Gut microbiota

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 eff

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.[3][4] The gut is the main location of the human microbiome.[5] 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.[4] Imbalances in the gut microbiota (dysbiosis) have been associated with numerous diseases, including inflammatory bowel disease, certain cancers, and even neurological disorders, prompting increased efforts to develop microbiome-targeted therapies.[6]

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.[7] Bacteria are the largest and to date, best studied component and 99% of gut bacteria come from about 30 or 40 species.[8] About 55% of the dry mass of feces is bacteria.[9] Over 99% of the bacteria in the gut are anaerobes, but in the cecum, aerobic bacteria reach high densities.[5] It is estimated that the human gut microbiota has around a hundred times as many genes as there are in the human genome.

Overview

In humans, the gut microbiota has the highest numbers and species of bacteria compared to other areas of the body.[10] The approximate number of bacteria composing the gut microbiota is about 1013–1014 (10 to 100 trillion).[11] In humans, the gut flora is established at birth and gradually transitions towards a state resembling that of adults by the age of two,[12] coinciding with the development and maturation of the intestinal epithelium and intestinal mucosal barrier. This barrier is essential for supporting a symbiotic relationship with the gut flora while providing protection against pathogenic organisms.[13][14]

The relationship between some gut microbiota and humans is not merely commensal (a non-harmful coexistence), but rather a mutualistic relationship.[5]: 700  Some human gut microorganisms benefit the host by fermenting dietary fiber into short-chain fatty acids (SCFAs), such as acetic acid and butyric acid, which are then absorbed by the host.[10][15] Intestinal bacteria also play a role in synthesizing certain B vitamins and vitamin K as well as metabolizing bile acids, sterols, and xenobiotics.[5][15] The systemic importance of the SCFAs and other compounds they produce are like hormones and the gut flora itself appears to function like an endocrine organ.[15] Dysregulation of the gut flora has been correlated with a host of inflammatory and autoimmune conditions.[10][16]

The composition of human gut microbiota changes over time, when the diet changes, and as overall health changes.[10][16] A systematic review from 2016 examined the preclinical and small human trials that have been conducted with certain commercially available strains of probiotic bacteria and identified those that had the most potential to be useful for certain central nervous system disorders.[17] It should also be highlighted that the Mediterranean diet, rich in vegetables and fibers, stimulates the activity and growth of beneficial bacteria for the brain.[18]

Classifications

The microbial composition of the gut microbiota varies across the digestive tract. In the stomach and small intestine, relatively few species of bacteria are generally present.[7][19] Fungi, protists, archaea, and viruses are also present in the gut flora, but less is known about their activities.[20]

Many species in the gut have not been studied outside of their hosts because they cannot be cultured.[19][8][21] While there are a small number of core microbial species shared by most individuals, populations of microbes can vary widely.[22] Within an individual, their microbial populations stay fairly constant over time, with some alterations occurring due to changes in lifestyle, diet and age.[7][23] The Human Microbiome Project has set out to better describe the microbiota of the human gut and other body locations.[citation needed]

The four dominant bacterial phyla in the human gut are Bacillota (Firmicutes), Bacteroidota, Actinomycetota, and Pseudomonadota.[24] Most bacteria belong to the genera Bacteroides, Clostridium, Faecalibacterium,[7][8] Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, and Bifidobacterium.[7][8] Other genera, such as Escherichia and Lactobacillus, are present to a lesser extent.[7] Species from the genus Bacteroides alone constitute about 30% of all bacteria in the gut, suggesting that this genus is especially important in the functioning of the host.[19]

Fungal genera that have been detected in the gut include Candida, Saccharomyces, Aspergillus, Penicillium, Rhodotorula, Trametes, Pleospora, Sclerotinia, Bullera, and Galactomyces, among others.[25][26] Rhodotorula is most frequently found in individuals with inflammatory bowel disease while Candida is most frequently found in individuals with hepatitis B cirrhosis and chronic hepatitis B.[25]

Archaea constitute another large class of gut flora which are important in the metabolism of the bacterial products of fermentation.

Industrialization is associated with changes in the microbiota and the reduction of diversity could drive certain species to extinction; in 2018, researchers proposed a biobank repository of human microbiota.[27]

Enterotype

An enterotype is a classification of living organisms based on its bacteriological ecosystem in the human gut microbiome not dictated by age, gender, body weight, or national divisions.[28] There are indications that long-term diet influences enterotype.[29] Three human enterotypes have been proposed,[28][30] but their value has been questioned.[31]

Composition

Bacteria

Due to the high acidity of the stomach, most microorganisms cannot survive there. The main bacteria of the gastric microbiota belong to five major phyla: Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteriota, and Proteobacteria. The dominant genera are Prevotella, Streptococcus, Veillonella, Rothia, and Haemophilus.[32] The interaction between the pre-existing gastric microbiota with the introduction of H. pylori may influence disease progression.[32] When there is a presence of H. pylori it becomes the dominant species of the microbiota.[33]