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Gut microbiota

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**Overview of Gut Microbiota:**
Gut microbiota consists of bacteria, archaea, fungi, and viruses in the digestive tracts of animals.
– The gastrointestinal metagenome is the sum of all genomes of the gut microbiota.
– The gut is the primary location of the human microbiome.
Gut microbiota impacts colonization, resistance to pathogens, immune function, and behavior via the gut-brain axis.
– The colon has the highest microbial density, with up to 1000 different species.

**Classification and Composition of Gut Microbiota:**
– The stomach and small intestine have fewer bacterial species compared to the colon.
– The colon contains the highest microbial density.
– Bacteria make up to 60% of the dry mass of feces.
– The gut flora has around a hundred times more genes than the human genome.
– The dominant bacterial phyla in the human gut are Firmicutes, Bacteroidetes, Actinomycetes, and Pseudomonades.
– Gut flora is established by one to two years after birth and synthesizes vitamins and metabolizes compounds.
– Dysregulation of gut flora is linked to inflammatory and autoimmune conditions.

**Enterotype and Bacteriome:**
– Enterotype is a classification based on the bacteriological ecosystem in the human gut microbiome.
– Long-term diet influences enterotype, with three proposed human enterotypes.
– The stomach has high acidity limiting microorganism survival, while the small intestine contains trace amounts of microorganisms.
– The large intestine houses the largest bacterial ecosystem with 99% obligate anaerobes.
– Factors like antibiotics, stress, and parasites can disrupt the flora, with feces containing 60% dry mass flora ideal for testing.

**Intestinal Microbiota Diversity and Variation:**
– The gut microbiota has around 300-1000 species, with 5 dominant phyla.
– Microbiome composition evolves during life, with maturation occurring in the first 3 years.
– Different enzyme prevalence in adult vs. infant microbiomes, influenced by geography and factors like malnourishment, diet, race, ethnicity, and socioeconomic status.
– The gut flora performs various vital functions, including direct defense against pathogens, fortification of host defense, and metabolizing indigestible compounds.

**Impact of Gut Microbiota on Health and Metabolism:**
Gut microbiota impacts health by regulating antibody production, producing short-chain fatty acids affecting the immune system, and influencing immune cells.
– Gut bacteria produce metabolites like indole, IPA, and SCFAs from tryptophan, aiding in neuroprotection and immune modulation.
– Gut flora helps with carbohydrate utilization, cellulose degradation, and drug metabolism, affecting drug efficacy and toxicity.
– Bacterial metabolites like secondary BAs play crucial roles in health and disease, influencing biochemical pathways and human health.

Gut microbiota (Wikipedia)

Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut microbiota. The gut is the main location of the human microbiome. The gut microbiota has broad impacts, including effects on colonization, resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, controlling immune function, and even behavior through the gut–brain axis.

Escherichia coli, one of the many species of bacteria present in the human gut

The microbial composition of the gut microbiota varies across regions of the digestive tract. The colon contains the highest microbial density of any human-associated microbial community studied so far, representing between 300 and 1000 different species. Bacteria are the largest and to date, best studied component and 99% of gut bacteria come from about 30 or 40 species. Up to 60% of the dry mass of feces is bacteria. Over 99% of the bacteria in the gut are anaerobes, but in the cecum, aerobic bacteria reach high densities. It is estimated that the human gut microbiota have around a hundred times as many genes as there are in the human genome.

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