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Extract from a medical journal in 1914:

‘The control of man’s diet is readily accomplished, but mastery over his intestinal bacterial flora is not…the innumerable examples of autointoxication that one sees in his daily walks in life is proof thereof. They are the cases that present…malaise, total lack of ambition so that every effort in life is a burden, mental depression often bordering upon melancholia, frequent attacks of indefinite abdominal pains due to flatulency, sudden attacks of acute diarrhea alternating with periods of constipation…A battle royal must be fought and when this first great struggle ends in victory for the Bacillus bulgaricus it must be kept on the field of battle forever at guard…’

Bond Stow, M.D., on autointoxication and Lactobacillus bulgaricus – Medical Record Journal of Medicine and Surgery, 1914

Fecal Microbiota Transplantation


American Gastroenterological Association (website) 

FMT Science (website) 

Fecal Microbiota Transplantation Now and in the Future (2015, video) 

Fecal Microbiota Transplantation: Moving Mainstream, Regulatory Hurdles and Potential Future Indications (2015) 

Fecal microbiota transplantation broadening its application beyond intestinal disorders (2015) 

FMT Stands Up To Antibiotics in Cost-Effectiveness Model (2014) 

Fecal microbiota transplantation: effectiveness, complexities, and lingering concerns (2014) 

Fecal microbiota transplantation: facts and controversies (2014) 

Fecal Transplant an Option Even in the Immunocompromised (2013) 

Microbiota Take 4 months to Colonise after FMT for Recurrent Clostridium difficile Infection (2013) 

New Evidence Reveals Impact of Fecal Transplantation upon Gut Flora and Digestive Health (2013) 

Fecal transplant: A safe and sustainable clinical therapy for restoring intestinal microbial balance in human disease? (2013) 

An overview of fecal microbiota transplantation, techniques, indications, outcomes (2013) 

Therapeutic Potential of Fecal Microbiota Transplantation  (2013) 

Fecal microbiota transplantation and donor standardization (2013) 

Fecal microbiota transplantation: past, present and future (2013) 

Fame and future of fecal transplantations (2013) 

Fecal Microbiota Transplant: We Know Its History, but Can We Predict Its Future?  (2013) 

IDSA: Oral Ingestion Viable for Fecal Microbiome Transplant (2013) 

Fecal Microbiota Transplant Using Frozen Inoculum Effective for Recurring Clostridium difficile (2013) 

Fecal Microbiota Transplantation – Techniques, Applications, and Issues (2012) 

FMT techniques, applications and issues (2012) 

Fecal microbiota transplantation and emerging applications (2011) 

Durable alteration of the colonic microbiota by the administration of donor fecal flora (2010) 

Bacteriotherapy using fecal flora: Toying with Human Motions  (2004)   


FMT Risks


Complicated fecal microbiota transplantation in a tetraplegic patient with severe Clostridium difficile infection (2015)

Navigating long-term safety in fecal microbiota transplantation. (2013) 

Bacteremia as an adverse event of fecal microbiota transplantation in a patient with Crohn’s disease and recurrent Clostridium difficile infection. (2013) 

Fecal microbiota transplantation: long-term safety issues. (2013) 

Transient flare of ulcerative colitis after fecal microbiota transplantation for recurrent Clostridium difficile infection. (2013)


FMT & Clostridium difficile


Evidence table: Fecal microbiota transplantation (FMT) for Clostridium difficile colitis (2015) 

Randomised clinical trial: faecal microbiota transplantation by colonoscopy vs. vancomycin for the treatment of recurrent Clostridium difficile infection (2015)

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection (2015) 

FMT a new standard treatment option for C Diff (2013) 

Fecal Transplant Beats Vancomycin For C. difficile (2013) 

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile (2013) 

Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis (2013) Mayo Clinic Statistics on FMT to Treat C Diff (2013) 

Long-term follow-up of colonoscopic fecal microbiota transplant for recurrent Clostridium difficile infection (2012) 

Treating C Diff with FMT Workgroup (2011)  

Systematic Review of Intestinal Microbiota Transplantation (Fecal Bacteriotherapy) for Recurrent Clostridium difficile Infection (2011)   


FMT & Other Pathogens / Dysbiosis


Fecal microbiota transplantation restores dysbiosis in patients with MRSA enterocolitis (2015)


Microbiome Resources

Gut Microbiota Watch 

ACG Glossary of Gut Microbiome

AGA Centre for Gut Microbiome Research and Education  

UMass Center for Microbiome Research 

Gut Microbes Journal  

Gut Health and Food Safety – UK 

Biome Onboard Awareness: The science behind food, disease, microbiome 

Make friends with your Gut Microbiota (2014 – good plain-english overview) 

Your changing Microbiome (2014 – kid-friendly overview) 

Microbiome: FAQs (good plain English overview) 

AGA Briefing to Congress on Microbiome (YouTube video – 55 minutes) 

The Human Microbiome, Diet, and Health: Workshop Summary (2012) 

Human Microbiome Science: Vision for the Future Conference (videos & slides) (2013)


Microbiome Research


How To Make Better Health Predictions From Our Gut Microbes (2015)

Daily changes in mouse gut bacteria moves with internal clock and gender (2015)

Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota (2015) 

Gut Microbiota: the good, the bad & the ugly  (2014) 

Ideas About Gut Microbiome and Diet Becoming Mainstream (2013) 

Human gut microbiome viewed across age and geography (2012) 

Characterization of the Human Predominant Fecal Microbiota (2012) – PhD Dissertation Unhealthy’ Changes in Gut Microbes Benefit Pregnant Women (2012) 

A Home for the Microbiome (2013) 

Host-microbial interactions and regulation of intestinal epithelial barrier function (2012) 

Gut Microbe Populations Stable Over Years, Probably Decades (2013) 

Prebiotics, fecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome (2013) 

VHIR researchers identify intestinal bacteria which cause abdominal gases (2013) 

Gut Microbes Contribute to Serious Malnutrition (2013) 

Rapid Evolution of the Human Gut Virome (2013) 

The Long-term Stability of the Human Gut Microbiota (2013) 

A Living Drug Cocktail (2013) 

TReg Induction by a Select Mixture of Microbiota (2013) 

The “City of Microbes” Within Our Bodies May Maintain Our Health, Expert Says (2013) 

Intestinal Bacteria May Fuel Inflammation and Worsen HIV Disease (2013) 

Replenishing our defensive microbes (2013) 

Association between Blood Group and Human Microbiota Composition (2013) 

Understanding Our Gut Microbes Could Lead to New Medicines (2013) 

Ecological Forces Structure Your Body’s Personal Mix of Microbes (2013) 

Biologists Identify How Beneficial Bacteria Reside and Thrive in GI Tract (2013) 

Researchers unravel genetic mechanism behind microbiome colonisation (2013) 

The Human Microbiome – Me, Myself & Us (2012) 

Enterotypes of the human gut microbiome (2011) 

The Gut Microbiota as a Target for Innovative Drug Development (2011) 

Role of the gut microbiota in defining human health (2010) 

Effect of bowel preparation and colonoscopy on post‐procedure intestinal microbiota composition (2006) 

The Rainforest in your Gut (video) 

Gut Microbiota (Audio – BBC Radio)   


Microbiota, FMT and Inflammatory Bowel Disease (Crohn's & UC)


Gut microbiota and inflammatory bowel disease: A selection of content from the Gut Microbiota for Health Experts Exchange 2014-2015 (2015, download PDF from this page) 

The July 2015 issue of Gastroenterology published the first two randomized, controlled studies assessing the use of FMT in the treatment of ulcerative colitis. An editorial in the same issue explored the reasons why one was negative and the other positive:
Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis
Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial
Fecal Microbiota Transplantation for Ulcerative Colitis: Not Just Yet (editorial)
FMT induces remission in active ulcerative colitis (overview article) 

Researchers test fecal transplantation to treat ulcerative colitis (2015) 

Fecal Microbial Transplant Effect on Clinical Outcomes and Fecal Microbiome in Active Crohn’s Disease (2015)
The published study only includes patients with CD, the original study also included UC patients. Patients with UC did not improve significantly. FMT was delivered by nasogastric tube.

When bacteria-killing viruses take over, it’s bad news for the gut (plain language overview)
Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease (full text article in Cell, 2015) 

Manipulation of the Microbiota for Treatment of IBS and IBD—Challenges and Controversies (2014) 

Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a deficient commensal bacteria implicated in Crohn’s disease (2014) 

Increased Prevalence of Methanosphaera stadtmanae in Inflammatory Bowel Diseases (2014)

Fecal transplantation in patients with moderately to severely chronic active ulcerative colitis (2014)

A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis (2013) 

FMT for severe enterocolonic fistulizing Crohns Disease (2013) 

Safety, Tolerability, and Clinical Response After Fecal Transplantation in Children and Young Adults With Ulcerative Colitis (2013) 

Experimental fecal transplants could revolutionize treatment of bowel diseases (2013) 

Fecal Transplant Shown To Treat Inflammatory Bowel Disease In Children (2013) 

The microbiota and inflammatory bowel disease: Insights from animal models (2013) 

Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases (2013) 

Persistent infection with Crohn’s disease-associated adherent-invasive Escherichia colileads to chronic inflammation and intestinal fibrosis (2014) 

The intestinal microbiota dysbiosis and Clostridium difficile infection: is there a relationship with inflammatory bowel disease? (2013) 

The biodiversity and composition of the dominant fecal microbiota in patients with inflammatory bowel disease (2013) 

Brain-gut interactions in inflammatory bowel disease (2013) 

Colon Cancer and IBD: Potential Links to Microbiota, Race (2013) 

Study identifies distinct microbiome in Crohn’s intestinal submucosa (2013) 

Temporal Bacterial Community Dynamics Vary Among Ulcerative Colitis Patients After Fecal Microbiota Transplantation. (2013) 

Dysfunctional gut microbiota closely linked to range of health issues (2013) 

Bacterial molecules may prevent inflammatory bowel disease (2013) 

Fecal Microbiota Transplantation in Ulcerative Colitis: Review of 24 Years Experience (2012)

Systematic review: fecal microbiota transplantation in the management of inflammatory bowel disease (2012) 

Does our food (environment) change our gut microbiome (‘in-vironment’): a potential role for inflammatory bowel disease? (2012) 

The microbiome and inflammatory bowel disease: is there a therapeutic role for fecal microbiota transplantation? (2012) 

Review article: fecal transplantation therapy for gastrointestinal disease (2011) Colonic Microbiota and Crohns Disease & FUT2  Genotype (2011) 

Antibiotic use and inflammatory bowel diseases in childhood (2010) 

Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiota (2010) FMT in UC: Spotlight on Patients’ E‘motions’ (2011?) 

Treatment of Ulcerative Colitis using fecal bacteriotherapy (2003) 


Microbiota & Autoimmune Disease


Metagenomic Study Finds Differences in Oral, Gut Microbiomes of Rheumatoid Arthritis Patients (2015) 

Increased Archaea Species and Changes with Therapy in Gut Microbiome of Multiple Sclerosis Subjects (2014) 


Microbiota & Food


Gut Microbiota, Diet & Nutrition: A selection of content from the Gut Microbiota for Health Experts Exchange 2013-2014  (2014, download PDF from this page) 

Intestinal microbiota, diet and health. (2013) 

The Metabolic and Ecological Interactions of Oxalate-Degrading Bacteria in the Mammalian Gut (2013) 

Gut Microbiota and Personalized Nutrition (2013) 

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota (2013) 

Effect of Sucrose on Gut Permeability and Intestinal Bacterial Colonization (2010)   


Microbiota & Anti-biotics


Hospital Stay Could Be Setting Up Patients for Sepsis (2015)

Manipulation of the Microbiota for Treatment of IBS and IBD—Challenges and Controversies (2013)

Team shows how antibiotics enable pathogenic gut infections (2013) 

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens (2013) 

Antibiotic exposure and the development of coeliac disease: a nationwide case–control study (2013)   


Microbiota & Irritable Bowel Syndrome


Microbiome composition associated with efficacy of low FODMAP diet in pediatric IBS (2015) 

Manipulation of the Microbiota for Treatment of IBS and IBD—Challenges and Controversies (2014) 

Intestinal microbiota in functional bowel disorders: a Rome foundation report (2013) 

Lactase deficiency in patients with postinfectious irritable bowel syndrome and the role of intestinal microflora in its development (2012) 

Intestinal microbiota and its role in irritable bowel syndrome (IBS) (2013) 

Effect of probiotic species on irritable bowel syndrome symptoms: A bring up to date meta-analysis (2013) 

The gut microbiota and irritable bowel syndrome: friend or foe? (2013)

Intestinal barrier function in health and gastrointestinal disease (2012) 

Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome. (2010) 

Small intestinal bacterial overgrowth in irritable bowel syndrome: systematic review and meta-analysis (2009) 

Is the Intestinal Microbiome altered in Irritable Bowel Syndrome (2004)  


Microbiota & CFS / ME

The GI Microbiome and its role in Chronic Fatigue Syndrome: a Summary of Bacteriotherapy (2012) 

Increased IgA responses to the LPS of commensal bacteria is associated with inflammation and activation of cell-mediated immunity in chronic fatigue syndrome (2012) 

Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome (2009) 

Gut inflammation in chronic fatigue syndrome (2010) Bacteriotherapy in CFS a retrospective review (1995)   


Microbiota & Obesity / Liver Health

Metabolism of Cholesterol and Bile Acids by the Gut Microbiota  (2014) 

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice (2013) 

Microbiota and gut-liver axis: their influences on obesity and obesity-related liver disease (2013) 

Human intestinal microbiota composition is associated with local and systemic inflammation in obesity (2013) 

Rich or poor in gut bacteria: we are not all equal facing obesity associated diseases (2013) 

Microbiota and gut-liver axis: their influences on obesity and obesity-related liver disease (2013) 

Gut microbiota and the development of obesity (2012) 

Potential mechanisms for the emerging link between obesity and increased intestinal permeability (2012) 

Obesity, diabetes, and gut microbiota: the hygiene hypothesis expanded? (2010) 

Microbiota and SCFA in lean and overweight healthy subjects (2010) 

Early differences in fecal microbiota composition in children may predict overweight (2008) 

Symbiotic modulation of gut flora: effect on minimal hepatic encephalopathy  (2004) 

Gut flora-based therapy in liver disease? The liver cares about the gut. (2004)   


Microbiota & the Brain / Neurotransmitters


Early Research Points to Autism-Microbiome Link (2015) 

Microbes help produce serotonin in gut (2015) 

Scientists show a link between intestinal bacteria and depression (2015)

A model for the induction of autism in the ecosystem of the human body: the anatomy of a modern pandemic? (2015)

Collective unconscious: How gut microbes shape human behavior (2015)

The gut microbiota influences blood-brain barrier permeability in mice (2014) 

Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders (2014) 

Microbiota-Generated Metabolites Promote Metabolic Benefits via Gut-Brain Neural Circuits (2014) 

Deciphering benefits of microbial fermentation via the Gut-Brain axis (2014) 

Gut bacteria’s influence on brain development (2014) 

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

In depression, bacterial translocation may drive inflammatory responses (2013) 

Gut-brain axis: how the microbiome influences anxiety and depression (2014) 

The adoptive transfer of behavioral phenotype via the intestinal microbiota: experimental evidence and clinical implications (2013) 

Clues about autism may come from the gut (2013) 

Fecal Microbiota and Metabolome of Children with Autism and Pervasive Developmental Disorder Not Otherwise Specified (2013) 

On Autism, Gut Microbes, and Contradictory Research Findings (2013) 

The adoptive transfer of behavioral phenotype via the intestinal microbiota: experimental evidence and clinical implications (2013) 

The microbiota-gut-brain axis: neurobehavioral correlates, health and sociality (2013) 

Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: Part I – autointoxication revisited (2013) 

Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: Part 2 – autointoxication revisited (2013) 

Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: Part 3 – autointoxication revisited (2013) 

Microbiota is essential for social development in the mouse (2013)  

Ingestion of Lactobacillus strain regulates emotional behavior (2011)   


Microbiota & the Immune System


Diversity of the cultivable human gut microbiome involved in gluten metabolism: Isolation of microorganisms with potential interest for coeliac disease. (2014) 

Diabetes is predominantly an intestinal disease (2014) 

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation (2013) 

Gut microbes closely linked to range of health issues (2013) 

The interplay between the gut immune system and microbiota in health and disease: nutraceutical intervention for restoring intestinal homeostasis (2013) 

Gut Bacteria Change Threshold of Immune Activation in Arthritis (2013) 

Specific Gut Commensal Flora Locally Alters T Cell Tuning to Endogenous Ligands (2013) 

Antibody response against gastrointestinal antigens in demyelinating diseases of the central nervous system. (2013) 

Alterations in the Gut Microbiota Associated with HIV-1 Infection (2013)  

How hormones and microbes drive the gender bias in autoimmune diseases (2013)

Does Parkinson’s Begin in the Gut? (2012) 

Gut Bacteria May Trigger Diseases such as Rheumatoid Arthritis (2012)   


Microbiota & Sex Hormones

   Gut bacteria may be a source of male steroid hormones (2014)


Microbiota & Blood Type

   Association between the ABO blood group and the human intestinal microbiota composition (2012)   


Microbiota & Genes

   Genetic Makeup and Diet Interact With the Microbiome to Impact Health (2013)   


Microbiota & Cancer

   Microbial dysbiosis is associated with human breast cancer (2014) 

Intestinal Bacteria and Lymphoma (2013) 

The Gut Microbiome Modulates Colon Tumorigenesis (2013)   


Microbiota & Heart Disease


The way to a man’s heart is through his gut microbiota’ – dietary pro- and prebiotics for the management of cardiovascular risk (2014) 

Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis (2013) 

Olfactory receptor responding to gut microbiota-derived signals plays a role in renin secretion and blood pressure regulation (2013)   


Microbiota & Toxic Metals


Exposing to cadmium stress cause profound toxic effect on microbiota of the mice intestinal tract (2014)     


Microbiota & Age


Altering the community of gut bacteria promotes health and increases lifespan (2014) 

Ageing and gut microbes: perspectives for health maintenance and longevity (2013) 

Human gut microbiome viewed across age and geography (2011)   


Microbiota & Infant / Maternal / Family transfer


The infant gut microbiome: New studies on its origins and how it’s knocked out of balance (2015)

Maternal prenatal stress is associated with the infant intestinal microbiota (2015)

BCM and Texas Children’s Study Finds Unique Placental Microbiome (2014)

The Human Microbiome: considerations for pregnancy, birth and early mothering (2014) 

The human microbiome. Early life determinant of health outcomes (2014) 

Newborn gut microbiome begins during birth (2014) 

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants (2014) 

Mom Knows Best: The Universality of Maternal Microbial Transmission (2013) 

Vertical mother–neonate transfer of maternal gut bacteria via breastfeeding (2013) 

Infant Gut Microbiota Influenced by Cesarean Section and Breastfeeding Practices; May Impact Long-Term Health (2013) 

Cohabiting family members share microbiota with one another and with their dogs (2013) 

The Long-Term Stability of the Human Gut Microbiota (2013)   


FMT in other cultures/eras


Poop Wine – Traditional Korean Remedy Should We Standardize the 1,700-Year-Old Fecal Microbiota Transplantation? 

Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis (1958) 

Fecal Transplants in the “Good Old Days” 

Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances 



If you find any issues with these links, please .


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