium preventing diet-induced obesity and metabolic disorders in mice (Jun 2021)

Dietary modulation of gut microbiota contributes to alleviation of both genetic and simple obesity in children (Jul 2015):

Nutrient poor environment causes bacteria to adapt, this causes host to store more fat. Direct communication with mitochondria (Apr 2017):

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity (May 2013)

A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice (Nov 2016):

An intestinal microbiota-farnesoid X receptor axis modulates metabolic disease. Mice lacking expression of FXR in the intestine were resistant to (High Fat Diet)HFD-induced obesity, insulin resistance and NAFLD thus confirming that intestinal FXR is involved in the potentiation of metabolic disease (Sep 2016): || Gut microbiota, FXR, and bile acids as regulators of host metabolism (Feb 2017):

Dual-specificity phosphatase 6 deficiency regulates gut microbiome and transcriptome response against diet-induced obesity in mice (Nov 2016):

Short Chain Fatty Acids Prevent High-fat-diet-induced Obesity in Mice by Regulating G Protein-coupled Receptors and Gut Microbiota (Nov 2016):

Dietary fat and gut microbiota interactions determine diet-induced obesity in mice (& difference between animal fat & vegetable fat) (Oct 2016)

TED talk by microbiome researcher, Rob Knight (obesity part around 11:30):

Freeze-dried poop pills being tested for obesity treatment (Jan 2016):

The gut microbiota affects calorie harvest and energy homeostasis. Germ-free mice have 40% less total body fat than conventional mice although they ingest 29% more calories than their conventionally raised littermates. Fecal microbiota transplanted from conventionally raised mice to germ-free mice triggered a 57 % increase in the amount of body fat and a dramatic increase in hepatic triglyceride levels and insulin resistance without modifying the amount of food consumed (Apr 2016): || Germ-free lab mice also suffer various problems: - (Oct 2016)

Children who take antibiotics gain weight faster (Oct 2015, n=163,820): - (Mar 2016, n=21,714) - (Jul 2016, n=979) - (Mar 2017, n=162) || Also seen in feed animals (along with pro & pre biotics) (Nov 2016):

Testosterone disruptor effect and gut microbiome perturbation in mice: Early life exposure to doxycycline (Jan 2019): "Early-life exposure to low-dose of doxycycline associates with increased risk of obesity."

Effect of diet soda on gut bacteria (Sep 2014):

Artificial sweeteners induce glucose intolerance by altering the gut microbiota (Sep 2014): | And block enzyme activity (Nov 2016): | Artificial Sweeteners May Change Our Gut Bacteria in Dangerous Ways (Apr 2015):

Changes in the microbiome may contribute to cognitive changes associated with eating a Western diet (May 2016, mice):

Effects of Gut Microbes on Nutrient Absorption and Energy Regulation (Feb 2012):

Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates (Aug 2014):

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice (Nov 2009):

Diet rapidly and reproducibly alters the human gut microbiome (Dec 2013):

Review, 2017: Influence of diet on the gut microbiome and implications for human health

Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior (Jan 2016): - (Feb 2016, rats):

Fast food fever: reviewing the impacts of the Western diet on immunity. Dietary impact on the gut microbiome and the mechanisms by which our poor dietary choices are encoded into our gut, our genes, and are passed to our offspring (Jun 2014):

Mendelian Randomization Analysis Reveals Causal Effects of the Human Gut Microbiota on Abdominal Obesity (Mar 2021, n=1126 twin pairs)

Diet-induced extinctions in the gut microbiota compound over generations (Jan 2016):

Other conditions:


Review, 2018: Microbiome and Allergic Diseases "Recent research points to a central role of the microbiome"

Review, 2018: Microbiota and Food Allergy "evidence suggests that the increasing prevalence of food allergies is associated with compositional and functional changes in our gut microbiota; mechanistic details not fully understood" | Another:

“expansion of a certain species of house dust fungus (Wallemia mellicola) can occur in the intestines of mice after they are treated with antibiotics and exposed to the fungus. By contrast, mice with an intact and healthy intestinal microbiota resist this expansion. After expansion of this fungal population, the mice are more prone to develop asthma-like inflammation in their lungs when exposed to allergens”

"Two separate consortia of five or six species of bacteria derived from the human gut could suppress food allergies in the mouse model, fully protecting the mice and keeping them resistant to egg allergy. Giving other species of bacteria did not provide protection.". Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy (June 2019)

Gut microbiota from infant with Cow's Milk Allergy promotes clinical and immune features of atopy in a murine model (Mar 2019):

Germ-Free Mice Exhibit Mast Cells With Impaired Functionality and Gut Homing and Do Not Develop Food Allergy (Feb 2019):

Gut Microbes from Healthy Infants Block Milk Allergy Development in Mice. Healthy infants harbor intestinal bacteria that protect against food allergy (2019):

Perinatal antibiotic exposure alters composition of murine gut microbiota and may influence later responses to peanut antigen (2018): "Our data suggest that early antibiotic exposure promotes a shift in the gut microbiota community that may in turn, influence how mice later respond to a TNF-α + antigen challenge"

"the gastrointestinal microbiota plays a definitive role in atopy development" (2017):

Commensal bacteria protect against food allergen sensitization (2014): "We show here that sensitization to a food allergen is increased in mice that have been treated with antibiotics or are devoid of a commensal microbiota"

Allergies/immune response patterns are shaped by microbial exposures and diet in the pregnant mother and during the infant’s first years: (more in the pregnancy & birth listing:

American adults with allergies have low gut microbe diversity: "Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project (2016)"

A metagenome-wide association study of gut microbiota in asthma in UK adults (2018): "The microbiota of the individuals with asthma consisted of fewer microbial entities than the microbiota of healthy individuals. The adult human gut microbiome of asthma patients is clearly different from healthy controls."

Newborn Gut Microbiome Predicts Later Allergy and Asthma:

Causality between certain gut microbiota and the development of allergic asthma has been shown in experiments conducted in neonatal mice:

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting (2017): "Our findings provide additional support for considering modulation of the gut microbiome as a primary asthma prevention strategy"

A distinct microbiota composition is associated with protection from food allergy in an oral mouse immunization model (2016):

Relationship between a viral detection system (MAVS), the composition of the gut microbiota, and the development of skin allergies (2018): after FMT from allergic mice the recipients "developed severe allergic reactions, showing that the transplanted gut bacteria were responsible"

Trans-maternal Helicobacter pylori exposure reduces allergic airway inflammation in offspring through regulatory T-cells (2018):

"proteases expressed by opportunistic pathogens impact host immune responses that are relevant to the development of food sensitivities, independently of the trigger antigen" (Mar 2019):


Re-framing the Theory of Autoimmunity in the Era of the Microbiome: Persistent Pathogens, Autoantibodies, and Molecular Mimicry (2018): - The theory of autoimmunity was developed at a time when the human body was regarded as largely sterile. Antibodies in patients with chronic inflammatory disease could consequently not be tied to persistent human pathogens. The concept of the "autoantibody" was created to reconcile this phenomenon. This calls for a paradigm shift in autoimmune disease treatment.

Review, 2022: Safety and efficacy of fecal microbiota transplantation for autoimmune diseases and autoinflammatory diseases: A systematic review and meta-analysis "effective and relatively safe, and it is expected to be used as a method to induce remission of active autoimmune diseases"

Perspective, 2022: Scientists have proposed a new mechanistic model (AD2) for Alzheimer's, looking at it not as a brain disease, but as a chronic autoimmune condition that attacks the brain. Alzheimer's disease as an innate autoimmune disease (AD2): A new molecular paradigm.

Review, 2022: Safety and efficacy of fecal microbiota transplantation for autoimmune diseases and autoinflammatory diseases: A systematic review and meta-analysis "FMT in the treatment of autoimmune diseases is effective and relatively safe, and it is expected to be used as a method to induce remission of active autoimmune diseases"

Review, 2020: Intestinal Dysbiosis in, and Enteral Bacterial Therapies for, Systemic Autoimmune Diseases

Review, 2019: Microbe-metabolite-host axis, two-way action in the pathogenesis and treatment of human autoimmunity "review summarizes the latest research of microbes and their related metabolites in AID. More importantly, it highlights novel and potential therapeutics, including fecal microbial transplantation, probiotics, prebiotics, and synbiotics"

Review, 2018: Antibiotics and autoimmune and allergy diseases: Causative factor or treatment? "Antibiotics use in children promotes the development of allergic disorders, whereas antibiotics use in adults seems to ameliorate inflammatory responses and reduce the severity of autoimmune diseases"

Translocation of a gut pathobiont drives autoimmunity in mice and humans (2018):

Autoimmunity-Associated Gut Commensals Modulate Gut Permeability and Immunity in Humanized Mice (Mar, 2019):

Identification of a Shared Microbiomic and Metabolomic Profile in Systemic Autoimmune Diseases (2019):

New Link Between Autoimmune Diseases and a Gut Bacterium (b. fragilis). Antigenic mimicry of ubiquitin by the gut bacterium Bacteroides fragilis : a potential link with autoimmune disease (2018): -


Review, Oct 2019: Hair regrowth following fecal microbiota transplantation in an elderly patient with alopecia areata: A case report and review of the literature:

Hair Growth in Two Alopecia Patients after Fecal Microbiota Transplant (2017)

Gut microbiota plays a role in the development of alopecia areata (2017)

Intestinal Dysbiosis and Biotin Deprivation Induce Alopecia through Overgrowth of Lactobacillus murinus in Mice (2017): -

Analysis of the gut microbiota in alopecia areata: identification of bacterial biomarkers (Aug 2019)

Scalp bacterial shift in Alopecia areata (April 2019): "Our results highlight, for the first time, the presence of a microbial shift on the scalp of patients suffering from AA"

Upcoming FMT clinical trial for hair loss (Aug 2019, Hong Kong):


Do Kimchi and Cheonggukjang Probiotics as a Functional Food Improve Androgenetic Alopecia? A Clinical Pilot Study (Aug 2019) "a kimchi and cheonggukjang probiotic product could promote hair growth and reverse hair loss without associated adverse effects such as diarrhea"

The effect of Lactobacillus plantarum hydrolysates promoting VEGF production on vascular growth and hair growth of C57BL/6 mice (Apr 2019)

Therapeutic, Prophylactic, and Functional Use of Probiotics: A Current Perspective (Sep 2020) - see Androgenetic Alopecia section. "various preclinical and clinical interventions model studies pointed out a potential therapeutic role of probiotic supplementations against androgenetic alopecia"

Probiotic Bacteria Induce a ‘Glow of Health’ (2013) "Eating probiotic yogurt triggered epithelial follicular anagen-phase shift with sebocytogenesis resulting in thick lustrous fur due to a bacteria-triggered interleukin-10-dependent mechanism" | Probiotic ‘glow of health’: it’s more than skin deep (2014)


The role of gut microbiota in lupus: what we know in 2018? "Current data demonstrates that, depending on the pattern of intestinal microorganisms or the presence of specific bacteria, different responses related to lupus physiology can be triggered. Fecal microbiota transplantation, live biotherapeutics, or dietary interventions targeting the microbiota will likely become a treatment for SLE."

Disordered intestinal microbes are associated with the activity of Systemic Lupus Erythematosus (Mar 2019): "SLE patients, especially the active patients, show an obvious dysbiosis in gut microbiota and its related metabolic pathways. Furthermore, the random forest models are able to diagnose SLE and predict disease activity."


Review, 2020: The Role of the Gut Microbiota in Coronary Heart Disease "Gut microbiota are causally associated with coronary heart disease."

Review, 2018: Role of gut microbiota in chronic low‐grade inflammation as potential driver for atherosclerotic cardiovascular disease: a systematic review of human studies

Review, 2018: Effects of products designed to modulate the gut microbiota on hyperlipidaemia "Products designed to modulate the gut microbiota results in changes of the plasma lipid concentrations and these changes may protect against cardiovascular disease"

Multiple reviews connecting cardiovascular disease to the gut microbiome:

Gut intraepithelial T cells calibrate metabolism and accelerate cardiovascular disease (2019): "Integrin β7− mice that lack natural IELs are metabolically hyperactive and, when fed a high-fat and high-sugar diet, are resistant to obesity, hypercholesterolaemia, hypertension, diabetes and atherosclerosis"

A gut bacterium tackles atherosclerosis (Oct 2022) Gut Parabacteroides merdae protects against cardiovascular damage by enhancing branched-chain amino acid catabolism

Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry (2018):

Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome (2018): "This study provides important evidence for a joint genetic and microbial effect in cardiovascular disease and provides directions for future applications in personalized medicine"

Microbial Transplantation With Human Gut Commensals Containing CutC Is Sufficient to Transmit Enhanced Platelet Reactivity and Thrombosis Potential (2018):

The gut microbiome in atherosclerotic cardiovascular disease (2017):

Gut Microbiota–Dependent Trimethylamine N-Oxide (TMAO) Predicts Risk of Cardiovascular Events in Patients With Stroke and Is Related to Proinflammatory Monocytes (2018):

Gut microbiome can influence common dietary compound (TMAO) linked to heart disease: | Targeting the gut microbiome to fight heart disease - Resveratrol reduces levels of TMAO and TMA:

Tomorrow’s Heart Drugs Might Target Gut Microbes. Scientists can stop gut bacteria in mice from making a chemical that causes arterial disease (2015):

Bacterial Fats, not Butter, May Be to Blame for Heart Disease (2017):

Bacteria Help Regulate Blood Pressure: Kidneys sniff out signals from gut bacteria for cues to moderate blood pressure after meals.

Gut Microbiome Associates With Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study Participants (2016):


Commensal Microbe-specific Activation of B2 Cell Subsets Contributes to Atherosclerosis Development Independently of Lipid Metabolism:

An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis (2018):

Bacterial butyrate prevents atherosclerosis by maintaining gut barrier function in mice. Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model (Nov 2018)

Stroke and transient ischemic attack:

Review, 2022: The effect of fecal microbiota transplantation on stroke outcomes: A systematic review "manipulating gut microbiota via FMT can be a possible therapeutic approach for treatment of stroke and recovery of post-stroke complications"

Review, 2020: The Gut Ecosystem: A Critical Player in Stroke

Review, 2016: The Gut Microbiome as Therapeutic Target in Central Nervous System Diseases: Implications for Stroke: - "Transplantation of balanced microbiota after cerebral ischemia improved stroke outcome"

Gut microbes impact stroke severity via the trimethylamine N-oxide pathway (Jun 2021, human-to-mouse FMT)

Short-chain fatty acids improve post-stroke recovery via immunological mechanisms (Dec 2019, mice)

Stroke Dysbiosis Index (SDI) in Gut Microbiome Are Associated With Brain Injury and Prognosis of Stroke (Apr 2019) "We developed an index to measure gut microbiota dysbiosis in stroke patients; this index was causally related to outcome in a mouse model of stroke"

Commensal microbiota affects ischemic stroke outcome by regulating intestinal γδ T cells (2016): "antibiotic-induced alterations in the intestinal flora reduce ischemic brain injury in mice, an effect transmissible by fecal transplants"

Microbiota Dysbiosis Controls the Neuroinflammatory Response after Stroke (2016):

Dysbiosis of Gut Microbiota With Reduced Trimethylamine‐N‐Oxide Level in Patients With Large‐Artery Atherosclerotic Stroke or Transient Ischemic Attack:

Heart failure:

Review, 2018: The gut microbiome and heart failure "exact mechanisms of action remain unclear; investigating the gut microbiome as a potential strategy for clinical intervention is highly warranted"

Review, 2018: Dietary metabolism, the gut microbiome, and heart failure

Review, 2017: Targeting the Microbiome in Heart Failure:

Pathogenic Gut Flora Tied to Heart-Failure Severity (2016): -

Heart failure is associated with depletion of core intestinal microbiota (2017):

Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients (2018):

Heart failure: Destroying gut bacteria could improve outcomes. Gut microbiota depletion preserves heart function, suppresses cardiac fibrosis and hypertrophy in a non-ischemic heart failure mouse model (2018): -


Bacteria pill is 'better than statins' in the war on cholesterol, say researchers. Trials of the new treatment showed cholesterol falling 37% in patients who were suffering from harmfully high levels in their system:

A link has been discovered between bacteria in the gut and body weight, triglyceride and good cholesterol levels. Researchers identified 34 specific digestive tract microorganism species that influence weight and lipid metabolism:

The intestinal microbiota regulates host cholesterol homeostasis (Nov 2019) "FMT from humans harboring elevated plasma cholesterol levels to recipient mice induced a phenotype of high plasma cholesterol levels in association with a low hepatic cholesterol synthesis and high intestinal absorption pattern"

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level (Jun 2020, n=1299)

Blood pressure:

Review, 2017: "In this review, we compile the recent findings and hypotheses describing the interplay between the microbiome and blood pressure":

Critical Role of the Interaction Gut Microbiota – Sympathetic Nervous System in the Regulation of Blood Pressure (Mar 2019):


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Review, 2018: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity

Review, 2018: Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome? This article provides a comprehensive review of the current evidence supporting microbiome alterations in ME/CFS patients.

Review, 2016: A Role for the Intestinal Microbiota and Virome in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)?

Review, 2009: Leaky gut in chronic fatigue syndrome: A review - "The purpose of this paper is to review the evidence that an increased translocation of gram negative bacteria is another inflammatory pathway that is involved in CFS"

FMT for CFS:

A Retrospective Outcome Study of 42 Patients with Chronic Fatigue Syndrome, 30 of Whom had Irritable Bowel Syndrome. Half were treated with oral approaches, and half were treated with Faecal Microbiome Transplantation (Jul 2019, Dove, Taymount) "the FMT group improved to a greater extent"

Fecal Microbiota Transplantation for Fibromyalgia: A Case Report and Review of the Literature (2017)

Thomas J Borody's 2012 CFS FMT study with 70% initial success rate: Bacteriotherapy in Chronic Fatigue Syndrome (CFS): A Retrospective Review -;dn=119626231492520;res=IELHEA - Full paper:

Insights from metabolites get us closer to a test for chronic fatigue syndrome. "Combining this data with data from an earlier microbiome study, the researchers now report they can predict whether or not someone has the disorder with a confidence of 84 percent" | Dorottya Nagy-Szakal et al, Insights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics, Scientific Reports (2018). DOI:

Chronic fatigue syndrome is in your gut, not your head. Cornell identifies biological markers (2016): -

The gut microbiome in Myalgic Encephalomyelitis (page 10, Cornell, 2017):

Increased D-Lactic bacteria in CFS patients:

A Pair of Identical Twins Discordant for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Differ in Physiological Parameters and Gut Microbiome Composition (2016):

2017 Columbia University study confirms "Chronic Fatigue Syndrome Associated with Abnormal Gut Microbes":

Exercise – induced changes in cerebrospinal fluid miRNAs in Gulf War Illness, Chronic Fatigue Syndrome and sedentary control subjects. Changes in brain chemistry -- observed in levels of miRNAs that turn protein production on or off -- were seen 24 hours after riding a stationary bike for 25 minutes. - See the "mechanisms" section for info on gut microbe's influence on miRNAs.

Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) (2015): "findings suggest a role for an altered gut microbiome and increased bacterial translocation following exercise in ME/CFS patients that may account for the profound post-exertional malaise experienced by ME/CFS patients"


Review, Jul 2020: Role of the gut microbiota in the pathogenesis of coeliac disease and potential therapeutic implications "Dysbiotic microbiota may lead to a dysregulated immune response that may contribute to the pathogenesis of coeliac disease"

Serendipity in Refractory Celiac Disease: Full Recovery of Duodenal Villi and Clinical Symptoms after Fecal Microbiota Transfer. (2016)

Duodenal Bacteria From Patients With Celiac Disease and Healthy Subjects Distinctly Affect Gluten Breakdown and Immunogenicity (2016):

Bacteria from celiac patients influence gluten’s digestion and its ability to provoke an immune response (2016):

Researchers discover enzyme created by oral bacteria (Rothia) that break down gluten, preventing the exaggerated immune response associated with celiac (2016)

"These findings suggest that enzymes produced by opportunistic pathogens and certain bacteria within the gut can trigger host immune responses that could increase susceptibly to food sensitivities" Advances in the understanding of how microbes promote food sensitivity (2019)

Celiac disease may be partly triggered by bacterial infection. Protein fragments from these bacteria are very similar to fragments from gluten. That means once the immune system finishes fighting off these bugs, it’s still all riled up when gluten proteins start showing up (Dec 2019, in vitro) T cell receptor cross-reactivity between gliadin and bacterial peptides in celiac disease.

Experimental hookworm infection and gluten microchallenge promote tolerance in celiac disease (2015): -

Association Between Antibiotics in the First Year of Life and Celiac Disease (Mar 2019):

Who Has the Guts for Gluten? (2013):


Antibiotics disrupt the beneficial bacteria found in the gut and make patients more likely to get C. difficile:


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Review, 2018: Gut microbiota in diabetes and HIV: Inflammation is the link

Review, 2016: Microbiome alterations in HIV infection a review:

Fecal microbiota transplantation in HIV: A pilot placebo-controlled study (Feb 2021, n=30) capsules (OpenBiome) or placebo for 8 weeks.

Gut bacteria may contribute to susceptibility to HIV infection, UCLA-led research suggests (Sep 2022, n=55) Gut dysbiosis and inflammatory blood markers precede HIV with limited changes after early seroconversion

Changes in gastrointestinal microbial communities influence HIV-specific CD8+ T-cell responsiveness to immune checkpoint blockade (Aug 2020, n=56, Openbiome)

Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection (April 2019): "findings support a role for the gut microbiome in HIV transmission in MSM, and rationale for investigating the gut MB as a risk factor for HIV transmission"

Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals (2018):

Bacteria in our gut affects HIV—is there a solution? (2016)

How Gut Microbiota Impacts HIV Disease. A new understanding of the role gut microbiota plays in HIV disease is beginning to emerge, suggesting potential new strategies to manage the infection (2016):

Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals (2016, n=37):

Understanding the Gut Microbiome and HIV (2016):

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen (2016):

Low nadir CD4+ T-cell counts predict gut dysbiosis in HIV-1 infection (2018): "low nadir CD4+ T-cell counts, rather than HIV-1 serostatus per se, predict the presence of gut dysbiosis in HIV-1 infected subjects. Such dysbiosis does not display obvious HIV-specific features; instead, it shares many similarities with other diseases featuring gut inflammation"

Extracellular vesicles from symbiotic vaginal lactobacilli inhibit HIV-1 infection of human tissues (Dec 2019, ex vivo)

"Vaginal microbiota dominated by lactobacilli protects women from sexually transmitted infection, in particular HIV-1" Extracellular Vesicles Generated by Gram-Positive Bacteria Protect Human Tissues Ex Vivo From HIV-1 Infection (Jan 2022)


Review, 2022: A Systematic Review and Meta-Analysis of Randomized Controlled Trials of Fecal Microbiota Transplantation for the Treatment of Inflammatory Bowel Disease "Conclusion. FMT is a safe, effective, and well-tolerated therapy. Studies have found that fresh fecal microbiota transplant can increase clinical remission rates"

Gaps in knowledge and future directions for the use of faecal microbiota transplant in the treatment of inflammatory bowel disease (Nov 2019)

Recent Research on Fecal Microbiota Transplantation in Inflammatory Bowel Disease Patients (Q&A with Monika Fischer, MD. Gastroenterol Hepatol, Jan 2019) | Similar one from 2018 with one of the authors:

Review, 2018: The role of fecal microbiota transplantation in inflammatory bowel disease. "Despite high heterogenity in all areas of procedure, overall, this review supports a positive effect of FMT on outcome of IBD and FMT was well tolerated for the majority of patients." | Another 2018 review: Current Evidence for the Management of Inflammatory Bowel Diseases Using Fecal Microbiota Transplantation

Review, 2018: Fecal microbiota transplant – a new frontier in inflammatory bowel disease "Clinical trials data are still poor but strongly support a future introduction of FMT in therapy to manage IBD microbiome. More studies are needed to assess the optimal route of administration and the frequency of FMT, the best matched donor for each patient as well as the risks associated with FMT in IBD"

Review, 2017: Gut microbiota in the pathogenesis of inflammatory bowel disease:

Review, 2016: The association between the gut microbiota and the inflammatory bowel disease activity: a systematic review and meta-analysis:

Inflammatory Bowel Disease Outcomes Following Fecal Microbiota Transplantation for Recurrent C. difficile Infection (Nov 2020, n=50, Crohn’s and UC) "This prospective trial assessing FMT in IBD-CDI patients suggests IBD outcomes are better than reported in retrospective studies. Among the Crohn’s disease cohort, 73.3% (11 of 15) had IBD improvement. Among the ulcerative colitis cohort, 62% (22 of 34) had IBD improvement."

Fecal microbiota transplantation results in bacterial strain displacement in patients with inflammatory bowel diseases (Oct 2019) "3 days after FMT, 11 out of 15 recipients were in remission"

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice (2019):

"In a population-based study, we found infection within the first year of life to be associated with a diagnosis of IBD. This might be due to use of antibiotics or a physiologic defect at a critical age for gut microbiome development." (Feb 2019)

Antibiotics induce remission in children with IBD failing a biologic. Efficacy of Combination Antibiotic Therapy for Refractory Pediatric Inflammatory Bowel Disease (Feb 2019, n=63)

Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease (2018): "findings support the idea that certain eukaryotic viruses might trigger intestinal inflammation and contribute to IBD pathogenesis and pave the way not only for the discovery of novel diagnostic biomarkers but also for the development of anti-viral drugs for the treatment of IBD"

Distinct Microbial Communities Trigger Colitis Development upon Intestinal Barrier Damage via Innate or Adaptive Immune Cells (2017):

Worm infection counters inflammatory bowel disease by drastically changing gut microbiome:

Breakdown products from microcin B17, a well-known toxin produced by E. coli, seem to trigger gut inflammation that is characteristic of IBD (2018):


FMT for Crohn’s disease:

Multiple fresh fecal microbiota transplants induces and maintains clinical remission in Crohn’s disease complicated with inflammatory mass (2017):

Repeated and multiple fecal microbiota transplantations plus partial enteral nutrition as the first-line treatment in active pediatric Crohn’s disease (Feb 2023, n=25) "At week 18-22, clinical remission was achieved in 72.7% and 20.0% of patients in the FMT and PEN groups". Lower route, no bowel prep, multiple fresh FMTs, 12 donors (relatives and trusted friends) - one donor per recipient.

Foodborne fungus impairs intestinal wound healing in Crohn's disease (Mar 2021) Debaryomyces is enriched in Crohn’s disease intestinal tissue and impairs healing in mice.

Malassezia (skin fungus) Is Associated with Crohn’s Disease and Exacerbates Colitis in Mouse Models (Mar 2019) "Collectively, these results suggest that targeting specific commensal fungi may be a therapeutic strategy for IBD"

The fecal microbiota as a biomarker for disease activity in Crohn’s disease (2016):

A microbial signature for Crohn's disease (2017):

Serologic microbial associated markers can predict Crohn's disease behaviour years before disease diagnosis (2016):

Genetic Variant Newly Linked to Crohn’s Disease Also Associated with Altered Gut Microbiome Composition (2016):

Case Western Reserve-Led International Team Identifies Fungus in Humans for First Time as Key Factor in Crohn’s Disease (2016):

A role for bacterial urease in gut dysbiosis and Crohn’s disease. Bacterial (E. coli) enzyme (urease) reconfigures the entire gut microbiome and worsens immune-mediated colitis:

Ulcerative Colitis:

Review, Jun 2022: Efficacy of Fecal Microbiota Transplantation in the Treatment of Active Ulcerative Colitis: A Systematic Review and Meta-Analysis of Double-Blind Randomized Controlled Trials "Clinical remission or response and endoscopic remission or response were significantly higher in patients who received FMT compared with placebo without any differences in serious or specific adverse events."

Review, Jun 2016: Fecal Microbiota Transplantation for Ulcerative Colitis: A Systematic Review and Meta-Analysis:

Review, Sep 2017: Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis: Pooled rate of clinical remission in all 4 trials was 42.1% in the group receiving donor FMT and 22.6% in those receiving control. | Discussion with one of the authors in 2018:

Capsulized Fecal Microbiota Transplantation Induces Remission in Patients with Ulcerative Colitis by Gut Microbial Colonization and Metabolite Regulation (Apr 2023, n=22) "FMT induced clinical remission and clinical response in 57.1% (12 of 21) and 76.2% (16 of 21) of UC patients"

Fecal microbiota transplantation for recurrent Clostridioides difficile infection in patients with concurrent ulcerative colitis (Apr 2023, n=34) "Twenty-four patients (69%) experienced remission or an amelioration of UC activity"

Fecal Transplants Effective (Jun 2016):

Fecal Microbiota Transplantation Ameliorates Active Ulcerative Colitis by Downregulating Pro-inflammatory Cytokines in Mucosa and Serum (Apr 2022, n=27) "16 (59.3%) achieved efficacious clinical response and 11 (40.7%) clinical remission"

Fecal microbiota transplantation versus glucocorticoids for the induction of remission in mild to moderate ulcerative colitis (Aug 2022, n=122) "FMT therapy was as effective as glucocorticoids to induce remission in active mild to moderate UC, accompanied by fewer adverse events"

Lyophilised oral faecal microbiota transplantation for ulcerative colitis (LOTUS): a randomised, double-blind, placebo-controlled trial (Dec 2021, n=35) "At week 8, eight (53%) of 15 patients in the FMT group were in corticosteroid-free clinical remission with endoscopic remission or response, as were three (15%) of 20 patients in the placebo group"

Efficacy of fecal microbiota therapy in steroid dependent ulcerative colitis: a real world intention-to-treat analysis (Nov 2018, n=345):

Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative Colitis. A Randomized Clinical Trial (Jan 2019): "1-week treatment with anaerobically prepared donor FMT compared with autologous FMT resulted in a higher (32% vs 9%) likelihood of remission at 8 weeks."

The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis (2017):

Fecal microbiome from patients with ulcerative colitis is potent to induce inflammatory responses. "fecal bacteria from UC patients cause stronger inflammatory responses than fecal bacteria from healthy controls" (2018):

"FMT from UC donors to normal recipient rats triggered UC symptoms, UC-prone microbial shift, and host metabolic adaption" (2018):

Microbiome profiling reveals associations with ulcerative colitis severity, treatment. Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course (Oct 2018): -

Gut mucosal virome alterations in ulcerative colitis (Mar 2019): "We demonstrated for the first time that UC is characterised by substantial alterations of the mucosa virobiota with functional distortion. Enrichment of Caudovirales bacteriophages, increased phage/bacteria virulence functions and loss of viral-bacterial correlations in the UC mucosa highlight that mucosal virome may play an important role in UC pathogenesis"


Numerous studies & reviews:

FMT for IBS:

Pre-Antibiotic Treatment Followed by Prolonged Repeated Faecal Microbiota Transplantation Improves Symptoms and Quality of Life in Patients with Irritable Bowel Syndrome: An Observational Australian Clinical Experience (Oct 2022, n=60)

Fecal microbiota transplantation relieves abdominal bloating in children with functional gastrointestinal disorders via modulating the gut microbiome and metabolome (Oct 2022, n=12) "Abdominal bloating was relieved in all pediatric FGID patients by FMT at 8 weeks. Pain and diarrhea improved"

Fecal microbiota transplantation in the treatment of irritable bowel syndrome: a single-center prospective study in Japan (Jul 2022, n=17) "about 60% of Japanese patients with IBS showed improvement in both the IBS-SI and BSFS, without severe side effects"

Effect of fecal microbiota transplantation in patients with slow transit constipation and the relative mechanisms based on the protein digestion and absorption pathway (Dec 2021, n=8) "clinical improvement reached 62.5% and rates of patients’ clinical remission achieved 75% after the 3rd treatment"

The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors (Dec 2021, n=18) "FMT can effectively alleviate the anxiety and depression behaviors of IBS-D patients and reduce the IBS-SSS score"

Efficacy of faecal microbiota transplantation for patients with irritable bowel syndrome in a randomised, double-blind, placebo-controlled study (Dec 2019, n=165) "89% response rate in patients who received 60g FMT. The use of a superdonor is necessary for successful FMT" - 1 year follow up, 3 year follow up.

Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial (2018):

The kinetics of gut microbial community composition in patients with irritable bowel syndrome following fecal microbiota transplantation (Nov 2018). "Patients’ microbiota profiles became more-or-less similar to donors. Questionnaire scores were significantly improved at all time points following FMT"

Fecal transplants from humans with irritable bowel syndrome and anxiety into mice lead to similar symptoms and anxiety-like behavior in the rodents, researchers report (2017):

Fecal microbiota transplantation in patients with slow-transit constipation: A randomized, clinical trial. (2017):

Gut Microbiota in Patients With Irritable Bowel Syndrome—A Systematic Review (Jul 2019) "All studies found differences between cases and controls, although the nature of these differences was inconsistent, and therefore no definitive conclusion can be reached as to whether any species might be harmful or protective" -

A Review of Microbiota and Irritable Bowel Syndrome: Future in Therapies (2018). Summary of dysbiosis findings in IBS (Table 1): - "There is growing evidence indicating that fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs) may result in bloating, pain and other IBS symptoms in approximately 70% of IBS patients"

Altered Molecular Signature of Intestinal Microbiota in Irritable Bowel Syndrome Patients Compared with Healthy Controls: a Systematic Review and Meta-analysis (2017): - | Another 2019 systematic review:

Review, 2017: We highlight the known effects of gut microbiota on mechanisms implicated in the pathophysiology of IBS including disrupted gut brain axis (GBA), visceral hypersensitivity (VH), altered GI motility, epithelial barrier dysfunction and immune activation

"a new battery of tests enables researchers to distinguish patients with IBS from healthy children and identifies correlations between certain microbes and metabolites with abdominal pain" (April 2019) Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome

Identification of Gut Microbiota and Metabolites Signature in Patients With Irritable Bowel Syndrome (Oct 2019)

Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome (2017):

Up to 50% of cases of chronic diahrrea/IBS-D is Bile Acid Malabsorption: - and bile acid absorption & metabolism is mediated by gut microbes:

Norwegian medical researchers have shown that the intestines of IBS patients do react to food in a special way (2014):

Removing fiber from diet decreases constipation symptoms and increases BM frequency (2012):

Antibiotics, gut microbiota, and irritable bowel syndrome: What are the relations? (Mar 2022) "Extensive research has established that antibacterial therapy induces remarkable shifts in the bacterial community composition that are quite similar to those observed in IBS. This suggestion is further supported by data from cohort and case-control studies, indicating that antibiotic treatment is associated with an increased risk of IBS"

Inflammation & arthritis:

Gut bacteria can cause, predict and prevent rheumatoid arthritis (2016):

Review, 2018: No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases

Review, 2017: Role of Gut Microbiota in Rheumatoid Arthritis. "In summary, Prevotella species are involved in the pathogenesis of arthritis."

Review, 2017: Role of Gut Microbiota in Rheumatoid Arthritis:

Review, 2016: The metabolic role of the gut microbiota in health and rheumatic disease: mechanisms and interventions:

Review, 2016: How the microbiota shapes rheumatic diseases:

Review, 2016: Microbiota and Arthritis: Correlations or Cause? - -

Fecal microbiota transplantation for rheumatoid arthritis: A case report (Dec 2020) "As far as we know, this is the first reported case that used FMT to treat RA successfully"

The Microbiome in Pediatric Rheumatic Diseases (2016):

A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis (July 2019). L. casei (ATCC334).

Two rheumatoid arthritis–specific autoantigens correlate microbial immunity with autoimmune responses in joints. In rheumatoid arthritis (RA), immunological triggers at mucosal sites, such as the gut microbiota, may promote autoimmunity that affects joints. (plus many more in comments):

"findings demonstrate a mechanism of RA pathogenesis through which a specific intestinal strain of bacteria can drive systemic autoantibody generation and joint-centered antibody deposition and immune activation" (Oct 2022) Clonal IgA and IgG autoantibodies from individuals at risk for rheumatoid arthritis identify an arthritogenic strain of Subdoligranulum.

Oregon study suggests some gut microbes may be keystones of health. "The inflammatory response in the third fish was completely controlled by the low-abundance species" (2015): -

Role of the Gut Microbiome in Modulating Arthritis Progression in Mice (2016): | Rifaximin Alters Intestinal Microbiota and Prevents Progression of Ankylosing Spondylitis in Mice (Mar 2019):

Bones and the Biome: The Link Between Our Microbiota and Rheumatologic Disease (2016):

Impact of the gut microbiota on inflammation, obesity, and metabolic disease (review, 2016): -

If being too clean makes us sick, why isn’t getting dirty the solution? (says getting dirty generally makes inflammation worse)


Intestinal Microbiota Distinguish Gout Patients from Healthy Humans:


Review, Jun 2022: Faecal Microbiota Transplantation and Chronic Kidney Disease

Review, 2019: Immunity, microbiota and kidney disease

Review, 2019: Modulation of the Gut Microbiota by Resistant Starch as a Treatment of Chronic Kidney Diseases: Evidence of Efficacy and Mechanistic Insights:

Review, 2019: Microbiome–metabolome reveals the contribution of gut–kidney axis on kidney disease:

Review, 2018: The gut microbiota and the brain–gut–kidney axis in hypertension and chronic kidney disease

Review, 2018: Mitochondrial dysfunction and gut microbiota imbalance: An intriguing relationship in chronic kidney disease

Review, 2018: Altered microbiome in chronic kidney disease: systemic effects of gut-derived uremic toxins

Review, 2018: Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients

Review, 2016: Gut hormones and gut microbiota: implications for kidney function and hypertension

Kidneys sniff out signals from gut bacteria for cues to moderate blood pressure after meals


Review, 2021: A New Perspective on Fecal Microbiota Transplantation in Liver Diseases

Review, 2019: Indoles: metabolites produced by intestinal bacteria capable of controlling liver disease manifestation

Review, 2018: Liver–Microbiome Axis in Health and Disease. "a liver–microbiome bidirectional crosstalk appears to be critical in health and various liver diseases and could be therapeutically targeted, such as by fecal microbiota transplantation"

Review, 2018: The gut–liver axis and the intersection with the microbiome

Review, 2017: The gut microbiome and liver cancer: mechanisms and clinical translation:


Review, Feb 2020: Fecal Microbiota Transplantation for Chronic Liver Diseases: Current Understanding and Future Direction

Effect of Fecal Microbiota Transplantation on Non-Alcoholic Fatty Liver Disease: A Randomized Clinical Trial (Jul 2022, n=75) "FMT could successfully improve the therapeutic effects on patients with NAFLD, and its clinical efficacy was higher in lean NAFLD than in obese NAFLD patients"

Fecal microbiota transplantation in alcohol-associated acute-on-chronic liver failure: an open-label clinical trial (Mar 2022, n=33, single FMT via naso tube from family member) "FMT is safe, improves short-term and medium-term survival, and leads to improvement in clinical severity scores"

Long-term Outcomes of Stool Transplant in Alcohol-associated Hepatitis—Analysis of Clinical Outcomes, Relapse, Gut Microbiota and Comparisons with Standard Care (Jan 2022, n=61) "healthy donor FMT is associated with significantly lesser ascites, infections, encephalopathy, and alcohol relapse (with a trend toward higher survival rates) than SoC"

Fecal Transplant Efficacy Examined for Chronic Liver Disease. Fecal microbiota transplantation (FMT) from a rationally selected donor seems safe and effective for patients with primary sclerosing cholangitis (PSC) (2017):

Fecal microbiota transplant improves brain function in hepatic encephalopathy (2018):

Neuroinflammation in Murine Cirrhosis is Dependent on the Gut Microbiome and is Attenuated by Fecal Transplant (June 2019)

Corticosteroids, nutrition, pentoxifylline, or fecal microbiota transplantation for severe alcoholic hepatitis (2018): "Healthy donor FMT for SAH improves survival beyond what is offered by current therapies"

Healthy Donor Fecal Microbiota Transplantation in Steroid-Ineligible Severe Alcoholic Hepatitis: A Pilot Study (2016): "1 week of FMT was effective and safe, and improved indices of liver disease severity and survival at 1 year"

Fecal Microbiota Transplantation in Patients With Primary Sclerosing Cholangitis: A Pilot Clinical Trial (Jan 2019): "To our knowledge, this is the first study to demonstrate that FMT in PSC is safe"

Genetically Obese Human Gut Microbiota Induces Liver Steatosis in Germ-Free Mice Fed on Normal Diet (2018):

Single bacterial strain causes liver damage: Enterobacter cloacae B29 administration induces hepatic damage and subcutaneous fat accumulation in high-fat diet fed mice (2018):

A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis (Jun 2020, n=163)

Microbial metabolite contributes to the accumulation of lipids in the liver and hence to nonalcoholic steatohepatitis (2018):

Gut microbiota translocation promotes autoimmune cholangitis (2018): "our data demonstrates the important role of gut microbiota and bacterial translocation in the pathogenesis of murine autoimmune cholangitis"

How gut bacteria may help to spot and address liver disease (2018):

Study finds gut microbiome can control antitumor immune function in liver. "if you treat mice with antibiotics and thereby deplete certain bacteria, you can change the composition of immune cells of the liver [due to bile acid changes], affecting tumor growth in the liver" (2018):

Gut microbiome composition in lean patients with NASH (nonalcoholic fatty liver disease) is associated with liver damage independent from caloric intake: a prospective pilot study (2018):

Probiotics Prevent Autoimmune-Related Liver Injury. A recent study examined the effect of Lactobacillus probiotic strains on liver injury in lupus-prone mice, demonstrating that gut bacteria plays an important role in autoimmune diseases. (2017)

Gut pathobionts as triggers for liver diseases (2019):

Microbiota Control of Malaria, Dengue, and Zika:

Bacteria Block Mosquitoes from Transmitting Zika, Brazilian Study Says. Wolbachia bacteria have already been used to control dengue:

Wolbachia Bacteria Could Be Answer To Malaria, Dengue: Bill Gates:

Microbiota Control of Malaria Transmission:

Composition of the gut microbiota modulates the severity of malaria:


Review, Feb 2022: Gut Dysbiosis in Pancreatic Diseases: A Causative Factor and a Novel Therapeutic Target

Review, Dec 2019: Microbiota in pancreatic health and disease: the next frontier in microbiome research

Gut Microbiota Regulate Pancreatic Growth, Exocrine Function and Gut Hormones (Feb 2022, mice & prediabetic men)

Also see



Urinary tract & bladder:


Probiotics section covering both oral and vaginal administration:

Summary post for /r/Healthyhooha (2019):

Review, Feb 2021: Lactic acid-containing products for bacterial vaginosis and their impact on the vaginal microbiota: A systematic review "There is a lack of high-quality evidence to support the use of lactic acid-containing products for BV cure or vaginal microbiota modulation"

Review, Nov 2019: Fecal Microbiota Transplantation: A Potential Tool for Treatment of Human Female Reproductive Tract Diseases

Review, Aug 2019: An Updated Conceptual Model on the Pathogenesis of Bacterial Vaginosis "It may be that healthy women are colonized by nonpathogenic Gardnerella species, whereas virulent strains are involved in BV development. As well as roles of Prevotella bivia and Atopobium vaginae"

Review, June 2019: The vaginal microbiota, HPV and cervical dysplasia: a systematic review and network meta-analysis. "Vaginal microbiota dominated by non-Lactobacilli species or Lactobacillus iners were associated with 3-5 times higher odds of any prevalent HPV and 2-3 times higher for high risk HPV and dysplasia/cervical cancer compared to Lactobacillus crispatus"

Nation’s first vaginal fluid transplants offer hope for millions (Aug 2022)

Lactic acid-containing products for bacterial vaginosis and their impact on the vaginal microbiota: A systematic review (Feb 2021) "lack of high-quality evidence to support the use of lactic acid-containing products for BV cure or vaginal microbiota modulation"

"Vaginal microbiota dominated by lactobacilli protects women from sexually transmitted infection, in particular HIV-1" Extracellular Vesicles Generated by Gram-Positive Bacteria Protect Human Tissues Ex Vivo From HIV-1 Infection (Jan 2022)

Does exposure to different types of menstrual protections affect the vaginal environment? (Sep 2022, n=138) "potential associations between cups use reporting and fungal genital infection"


Effect of the Gut Microbiota on Obesity, gut permeability, inflammation, immune system, metabolism, probiotics, diet, FMT: an Update (2015)

Therapeutic opportunities in the human microbiome (2012):

Gut Microbes Can Evolve From Foe to Friend—And Do It Fast:

Google drive study archive – "substantial emerging literature on intestinal overgrowth, gut barrier permeability, endotoxemia, systemic inflammation, and chronic disease":



Gut microbiome's impact on drugs:

Gut microbiome interactions with drug metabolism, efficacy, and toxicity (Jan 2017):

Review, 2018: Gut microbiota modulates drug pharmacokinetics

Yale researchers identified human gut microbes that metabolize over 150 therapeutic drugs, a finding that highlights the role bacteria play in determining how well individuals respond to medications. Mapping human microbiome drug metabolism by gut bacteria and their genes (Jun 2019)

"The gut microbiota has been shown to metabolize over 40 drugs and might contribute to the therapeutic efficacy of many more [62]." (Review, April 2019):

Common medications accumulate in gut bacteria, which may reduce drug effectiveness and alter the gut microbiome (Sep 2021) Bioaccumulation of therapeutic drugs by human gut bacteria

Gut microbiota and intestinal FXR mediate the clinical benefits of metformin (2018):

Gut microbiota specifically mediates the anti-hypercholesterolemic effect of berberine (BBR) and facilitates to predict BBR’s cholesterol-decreasing efficacy in patients (Jul 2021, n=83)

Gut microbiota mediated the therapeutic efficacies and the side effects of prednisone in the treatment of MRL/lpr mice (Sep 2021)

Impact of gut microbiota on drug metabolism: an update for safe and effective use of drugs (2017):

Xenobiotic biotransformation (2018):

Microbiome could be culprit when good drugs do harm Separating host and microbiome contributions to drug pharmacokinetics and toxicity (Feb 2019).

Antibiotics can limit body's ability to uptake analgesics. Manipulation of the Gut Microbiome Alters Acetaminophen Biodisposition in Mice (Mar 2020)

Oral and gut microbes can inactivate an antidiabetic drug (Nov 2021) The human microbiome encodes resistance to the antidiabetic drug acarbose

An intact microbiota is required for the gastrointestinal toxicity of the immunosuppressant mycophenolate mofetil (2018):

Gut Microbiota Modulation Attenuated the Hypolipidemic Effect of Simvastatin in High-Fat/Cholesterol-Diet Fed Mice:

Drug's impacts on the gut microbiome:

General Anesthesia Alters the Diversity and Composition of the Intestinal Microbiota in Mice (2018):

Anesthesia and surgery induce age-dependent changes in behaviors and microbiota (Jan 2020, mice)

Wide range of drugs affect growth of gut microbes (2018): and promote antibiotic resistance [1][2].

A key ingredient in common antidepressants such as Prozac could be causing antibiotic resistance - Antidepressant fluoxetine induces multiple antibiotics resistance in Escherichia coli via ROS-mediated mutagenesis (2018): - maybe not relevant at the dosages studied: -

Cannabidiol is a powerful new antibiotic (June 2019)

Perturbation of the human gut microbiome by a non-antibiotic drug contributes to the resolution of autoimmune disease (April 2019):

Alterations of the Host Microbiome Affect Behavioral Responses to Cocaine (2016): - "Animals with reduced gut bacteria showed an enhanced sensitivity to cocaine reward and enhanced sensitivity to the locomotor-sensitizing effects of repeated cocaine administration. These behavioral changes were correlated with adaptations in multiple transcripts encoding important synaptic proteins in the brain’s reward circuitry. This study represents the first evidence that alterations in the gut microbiota affect behavioral response to drugs of abuse."

Rosuvastatin significantly influenced the microbial community in both the caecum and faeces, causing a significant decrease in alpha diversity in the caecum and resulting in a reduction of several physiologically relevant bacterial groups. RSV treatment of mice significantly affected bile acid metabolism and impacted upon expression of inflammatory markers known to influence microbial community structure (including RegIIIγ and Camp) in the gut (2017):

Gut microbiota are very sensitive to drugs, diet, and even environmental pollutants (2017):

Acid suppression medicines associated with increased pathogens:

Omeprazole (PPI) caused considerable changes in stool culture results:


Gut microbiome affects efficacy of cancer drugs: -

Microbiota: a key orchestrator of cancer therapy:

Bacteria in the gut modulates response to immunotherapy in melanoma (FMT, 2017):

Researchers found certain bacteria hiding out among cancer cells, gobbling up chemotherapy drugs intended to demolish tumors.

Chemotherapy-driven dysbiosis in the intestinal microbiome. (2015): -

Fecal Microbiota Transplants (FMT):


Impact of genetics on the microbiome:


Review, 2022: Intestinal Flora Affect Alzheimer's Disease by Regulating Endogenous Hormones

Review, 2018: Gut Microbiota and the Neuroendocrine System: - "the gut microbiota is the body’s major neuroendocrine system that controls various body processes in response to stress, the hypothalamic–pituitary–adrenal (HPA) axis"

Review, 2017: Steroids, Stress, and the Gut Microbiome-Brain Axis. "steroids can influence the gut microbiota, and in turn the gut microbiota can influence hormone levels"

Review, 2014: Gut Microbiota: The Neglected Endocrine Organ

Humans have evolved enzymes, receptors, and transporters for the compounds produced by our microbial communities so that the microbiome functions essentially as an endocrine organ:

The gut microbiota is a major regulator of androgen metabolism in intestinal contents (2019, mice and 8 healthy men) "We also observed GM-dependent changes in androgen action in extra-intestinal tissues. Overall, these findings identify the GM as a major regulator of local androgen action in the intestine as well as in other peripheral tissues"

3β-Hydroxysteroid dehydrogenase expressed by gut microbes degrades testosterone and is linked to depression in males (Feb 2022, n=107)

Probiotic Bifidobacterium lactis V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis (April 2019)

Male steroid hormones: -

Probiotic Microbes Sustain Youthful Serum Testosterone Levels and Testicular Size in Aging Mice (L. reuteri, 2014)

Researchers found predictive relationships between the fecal microbiota and serotonin and cortisol:

Gut microbiota induce IGF-1 and promote bone formation and growth (in mice). In contrast, antibiotic treatment does opposite:

Researchers find, correct a cause of rhino infertility. Gut microbes in the female southern white rhino metabolize phytoestrogens, estrogenlike plant compounds, in a way that reduces fertility (Apr 2019)

In humans, eradicating H. pylori affects the regulation of two hormones produced in the stomach and involved in energy balance, ghrelin and leptin (2011) -

Vitamin D:

Oral supplementation with probiotic L. reuteri NCIMB 30242 increases mean circulating 25-hydroxyvitamin D: a post hoc analysis of a randomized controlled trial:

Gut microbes may partner with a protein to help regulate vitamin D (2018):

Study reveals connection between gut bacteria and vitamin D levels. Link between active vitamin D and overall microbiome diversity, plus 12 types of bacteria (Nov 2020, n=567) Vitamin D metabolites and the gut microbiome in older men.

Causal relationship between gut microbiota and serum vitamin D: evidence from genetic correlation and Mendelian randomization study (Jan 2022)

Immune system:

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Intestinal Permeability:

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Mechanisms whereby the gut microbiome impacts, regulates, & interacts with the entire body:

Gut microbes are responsible for: Synthesis of vitamins, absorption of minerals, production of epithelial nutrients such as SCFAs, degradation of food components, stimulation of immune system, production of digestive & protective enzymes, prevention of colonization by opportunistic & pathogenic microbes, and more. - -

Humans have evolved enzymes, receptors, and transporters for the compounds produced by our microbial communities so that the microbiome functions essentially as an endocrine organ:

Review, 2018: Gut Microbiota and the Neuroendocrine System: - "the gut microbiota is the body’s major neuroendocrine system that controls various body processes in response to stress, the hypothalamic–pituitary–adrenal (HPA) axis"

In addition to secreting neuropeptides, enteroendocrine cells rapidly convey information about nutrients in the gut by releasing neurotransmitters (glutamate) to excite vagal and spinal sensory neurons. (2018): "The finding that gut enteroendocrine cells form glutamatergic synapses identifies a first relay in the neural circuit through which the brain detects gastrointestinal contents, such as nutrients and microbes, to control satiety, metabolism, and digestion."

Influence the activation of peripheral immune cells, which regulate responses to neuroinflammation, brain injury, autoimmunity and neurogenesis:

Amyloid produced by commensal bacteria may cause changes in protein folding and neuroinflammation in the central nervous system through the autonomic nervous system (particularly the vagus nerve), the trigeminal nerve in the mouth and nasopharynx, and the gut (including mouth, esophagus, stomach and intestines), as well as via the olfactory receptors in the roof of the nose.

Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve:

The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis (2018):

Gut microbes can communicate with the brain through a variety of routes, including the vagus nerve, short-chain fatty acids (SCFAs), cytokines, and tryptophan:

Researchers Uncover Gut Bacteria's Potential Role In Multiple Sclerosis. "We essentially discovered a remote control by which the gut flora can control what is going on at a distant site in the body, in this case the central nervous system" (2018)

Gastrointestinal neuromuscular apparatus:

TLR2 may act in intestinal pathophysiology, not only by its inherent innate immune role, but also by regulating the intestinal serotoninergic system -

Bacterial Signaling to the Nervous System via Toxins and Metabolites:

Gut microbial metabolites as multi-kingdom intermediates (Sep 2020 review)

Immunoregulatory circuits engaging epithelial and mesenchymal cells in the intestine, airways, and skin. Immune communications with hematopoietic cells and the microbiota orchestrate local immune homeostasis and inflammation:

Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota (2017):

Bidirectional signaling between the brain and the gastrointestinal tract is regulated at neural, hormonal, and immunological levels.

Quorum sensing & electrical signaling: -

Extracellular Vesicles:

Gut's microbial community shown to influence host gene expression; epigenetics; epigenomic regulation: - - -

Redox signaling mediated by the gut microbiota. Redox imbalances have been correlated with every single disease. -


"These results provide novel and provocative evidence that modulation of the gut microbiome via FMT induces alterations in circulating and intestinal tissue miRNAs" (Apr 2021)

microRNAs (miRNAs) act at the epicenter of the signaling networks regulating intestinal homeostasis: -

Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through a small GTPase ARF4:

Review, 2017: MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome

Microbiota may control intestinal epithelial stem cell (IESC) proliferation in part through microRNAs (miRNAs). | review:

Gut microbes seem to influence miRNAs in the amygdala and the prefrontal cortex:

"bacteria secrete a specific molecule--nitric oxide--that allows them to communicate with and control their hosts' DNA, and suggests that the conversation between the two may broadly influence human health" Regulation of MicroRNA Machinery and Development by Interspecies S-Nitrosylation (Feb 2019).

Eukaryotic/host miRNAs play a role in the replication/propagation of viruses, affect life-cycles & infection pathways: More virus-host genome interactions:

Bacterium orchestrates gastric epithelial stem cells and gland homeostasis:

Maintain oxygen balance & homeostasis in the gut via peroxisome proliferator-activated receptor-γ (PPARγ):

Nutrient poor environment causes bacteria to adapt, this causes host to store more fat. Direct communication with mitochondria:

How dietary fiber (DF) intake elicits a wide range of physiologic effects, not just locally in the gut, but systemically.

Most of effects are mediated through metabolites acting as energy sources, signaling molecules, receptor ligands and substrates for host enzymes.

Enteric nervous system modulates gut microbiota community:

Researchers identify mechanisms through which H. pylori bacteria cause gastric cancer (2017):

Microbial metabolite contributes to the accumulation of lipids in the liver and hence to nonalcoholic steatohepatitis (2018):

A single genetic change in gut bacteria alters host metabolism via bacterial enzyme impacting bile metabolism (2018):

Accelerate Wound Healing via multiple mechanisms [1][2].

More effects of antibiotics:

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Systemic (more systemic impacts of the gut microbiome):

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