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Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. [ 1 ] [ 2 ] The gastrointestinal metagenome is the aggregate of all the genomes of the gut microbiota .
Human microbiota are microorganisms (bacteria, viruses, fungi and archaea) found in a specific environment. They can be found in the stomach, intestines, skin, genitals and other parts of the body. [1] Various body parts have diverse microorganisms. Some microbes are specific to certain body parts and others are associated with many microbiomes.
Diets in developed countries have lost microbiota-accessible carbohydrates which is the cause of a substantial depletion of gut microbiota taxa. This loss of microbiota diversity is likely involved in the increasing propensity for a broad range of inflammatory diseases, such as allergic disease, asthma, inflammatory bowel disease (IBD), obesity ...
The bacteria and fungi live together in the gut and there is most likely a competition for nutrient sources present. [99] [100] Seelbinder et al. found that commensal bacteria in the gut regulate the growth and pathogenicity of Candida albicans by their metabolites, particularly by propionate, acetic acid and 5-dodecenoate. [98]
"Microbiome is a term that describes the genome of all the microorganisms, symbiotic and pathogenic, living in and on all vertebrates. The gut microbiome consists of the collective genome of microbes inhabiting the gut including bacteria, archaea, viruses, and fungi". [70]
Microbial metabolism is the means by which a microbe obtains the energy and nutrients (e.g. carbon) it needs to live and reproduce.Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics.
Some bacteria are limited to only one nutritional group, whereas others are facultative and switch from one mode to the other, depending on the nutrient sources available. [16] Sulfur-oxidizing , iron , and anammox bacteria as well as methanogens are chemolithoautotrophs , using inorganic energy, electron, and carbon sources.
The gut microbiota comprises all microorganisms that reside along the gastrointestinal tract, including commensal, symbiotic and pathogenic organisms. FMT is the transfer of fecal material containing bacteria and natural antibacterials from a healthy individual into a diseased recipient.