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If you're curious about a condition not listed here, do a google, 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

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many long standing positions are being debunked, and even much of what you read (here or elsewhere) can become quickly outdated.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 this testing section for examples of current status/limitations of detecting & identifying human microbes.

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Kurzgesagt – How Bacteria Rule Over Your Body – The Microbiome - A good, simple intro, but some things might be wrong/outdated.

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 Hanza 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:


Brain function:

Gut bacteria produce and consume neurotransmitters: - - Along with gasotransmitters that affect our brain, mind and behavior: || As do gut fungi:

Gut microbes regulate serotonin:

Microbial Genes, Brain & Behaviour - Epigenetic Regulation of the Gut-Brain Axis: To date, there is rapidly increasing evidence for host-microbe interaction on virtually all levels of complexity, ranging from direct cell-to-cell communication to extensive systemic signalling, and involving various organs and organ systems, including the central nervous system. As such, the discovery that differential microbial composition is associated with alterations in behavior and cognition has significantly contributed to establish the microbiota-gut-brain axis as an extension of the well-accepted gut-brain axis concept. (2013)

Gut bacteria regulate nerve fibre insulation. Research suggests that gut bacteria may directly affect brain structure and function, offering new ways to treat multiple sclerosis and psychiatric conditions (2016):

Gut bacteria essential for neurogenesis; Antibiotics that kill gut bacteria also stop growth of new brain cells: -

Neuron destruction processes in the brain could be triggered by proteins produced by gut microbiota:

The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice:

The adoptive transfer of behavioral phenotype via the intestinal microbiota: experimental evidence and clinical implications (2013): "raising the possibility of using FMT for disorders of the central nervous system, and prompting caution in the selection of FMT donors"

Correlation between gut microbiota and personality in adults: A cross-sectional study (2017):

Associations among diet, the gastrointestinal microbiota, and negative emotional states in adults (2019): "results suggest GI microbes are related to mood in adults without diagnosed mood disorders and that these relationships differ by sex and are influenced by dietary fiber intake"

The Virus That Could Cure Alzheimer’s, Parkinson’s, and More:

Gut microbiome populations are associated with structure-specific changes in white matter architecture (2018):

"Although the results cannot prove causality, these findings provide evidence for the involvement of infections and the immune system in the etiology of a wide range of mental disorders in children and adolescents" A Nationwide Study in Denmark of the Association Between Treated Infections and the Subsequent Risk of Treated Mental Disorders in Children and Adolescents (Dec 2018).

Review, 2018: Microbiome—The Missing Link in the Gut-Brain Axis: Focus on Its Role in Gastrointestinal and Mental Health "mounting data that gut microbiota is the source of a number of neuroactive and immunocompetent substances, which shape the structure and function of brain regions involved in the control of emotions, cognition, and physical activity"

Review, 2018: Microorganisms’ Footprint in Neurodegenerative Diseases "The negative direct or indirect contributions of various microorganisms in onset or severity of some neurodegeneration disorders and interaction between human immune system and pathogenic microorganisms has been portrayed in this review article"

Review, 2018: The Brain-Gut-Microbiome Axis

Review, 2017: Neuromicrobiology: how microbes influence the brain: | via sci-hub:

Review, 2017: Gut reactions: How the blood–brain barrier connects the microbiome and the brain:

Review, 2017: Feeding the Microbiota-Gut-Brain Axis: Diet, Microbiome and Neuropsychiatry:

Review, 2016: Cognitive Function and the Microbiome, International Review of Neurobiology:

Review, 2015: Serotonin, tryptophan metabolism and the brain-gut-microbiome axis:

Review, 2015: The impact of gut microbiota on brain and behaviour: implications for psychiatry: - "The current narrative suggests that certain neuropsychiatric disorders might be treated by targeting the microbiota either by microbiota transplantation, antibiotics or psychobiotics."

Review, 2014: The effects of inflammation, infection and antibiotics on the microbiota-gut-brain axis:

Review, 2013: Microbial Endocrinology in the Microbiome-Gut-Brain Axis: How Bacterial Production and Utilization of Neurochemicals Influence Behavior:

Review, 2013: The role of gut microbiota in the gut-brain axis: current challenges and perspectives:

Review, 2012: The impact of the gut microbiota on brain and behaviour:

Review, 2012: Regulation of the stress response by the gut microbiota: implications for psychoneuroendocrinology:

Review, 2011: The microbiome-gut-brain axis: from bowel to behavior:

"In conclusion, we demonstrate a molecular basis for how the host microbiome is crucial for a normal behavioural response during social interaction. Our data further suggest that social behaviour is correlated with the gene-expression response in the amygdala, established during neurodevelopment as a result of host-microbe interactions." (2018)

A new pathway for the gut microbiota to modulate the brain: activation of pattern-recognition receptors by microbial products (peptidoglycan-sensing molecule Pglyrp2) (2017):

Microbiota and host determinants of behavioural phenotype in maternally separated mice: - "MS-induced changes in host physiology lead to intestinal dysbiosis"

Zika, Herpes, and West Nile viruses damage adult brains: - - - -

More in probiotic-specific page:


ADHD-originating in the gut? The emergence of a new explanatory model (2018):


Potential roles of gut microbiome and metabolites in modulating ALS in mice (July 2019) "In humans, we identify distinct microbiome and metabolite configurations"

Rebalancing gut microbiome lengthens survival in mouse model of ALS. Target Intestinal Microbiota to Alleviate Disease Progression in Amyotrophic Lateral Sclerosis (2017)

People with amyotrophic lateral sclerosis (ALS) have an altered composition of their gut microbial community, with an increase in harmful microbes and a decrease in beneficial microorganisms, according to a new small study Intestinal microbiota composition in patients with amyotrophic lateral sclerosis (Aug 2019).


Review, Mar 2019: The Role of Gut Microbiota in Pathogenesis of Alzheimer's Disease

Review, 2018: The Gut Microbiome Alterations and Inflammation-Driven Pathogenesis of Alzheimer’s Disease—a Critical Review:

Review, 2018: Microbiome-Mediated Upregulation of MicroRNA-146a in Sporadic Alzheimer’s Disease

Review, 2016: Alzheimer’s disease and gut microbiota:

Review, 2016: Role of gut microbiota and nutrients in amyloid formation and pathogenesis of Alzheimer disease:

Corroboration of a Major Role for Herpes Simplex Virus Type 1 in Alzheimer’s Disease (2018):

Infectious Theory of Alzheimer's Disease Draws Fresh Interest (2018):

Periodontal disease bacteria may kick-start Alzheimer's. Chronic oral application of a periodontal pathogen results in brain inflammation, neurodegeneration and amyloid beta production in wild type mice (2018):

A Common Gum Infection Bacteria (P. gingivalis) May Also be Causing Alzheimer’s. Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors (Jan 2019)

Association between Alzheimer’s Disease and Oral and Gut Microbiota: Are Pore Forming Proteins the Missing Link? (2018):

Mapping The Brain's Microbiome: Can Studying Germs In The Brain Lead To A Cure For Alzheimer's? (2017) | Alt links: p1 p2

Antibiotics weaken Alzheimer's disease progression through changes in the gut microbiome (2016):

Researchers Identify Virus and Two Types of Bacteria as Major Causes of Alzheimer’s (2016). “We are saying there is incontrovertible evidence that Alzheimer’s Disease has a dormant microbial component, and that this can be woken up by iron dysregulation."

The gut microbiota-derived metabolite trimethylamine N-oxide [that has been implicated in human disease pathogenesis] is elevated in Alzheimer’s disease (2018):

Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota (2017):

Protective Roles of Intestinal Microbiota derived Short Chain Fatty Acids in Alzheimer's Disease-type Beta-Amyloid Neuropathological Mechanisms (2017):

Gut microbiome alterations in Alzheimer’s disease (2017).


Review, 2019: Crosstalk Between the Microbiome and Gestational Immunity in Autism-Related Disorders "recent findings identify the immune system as a link between gut microbiota and the brain in neurodevelopmental disorders, and suggest that targeting the microbiome and maternal immune responses during gestation may offer strategies to limit autism development in at-risk pregnancies"

Review, 2018: The Perturbance of Microbiome and Gut-Brain Axis in Autism Spectrum Disorders

Review, 2018: Early Disruption of the Microbiome Leading to Decreased Antioxidant Capacity and Epigenetic Changes: Implications for the Rise in Autism

Review, 2016: Gut Microbiota and Autism: Key Concepts and Findings:

Autism Risk Determined by Health of Mom’s Gut, UVA Research Reveals. "as a result of microflora-associated calibration of gestational IL-17a (inflammatory molecule interleukin-17a) responses" (2018): - Cutting Edge: Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism (2018)

Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment (Apr 2019) "The identified patterns of mother–child gut microbiome profiles may be important for assessing risks during the early stage and planning of personalized treatment and prevention of ASD via microbiota modulation"

The microbiota modulates gut physiology and behavioral abnormalities associated with autism/neurodevelopmental disorders (2013): -

Alteration of gut microbiota-associated epitopes (MEs) in children with autism spectrum disorders (2018): "thirty-four MEs identified were potential biomarker of ASD, and alterations in MEs may contribute to abnormalities in gut immunity and/or homeostasis in ASD children"

Autism, antibiotics & probiotics: -

A single species of gut bacteria can reverse autism-related social behavior in mice. Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring (2016): | Nearly identical 2018 follow up study: Mechanisms Underlying Microbial-Mediated Changes in Social Behavior in Mouse Models of Autism Spectrum Disorder

ASU 10 week FMT trial shows improvements (2017): - | 2 year follow up sees nearly 50% reduction in symptoms (April 2019):

Depression and anxiety:

Review, 2019: Effects of regulating intestinal microbiota on anxiety symptoms: A systematic review "more than half of the studies included showed it was positive to treat anxiety symptoms by regulation of intestinal microbiota. Non-probiotic interventions were more effective than the probiotic interventions"

Review, 2018: Gut microbiome and depression: what we know and what we need to know:

Review, 2018: The Role of Microbiome in Insomnia, Circadian Disturbance and Depression

The effect of fecal microbiota transplantation on psychiatric symptoms among patients with irritable bowel syndrome, functional diarrhea and functional constipation: An open-label observational study (2018): - FMT improves psych symptoms even when it doesn't change IBS symptoms.

FMT transfer of depression-like behavior; this study demonstrates that dysbiosis of the gut microbiome may have a causal role in the development of depressive-like behaviors (2016):

The neuroactive potential of the human gut microbiota in quality of life and depression (2019): "Our results provide population-scale evidence for microbiome links to mental health, while emphasizing confounder importance"

Gut microbiota regulates mouse behaviors through glucocorticoid receptor pathway genes in the hippocampus (2018):

Microbiota Modulate Anxiety-Like Behavior and Endocrine Abnormalities in Hypothalamic-Pituitary-Adrenal Axis (2017):

Immobilization stress-induced Escherichia coli causes anxiety by inducing NF-κB activation through gut microbiota disturbance (2018): "However, the amelioration of gastrointestinal inflammation by treatment with probiotics including L. johnsonii can alleviate anxiety"

Link between intestinal bacteria, depression found (2015):

Effects of intestinal microbiota on anxiety-like behavior (2011):


Review, 2018: Gut microbiota, cognitive frailty and dementia in older individuals: a systematic review "Gut microbiota modulation of cognitive function represents a promising area of research for identifying novel preventive and treatment strategies against dementia"

Analysis of the relationship between the gut microbiome and dementia: a cross-sectional study conducted in Japan (Jan 2019): "We have shown that components of the gut microbiome, in particular Bacteroides and ‘other’ bacteria, are independently associated with dementia, and these associations are stronger than those of traditional dementia biomarkers"

Herpes virus infection may increase likelihood of dementia (2018): - Herpes Viruses and Senile Dementia: First Population Evidence for a Causal Link (2018):

Gastrointestinal tract microbiota are directly linked to dementia pathogenesis through triggering metabolic diseases and low-grade inflammation progress (2016)

Multiple sclerosis (MS):

Review, 2018: The Gut Microbiome and Multiple Sclerosis - "We propose considering the gut microbiome as the major environmental risk factor for CNS demyelinating disease"

Review, 2017: Gut microbiome in multiple sclerosis: The players involved and the roles they play

A new study reports T cells are activated in the intestines and migrate to the brain, causing an inflammatory cascade that may lead to multiple sclerosis. Researchers say the gut microbiome may play a more significant role in the development and progression of MS than previously believed. (Oct 2018)

Researchers at the University of Toronto and UC San Francisco have discovered that the intestine is the source of immune cells that reduce brain inflammation in people with multiple sclerosis (MS) Recirculating Intestinal IgA-Producing Cells Regulate Neuroinflammation via IL-10 (2019):

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)

Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria (2018):

The makeup of the microbial world in the gut is increasingly recognized as a potential link to the development of the debilitating neurological disease multiple sclerosis. (2016)

Gut bacteria at a young age can contribute to multiple sclerosis disease onset and progression (2017):

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models

Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice (2017)

Human gut microbe may lead to treatment for multiple sclerosis. Research team tested gut microbial samples from patients on a mouse model of MS. Of three bacterial strains, they discovered that one microbe, Prevotella histicola, effectively suppressed immune disease in the preclinical model of MS. (2017)

High frequency of intestinal TH17 cells correlates with microbiota alterations and disease activity in multiple sclerosis. Our data demonstrate that brain autoimmunity is associated with specific microbiota modifications and excessive TH17 cell expansion in the human intestine.

Hidden herpes virus may play key role in MS, other brain disorders. The ubiquitous human herpesvirus 6 may play a critical role in impeding the brain's ability to repair itself in diseases like multiple sclerosis. (2017)

Fecal microbiota transplantation associated with 10 years of stability in a patient with SPMS (2018): - A few other cases.


Review, 2019: The impact of indigenous microbes on Parkinson's disease "the gastrointestinal microbiome influences every organ system in the body; there is growing appreciation for the roles of both gastrointestinal function and its resident microbes within this disease state"

Review, 2019: Microbiome, Parkinson’s Disease and Molecular Mimicry "This has supported the hypothesis that the resident microbial community, commonly referred to as microbiota, might play a causative role in the development of PD"

Review, 2018: Stomaching the Possibility of a Pathogenic Role for Helicobacter pylori in Parkinson’s Disease

Review, 2018: Can the gut be the missing piece in uncovering PD pathogenesis?

Review, 2017: Microbes Tickling Your Tummy: the Importance of the Gut-Brain Axis in Parkinson’s Disease

There's Mounting Evidence That Parkinson's Starts in The Gut - Not The Brain (Mar 2019):

Does Parkinson’s Begin in the Gut? A growing body of evidence links the neurodegenerative disease to the gastrointestinal tract, opening new possibilities for treatment (May 2018):

New study adds to growing body of evidence that Parkinson’s may start in the gut. Researchers found gut-to-brain propagation of alpha-synuclein spread via the vagus nerve. Transneuronal Propagation of Pathologic α-Synuclein from the Gut to the Brain Models Parkinson’s Disease (Jun 2019, mice)

A gut-brain link for Parkinson’s gets a closer look. The misfolded proteins may start with microbes in the digestive system (Dec 2018):

Transplantation of fecal microbiota, from normal mice on Fasting Mimicking Diet (FMD) to antibiotic-pretreated Parkinson’s Disease (PD) mice increased dopamine levels in the recipient PD mice, suggesting that gut microbiota contributed to the neuroprotection of FMD for PD (Feb 2019) Neuroprotection of Fasting Mimicking Diet on MPTP-Induced Parkinson’s Disease Mice via Gut Microbiota and Metabolites.

Parkinsons disease and bacteriophages as its overlooked contributors (2018):

Neuroprotective effects of fecal microbiota transplantation on MPTP-induced Parkinson’s disease mice: Gut microbiota, glial reaction and TLR4/TNF-α signaling pathway (2018):

A specific gut bacterium directly induces PD symptoms and dopaminergic neuronal damage in the mouse brain (2018):

Gut microbiota are related to Parkinson's disease and clinical phenotype: - -

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease (2016): || Good article coverage:


PTSD could be prevented with gut microbes (2016):

Role of gut microbiome in posttraumatic stress disorder. The bacteria in your gut could hold clues to whether or not you will develop posttraumatic stress disorder (PTSD) after experiencing a traumatic event (2017):

Schizophrenia and bipolar disorder:

Review, 2019: The gut microbiota promotes the pathogenesis of schizophrenia via multiple pathways

Review, 2018: Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder:

Review, 2017: The microbiome, immunity, and schizophrenia and bipolar disorder

From Infection to the Microbiome: An Evolving Role of Microbes in Schizophrenia (Mar 2019):

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia (2018):

The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice (2019):

Schizophrenia Linked with Abnormal Immune Response to Epstein-Barr Virus (2019):

He Got Schizophrenia. He Got Cancer. And Then He Got Cured. (2018): "man with leukemia received a bone-marrow transplant from a schizophrenic brother"

Case study: Bartonella and sudden-onset adolescent schizophrenia (Mar 2019): -

Obesity & diet:

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

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:

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 (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)

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:

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

Study Links BMI, Lipid Levels to Gut Microbes. || Including fungal mycobiota:

Fat and thin people have different gut bacteria: - -

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

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.

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

Transfer of Obesity via the Gut Microbiome is Mediated Specifically through Suppression of Non-Aerobic Resting Metabolism: || They found it wasn't 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:

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: -

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

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

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

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

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: Gut microbiota, FXR, and bile acids as regulators of host metabolism:

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

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

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

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

Freeze-dried poop pills being tested for obesity treatment:

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: || Germ-free lab mice also suffer various problems: -!/content/playContent/1-s2.0-S0306452216305127

Children who take antibiotics gain weight faster: - - || Also seen in feed animals (along with pro & pre biotics): -

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:

Artificial sweeteners induce glucose intolerance by altering the gut microbiota: | And block enzyme activity: Artificial Sweeteners May Change Our Gut Bacteria in Dangerous Ways:

Changes in the microbiome may contribute to cognitive changes associated with eating a Western diet:

Effects of Gut Microbes on Nutrient Absorption and Energy Regulation:

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

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

Diet rapidly and reproducibly alters the human gut microbiome:

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

Resistant starch alters intestinal microbiota: -

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:

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

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): -


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, 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"

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, 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"

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:

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):


Review, 2018: The Complex Interplay between Chronic Inflammation, the Microbiome, and Cancer: Understanding Disease Progression and What We Can Do to Prevent It. "To date, microbes can be linked to almost every cancer, including colon, pancreatic, gastric, and even prostate."

Review, 2017: The human microbiome and cancer: -

Review, 2017: Research now suggests that the microbiota — commensal microorganisms including bacteria, fungi, and viruses that inhabit an organism — plays an important role in carcinogenesis, cancer progression, and treatment response:

Review, 2016: Microbiota dysbiosis: a new piece in the understanding of the carcinogenesis puzzle:

Review, 2013: The microbiome and cancer:

Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis:

Breast Microbiome Changes May Alter Breast Cancer Risks:

Microbiome Makeup Determines Whether Rats Get Colon Cancer:

Gut bacteria could help prevent cancer. New research offers evidence that anti-inflammatory 'health beneficial' gut bacteria can slow or stop the development of some types of cancer:

Microbes Meet Cancer. Understanding cancer’s relationship with the human microbiome could transform immune-modulating therapies:

What gut bacteria can teach us about cancer treatment. Studies probe link between gut bacteria and treatment effectiveness:

How Gut Bacteria Are Shaking Up Cancer Research:

Disparities in Gut Microbiome Could Lead to Biomarkers for Estrogen-driven Breast Cancer:

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota (2015):



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)?

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)

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"

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":

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:

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"


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):

"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)

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:



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"

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

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):

Male steroid hormones:

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)


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

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

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?

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:

Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals:

Understanding the Gut Microbiome and HIV:

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

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"


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:

"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)

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

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):


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"

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

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:

Fecal Transplants Effective:

Efficacy of fecal microbiota therapy in steroid dependent ulcerative colitis: a real world intention-to-treat analysis (2019):

Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative Colitis. A Randomized Clinical Trial (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."

Fecal Microbiota Transplantation for Ulcerative Colitis: A Systematic Review and Meta-Analysis (2016):

Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis (2017). 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:

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:

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"

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"

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

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

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):

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):

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? - -

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):

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, 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, 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:

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

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):


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):

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:



Urinary tract & bladder:


Summary post for /r/TheGirlSurvivalGuide (Feb 2019):

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"


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:

Reddit search results (q&a's with researchers, etc.):

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


Bile is a major player in shaping the gut microbiome and its influence on various disease states. Bile acid metabolism & absorption is also a gut-microbe-mediated process.

Fecal Microbiota Transplants (FMT):


Impact of genetics on the microbiome:

Immune system:

Intestinal Permeability:




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:

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; epigenomic regulation: - - - -

Gut microbiota has a widespread and modifiable effect on host gene regulation (2018):

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


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:

Review, 2018: Fire in the Forest: Adverse Effects of Antibiotics on the Healthy Human Gut Microbiome "Short-term antibiotic treatment is able to change the richness and diversity of species into a long-term dysbiotic state"

Review, 2018: Antibiotics and the nervous system: More than just the microbes? "clinical as well as experimental literature, largely neglected through the past decade, has clearly demonstrated that broad classes of antibiotics are neuroactive or neurotoxic. This is true even for some antibiotics that are widely regarded as not absorbed in the intestinal tract"

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"

Review, 2017: Antibiotic use and microbiome function:

Some of the changes caused by antibiotics are transient and can be reversed at the end of the treatment, while others seem irreversible. Most importantly, it has been observed that gut bacteria present a lower capacity to produce proteins, as well as display deficiencies in key activities, during and after the antibiotic treatment. For instance, antibiotics decrease the ability to absorb iron, to digest certain foods and to produce essential molecules. Previously it was assumed that short-term antibiotic treatment would alter gut microbe composition only for a short time, however, this is not the case. Even a relatively short course of antibiotics can lead to alteration in gut microbiota, which in turn can lead to severe consequences such as inflammation, immune dysregulation, allergies, infections, cardiovascular diseases, diabetes, metabolic issues, GI disease such as Crohn’s, IBD, yeast overgrowth, chronic constipation and diarrhea (2018)

According to a modelling study by UCL researchers, a single course of antibiotics can change the composition of oral and gut microbiomes for at least a year, perhaps permanently. - Modelling microbiome recovery after antibiotics using a stability landscape framework (Mar 2019)

Antibiotic Scars Left on the Gut Microbiota from the Stringent Response (2018): - "Current research is primarily focused on compositional shifts and alterations in the metabolic status of the gut microbiota to elucidate the damage caused by antibiotics. However, the impact of the stringent response, which is governed by a global gene regulatory system conserved in most gut bacteria, should not be overlooked."

"Alterations to microbial metabolic capacity occurred following antimicrobial exposure even in participants without substantial taxonomic disruption. Our findings suggest that metabolic potential is an important consideration for complete assessment of antimicrobial impact on the microbiome" (2018):

Pre-transplant recovery of microbiome diversity without recovery of the original microbiome (2018): "our findings suggest that recovery of diversity alone is not an adequate surrogate for microbiome recovery. Microbiota composition and its potential functionality should be considered along with diversity in drawing conclusions from microbiome studies"

Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans (Nov 2018) "combined treatment with broad-spectrum antibiotics has a profound & long-lasting effect on microbiota composition, the consequences of which remain largely unknown"

"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"

"We identified valerate as a metabolite that is depleted with clindamycin and only recovered with FMT." "Inhibiting Growth of Clostridioides difficile by Restoring Valerate, Produced by the Intestinal Microbiota (2018)"

Substantial reduction in microbiota diversity in subjects who took either amoxicillin or azithromycin and that those reductions were sustained throughout the 6-month study (2016):

Early life antibiotic exposure affects pancreatic islet development and metabolic regulation. Changes in the expression of key genes involved in short-chain fatty acid signaling and pancreatic development were detected in later life (2017):

Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior (2017):

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

Infant antibiotic use linked to adult diseases (2015): - Antibiotics, Pediatric Dysbiosis, and Disease

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic (ciprofloxacin) perturbation (2011):

Antibiotics that kill gut bacteria also stop growth of new brain cells:

Antibiotics impair murine hematopoiesis by depleting intestinal microbiota (2016):

Bactericidal Antibiotics Induce Mitochondrial Dysfunction and Oxidative Damage in Mammalian Cells (2013):

Inhibited mitochondrial gene expression and amounts of active mitochondria, increasing epithelial cell death. Kill intestinal epithelium cells (2015): -

Linked to Sepsis risk (2016):

Encourage spread of c.diff to people who haven't taken antibiotics (2016):

Reduces gut diversity of housemates who haven’t taken antibiotics: Microbial diversity in individuals and their household contacts following typical antibiotic courses (2016).

Negative impact on the phageome; low doses can make phages go extinct by making bacteria resistant to them (2016):

In antibiotics-treated mice, serotonin, tryptophan hydroxylase 1, and secondary bile acids levels were decreased: Antibiotics-induced depletion of mice microbiota induces changes in host serotonin biosynthesis and intestinal motility (2017).

Depletion of the gut microbiome by antibiotics impairs the body's ability to eliminate toxins like arsenic and mercury.

Damage immune system:

Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function (2017): -

Antibiotics found to weaken the immune system's ability to fight off disease (neutrophils, 2017):

Once the microbiota is destroyed by antibiotics, the immune reaction no longer occurs (Mar 2019): A Weaning Reaction to Microbiota Is Required for Resistance to Immunopathologies in the Adult.

A single early-life macrolide antibiotic course can alter the microbiota and modulate host immune phenotypes that persist long after exposure has ceased (2017):

This mouse study suggests FMT may not completely restore immune function damaged by antibiotics (2017): "Immune Responses to Broad-Spectrum Antibiotic Treatment and Fecal Microbiota Transplantation in Mice"

"Although the results cannot prove causality, these findings provide evidence for the involvement of infections and the immune system in the etiology of a wide range of mental disorders in children and adolescents" A Nationwide Study in Denmark of the Association Between Treated Infections and the Subsequent Risk of Treated Mental Disorders in Children and Adolescents (Dec 2018).

[Broad-spectrum] Antibiotics induce sustained dysregulation of intestinal T cell immunity by perturbing macrophage homeostasis (Oct 2018, mice) - FMT was not able to reverse the damage, but butyrate supplementation was able to prevent it.

Association between prior antibiotic therapy and subsequent risk of community-acquired infections: a systematic review (2017):

More studies showing long-term negative affects here: and by using the "antibiotics" flair in the sidebar:


Systemic (more systemic impacts of the gut microbiome):

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