Human microbiome
Atomic claims
The human microbiome is the collection of microorganisms and their genes that inhabit the human body.
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The human microbiome includes bacteria.
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The human microbiome chiefly inhabits the gut, skin, mouth, and urogenital tract.
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The human microbiome contributes to digestion.
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Altered microbial communities are associated with many diseases.
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Causality between altered microbial communities and disease is established for only a few conditions.
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The term "microbiome" in its current sense is commonly attributed to Joshua Lederberg.
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Joshua Lederberg described the microbiome as the ecological community of commensal, symbiotic, and pathogenic microorganisms sharing the body space.
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The NIH Human Microbiome Project (HMP) launched in 2007.
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The HMP sampled 242 healthy US adults.
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The HMP sampled men at 15 body sites.
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The HMP found large variation in microbial composition between individuals.
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The HMP found that metabolic pathway content was comparatively stable across individuals.
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A reference human body (70 kg male) is estimated to contain about 3.8 × 10^13 bacterial cells.
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The ratio of bacterial cells to human cells in a reference body is near 1:1.
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The 1:1 ratio estimate revised the long-cited 10:1 figure for the ratio of bacterial to human cells.
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The total mass of bacteria in a reference 70 kg human body is estimated at about 0.2 kg.
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The colon holds the large majority of the human body's bacteria.
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The MetaHIT consortium catalogued 3.3 million non-redundant gut microbial genes.
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The healthy adult gut community is dominated by the bacterial phylum Bacteroidetes.
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Microbial community composition differs markedly by body habitat.
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Body habitat site explains more variation in microbial community composition than individual identity.
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Delivery mode shapes the initial neonatal microbiota.
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Vaginally delivered infants acquire microbial communities resembling maternal vaginal microbiota.
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Gut microbiota composition in children converges toward an adult-like configuration within approximately the first three years of life.
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Gut bacteria ferment dietary fibre to short-chain fatty acids.
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Short-chain fatty acids produced by gut bacteria include acetate, propionate, and butyrate.
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Short-chain fatty acids serve as an energy source for colonocytes.
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Diet can alter gut community composition within days.
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Germ-free animals show defects in immune system development.
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Defects in germ-free animals indicate a microbial role in immune maturation.
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Fecal microbiota transplantation was superior to vancomycin for recurrent Clostridioides difficile infection in a randomized trial.
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The US FDA approved the first fecal microbiota product, Rebyota, in November 2022.
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Rebyota was approved for prevention of recurrent C. difficile infection.
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Principal microbiome study methods are 16S rRNA gene amplicon sequencing and shotgun metagenomics.
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Altered microbiota are associated with obesity.
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Whether microbiome changes cause disease, result from it, or reflect confounders is unresolved for most conditions.
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A critique argued that many rodent transfer studies claiming causality are over-interpreted.
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Early studies reported an increased Firmicutes/Bacteroidetes ratio in obesity.
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Later meta-analyses found the association between the Firmicutes/Bacteroidetes ratio and obesity to be weak or inconsistent.
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A 2011 proposal suggested human gut communities fall into three discrete enterotype clusters.
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The discrete enterotype cluster proposal has been disputed by analyses suggesting continuous gradients.
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A reported placental microbiome has been challenged as likely contamination.
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Later work found no evidence of a placental microbiome.
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A 2020 Nature paper reporting cancer-type-specific microbial signatures was retracted in 2024.
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The 2020 Nature paper on tumour microbiome signatures was retracted after critiques of its data handling.
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The efficacy of probiotics in healthy people is disputed.
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Evidence for the efficacy of probiotics is strain- and condition-specific.
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The human microbiome refers to the collective genomes of the microorganisms that reside on and within the human body.
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Microorganisms in the human microbiome include archaea.
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Human microbial communities predominantly inhabit the gastrointestinal tract.
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Microbial communities play an integral role in host metabolism.
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The resident microbiota was historically viewed primarily as potential agents of infectious disease.
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The scientific community widely recognizes the resident microbiota as a critical component of healthy human physiology.
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The term 'microbiome' describes the collective genomes of the microbiota residing in an environmental niche.
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A standard adult human body contains roughly 38 trillion bacterial cells.
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The largest concentration of human-associated microbes resides in the gastrointestinal tract.
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The goal of the Human Microbiome Project (HMP) was to map and characterize the microbial communities found at multiple human body sites.
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Gut bacteria synthesize essential nutrients that are absorbed by the human host.
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Gut bacteria synthesize vitamin K.
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The microbiome directly interacts with the mammalian immune system.
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The microbiome influences the development of gut-associated lymphoid tissue (GALT).
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Initial major microbial colonization of the human body occurs during birth.
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The mode of delivery significantly determines the early compositional structure of the infant's microbiome.
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Broad-spectrum antibiotics significantly perturb the microbiome's composition.
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Broad-spectrum antibiotic perturbation can result in long-term or permanent reductions in microbial diversity.
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Dysbiosis is defined as an imbalance or maladaptation in microbial composition.
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Dysbiosis is clinically associated with inflammatory bowel disease (IBD).
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Fecal microbiota transplantation (FMT) is the transfer of stool from a healthy donor to a patient's gastrointestinal tract.
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Fecal microbiota transplantation (FMT) is an established and highly effective clinical treatment for recurrent Clostridioides difficile (C. diff) infections.
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Microbiome dysbiosis is linked in literature to obesity.
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The scientific community debates whether microbial changes are the underlying cause of linked systemic, metabolic, and neurological conditions, or merely a secondary consequence.
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Historically, the scientific consensus held that a healthy human fetus develops in a sterile environment.
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Historically, the scientific consensus held that microbial colonization begins strictly at birth.
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Some studies have reported detecting bacterial DNA in the placenta.
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The detection of bacterial DNA in fetal environments has led to the proposal of an "in utero colonization" hypothesis.
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The "in utero colonization" hypothesis remains highly contested in the scientific community.
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Counter-studies argue that bacterial signals detected in fetal environments are the result of reagent contamination.
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External references: Wikidata Q1500347