Human oral microbiome database

Skin microbiome (Pubmed)

The New Science of Metagenomics - (Free NCBI textbook)

Organised wisdom Microbiome

Search Amazon.com for microbiome

A BBC podcast on the microbiome

Microbiome Jobs from Indeed


Powered by The microbiome represents diverse viral, bacterial fungal and other species that live on and within us. They are a part of us and we are a part of this complex ecosystem. Their proteins bind to ours, and their metabolism influences ours and vice versa. The gut microbiome seems to be divided into three major enterotypes Arumugam et al, 2011. A well balanced microbiome may keep us healthy, while imbalances may be a factor in causing disease. Certain diseases can be affected by manipulating the microbiome and some microbiome effects are catalogued here.

Viruses , bacteria and other pathogens are risk factors in many diseases, and in several cases can cause disease.These are summarised for several diseases. Unlike genes, pathogens can be attacked and sometimes eliminated.

Host pathogen interactomes for :Bornavirus; Borrelia Burgdorferi; Candida albicans; Chlamydia Pneumoniae ; Cryptococcus Neoformans; Ebola virus; Epstein-Barr virus; Helicobacter pylori; Hepatitis C virus; Herpes simplex (HSV-1); HERV-W; HIV-1, Human Protein Interaction Database (NCBI); Human cytomegalovirus; Influenza A virus; Porphyromonas Gingivalis; Toxoplasma Gondii; Trypanosoma Cruzi : KEGG pathway analysis of these interactomes can be accessed here

The Pubmed icons click to the term + microbiome and some examples are given: Other Pubmed searches (e.g. probiotic) are programmed: Summaries of the searches are provided.......................in progress

PANDAS Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infections

Control of antiviral immunity by pattern recognition and the microbiome. Pang and Iwasaki 2011

AIDS PubMed Logo

  • Microbiome Increased Enterobacteriales in HIV-positive subjects: Enterobacteriales and Bacteroidales levels correlate with duodenal CD4 T-cell depletion and peripheral CD8 T-cell activation, respectively Ellis et al, 2011
  • Probiotic
    • Yoghurt containing probiotic Lactobacillus rhamnosus and L. reuteri RC-14 help resolve moderate diarrhea and increase CD4 count in HIV/AIDS patients Anukam et al, 2008. see also Irvine et al, 2010
    • Bifidobacterium bifidum with Streptococcus thermophilus have immunostimulatory properties Trois et al, 2008

Alzheimer's disease PubMed Logo Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Claesson et al, 2011

Atherosclerosis PubMed Logo Human oral, gut, and plaque microbiota in patients with atherosclerosis. Koren et al, 2011

Arthritis PubMed Logo A large flora is involved, due to sepsis-induced arthritis.

Asthma PubMed Logo

Attention deficit hyperactivity disorder PubMed Logo


Autism PubMed Logo See also:- Normal gut microbiota modulates brain development and behavior Heijtza et al, 2011 in relation to neurodevelopmental disorders

Bipolar disorder PubMed Logo

Cancer PubMed Logo


Childhood obesity PubMed Logo

Chronic fatigue / fibromyalgia PubMed Logo


Coeliac disease PubMed Logo

Crohn's disease PubMed Logo

  • Bacteria [Dysbiosis Joosens et al, 2011: Decrease: Bifidobacterium adolescentis Clostridium cluster XIVa Dialister invisus Faecalibacterium prausnitzi: Increase Ruminococcus gnavusi]

Cystic fibrosis Microbiome refs

  • Hypercolonisation with many bacteria , particularly S.Aureus , P.Aeruginosa and S.Maltophilia and many other bacteria, fungi and viruses Listed here
  • Probiotics have been reported to improve symptomatology

Depression PubMed Logo

Diabetes Type 1 PubMed Logo The intestinal microbiome: relationship to type 1 diabetes. Neu et al, 2011

Type 2 Diabetes Microbiome references

EpilepsyPubMed Logo

Irritable bowel syndrome PubMed Logo


Multiple sclerosis PubMed Logo


Parkinson's diseasePubMed Logo


Schizophrenia PubMed Logo

Sydenham's chorea

  • Caused by childhood infection with Group A beta-hemolytic Streptococci leading to an autoimmune response that destroys cells in the basal ganglia Pubmed

Tourettes syndrome

Ulcerative colitis PubMed Logo

Diseases caused by bacteria viruses and pathogens ( apart from their immediate acute effects e.g. cold sores, flu, common cold)

See pathogenic viruses

Bacteria use some of the same metabolites as us and infection can markedly affect the levels of important compounds such as cholesterol, glutathione, tryptophan, methionine S-adenosyl-methionine, and homocysteine. Levels of these metabolites are modified in many human diseases.

Cholesterol PubMed Logo

Glutathione PubMed Logo


Homocysteine PubMed Logo Homocysteine, folate and glutathione metabolism are linked, as shown in this figure

One carbon metabolism and the transsulfuration pathway By Michael C Reed , Rachel L Thomas , Jovana Pavisic , S Jill James , Cornelia M Ulrich and H Frederik Nijhout (A mathematical model of glutathione metabolism) [CC-BY-2.0 (www.creativecommons.org/licenses/by/2.0)], via Wikimedia Commons

Folic acid

Methionine PubMed Logo

Propionic acid PubMed Logo

Tryptophan PubMed Logo

  • Many bacteria and other pathogens acquire tryptophan from the host: A common defense mechanism is the induction of the host's Indoleamine 2,3-dioxygenase (IDO1) pathway which degrades L-tryptophan to N-formylkynurenine.This will impact upon tryptophan and 5-hydroxy-tryptophan levels, and ultimately on serotonin synthesis: The synthesis of Kynurenic acid, an NMDA receptor antagonist will also be affected as shown in this KEGG pathway (IDO1: EC number Pubmed e.g. T.Gondii : This pathway is also affected by viruses: Infection can therefore impact directly upon key neurotransmitter networks.

Tryptophan and madness from Adonis Sfera, MD The fates of trytophan, kynurenines and quinolinate and the immune system



Diseases: Viruses, bacteria, other pathogens and risk factors implicated in:-

You and Your Ten Thousand Trillion Microbes

From YouTube: For every human cell in your body, there are hundreds or thousands of bacterial cells. So who is hosting whom? Even though our on-board microbial hordes—known also as our microbiome—sometimes threaten and deprive us of our health and our lives, they are central to our survival and our daily well being.

A discussion brought to you by the DC Science Writers Association and the USA Science and Engineering Festival filmed on Tuesday, April 17 at Busboys and Poets on 5th and K Sts., NW, Washington, D.C., that might convince you to love your microbial partners in life, albeit with a healthy respect for the ways they can become dangerous. Leading the discussion is microbiologist Liliana Losada of the J. Craig Venter Institute, an independent research laboratory in Rockville, Md., that has been greatly expanding our fundamental knowledge of the microbes in our world; and Alison O'Brien, former president of the American Society of Microbiology, professor of microbiology and immunology at the Uniformed Services University of the Health Sciences, and an expert in the gut bacterium known as E. coli, a major player in human health, basic science and biotechnology.


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 Last update: November 2, 2016

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