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Gut microbiota is influenced by many factors. Host-dependent factors include genetics, sex, age, and the immune system. These are hard to change voluntarily. Behaviors can also affect gut microbiota. Examples are antibiotic use, anti-acid use, and certain surgeries like gastric bypass. In the last 20 years, data shows diet impacts gut microbiota. Nutrients like fatty acids and non-digestible carbohydrates play a role. Prebiotics and polyphenols are also important.
Intrinsic factors such as gender, ethnicity, and age (; ) and extrinsic factors such as diet, hygiene, antibiotic use, and mode of delivery () modulate the composition of the gut microbiome. Most of all, diet is a major environmental factor that shapes gut microbial communities ().
African children showed a distinct composition of the intestinal bacterial community with enhanced abundance of Bacteroidetes and lower abundance of Firmicutes, as well as increased levels of SCFAs propionate and butyrate , which was at least four times higher than those of European children. These characteristics were directly linked with the low prevalence of allergies and autoimmune disease in this African population
The gut microbiota exhibit varying survival mechanisms in aerobic environments. There is an inverse relationship between their ability to survive aerobically and the frequency or duration of their colonization in the intestinal tract.
Across different diseases and diets, some gut bacteria always form strong relationships, acting together in groups. These are called “guilds.” One guild includes bacteria that help digest fiber and create beneficial substances like butyrate, supporting health. The other guild has bacteria with more genes for antibiotic resistance and potential virulence, which may be harmful. The balance between these two guilds is linked to health: more of the fiber-digesting group means better health; more of the potentially harmful group relates to poorer health outcomes.This pattern was the same in people from different countries, with different diseases, and even influenced how well people responded to treatments like immunotherapy.
Bacteroidetes to Firmicutes ratio is linked to SCFA production
Initially, facultative anaerobes such as Staphylococcus, Streptococcus, Enterobacteriaceae, and Lactobacillus colonize the gut. These create conditions that allow obligate anaerobes like Bifidobacterium, Clostridium, and Bacteroides to succeed, further diversifying the gut microbiota.
Most of the digestive tract is populated by anaerobic bacteria and the cecum by Aerobic Bacteria / Aerobic Organism
157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis
Gut microbiota comprises approximately 3 × 10^13 bacterial cells
Accordingly, whereas about one-third of microorganism composition of the gut microbiota is common in most people, the rest of two-thirds is specific to each individual
The composition of the microbiota is highly variable at different locations of the intestinal tract
The microbiome's composition varies significantly between individuals: the species, the relative ratios among different bacteria, and the identity of the dominant species
It has been suggested that the microbiota of most individuals can be categorized into one of three variants or “enterotypes” (enterotype 1, enterotype 2, enterotype 3) based on the dominant genera (Bacteroides, Prevotella, or Ruminococcus)
It is largely composed of symbiotic commensals with a few species functioning as pathobionts .
A significant difference exists between the kind of microbiota in the lumen and the microbiota embedded in the mucus layer of the gut
Regarding dominant phyla, warm-blooded omnivores, including birds and mammals, have gut microbiota with about 1000 bacterial species. These bacteria mainly belong to two phyla: Firmicutes and Bacteroidetes. Minor phyla include Proteobacteria and Actinomycetota. Some individuals may also have bacteria from phyla like Verrucomicrobia, Spirochetes / Spirochaete, Fusobacteria, Elusimicrobia, or Synergistetes
Fifty-three bacterial species were selected from the Human Microbiome Project to represent the spectrum of phyla and genera in the human gut microbiota and cover the five dominant phyla: Bacteroidetes , Firmicutes , Proteobacteria , Actinobacteria , and Fusobacteria / Fusobacteriota
Phylum-level variability is not individual-specific. More than 90% of gut bacteria are members of just two phyla, Bacteroidetes and Firmicutes. Bacteroidetes predominate in some individuals, and Firmicutes predominate in others - the latter predominate.
The human gut microbiota consists of more than 1,000 species and over 7,000 subspecies of microorganisms. The human intestine is colonized by an estimated 100 trillion bacteria. The gut microbiota is essentially composed of five phyla:
The 16S rRNA sequences mainly belonged to the phyla Firmicutes (79.4%), Bacteroidetes (16.9%), Actinomycetota (2.5%), Proteobacteria (1%) and Verrucomicrobia / Verrucomicrobiota (0.1%). in healthy humans
According to the ribosomal database project browser, Firmicutes account for 65%, Bacteroidetes 30%, Proteobacteria 2%, Verrucomicrobia 2%, Actinomycetota 1%, and others <1% of the gut bacteria
Yang et al. 2009 Gastroenterology 137: 588–597
The majority of sequences were associated with only four phyla of the Bacteria: Actinomycetota (5%), Bacteroidetes (23%), Firmicutes (49%), Proteobacteria (21%)
Regarding the dominant genera, the most common bacterial genera in human beings are Bacteroides, Clostridium, Peptococcus, Bifidobacterium, Eubacterium, Ruminococcus, Faecalibacterium, and Peptostreptococcus
Maier et al. showed 21 core genera in the human gut microbiota of healthy individuals, accounting for 78% of the median assignable relative abundance (mra) of the human gut microbiota at the genus level. The main selection criteria were prevalence, abundance in the human intestine, and phylogenetic diversity:
The genera include 38 representative bacterial species. Escherichia coli and Bacteroides fragilis are represented by the strains Escherichia coli IAI1 , Escherichia coli ED1a , and Enterotoxigenic Bacteroides fragilis (ETBF) as pathobiont
Bifidobacteria and Bacteroides comprise 85-98 % of intestinal microflora
Regarding the species , 99% of 10^12 bacteria per gram of colonic matter come from about 40 species
The adult gut microbiota is also partially stable, as a core of ~40 bacterial species (accounting for 75% of the gut microbiota in terms of abundance) persists for at least a year in individuals.
A more extensive longitudinal study found that 60% of all bacterial strains within an individual persisted for five years.
The entire cohort harbours between 1000 and 1150 prevalent bacterial species and each individual at least 160 such species, and that only 30-40 species as the bulk of microbiota are shared among individuals
Most relevant in gut microorganisms: Bifidobacterium longum, Bifidobacterium breve, Bifidobacterium bifidum, Bifidobacterium animalis lactis
Regarding the genomic level, genome-wide association studies (GWASs) have identified genomic factors linked to gut microbiota composition.
The previously known Unified Human Gut Microbiome (UHGM) with >200,000 human gut microbial genomes suggests the number of 4644 prokaryotes
The MetaHIT (Metagenomics of the Human Intestinal Tract) Consortium defined a “core” set of lineages as those present in half of the subjects studied, although essentially, no genes were present in all subjects
This gene pool of the host microbiota is referred to as its microbiome and is composed of the bacteriome (bacterial gene pool), the virome (viral gene pool), and the mycobiome (fungal gene pool)
Over 99% of the genes are bacterial. The entire cohort harbours between 1000 and 1150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared
Over 100 trillion microorganisms have been identified in the human GI tract, encoding over three million genes, compared with the 23,000 genes within the human genome
Transient Microorganisms
The yogurt starters Lactobacillus delbrueckii bulgaricus and Streptococcus thermophilus, as well as other lactic acid bacteria and Bifidobacteria in probiotic fermented milks, such as Lacticaseibacillus casei and Bifidobacterium animalis, are some examples of transient microorganisms
The variable gut microbiota includes autochthonous species that colonize the intestine, while others are allochthonous species that have shown the ability to transiently integrate into the resident gut microbiota and are mainly derived from the diet
see also:
Aerotolerance / Aerotolerant anaerobes
Autoimmune Diseases & Gut microbiota
Breastfeeding
Development of Gut Microbiota & Early Childhood / Neonates
Dispersal (immigration, Emigration) / Transmission
Drugs / Medications & Gut microbiota
Facultative aerobic bacteria / Facultative anaerobic organism
Food / Diets / Nutrients & Gut microbiota
Gut bacteria
Gut microbiota
Gut microbiota & Variability
Gut microbiota & Physical well-being / Health
Host - Microbiota interactions
Gut microbiota & Influencing factors
Prebiotics
Probiotics (living agents)
Sporulation / Spore