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 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. Imbalances in the gut microbiota have been associated with numerous diseases, including inflammatory bowel disease, certain cancers, and even neurological disorders, prompting increased efforts to develop microbiome-targeted therapies.
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. About 55% 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 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. The approximate number of bacteria composing the gut microbiota is about 1013–1014. In humans, the gut flora is established at birth and gradually transitions towards a state resembling that of adults by the age of two, 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.The relationship between some gut microbiota and humans is not merely commensal, but rather a mutualistic relationship. Some human gut microorganisms benefit the host by fermenting dietary fiber into short-chain fatty acids, such as acetic acid and butyric acid, which are then absorbed by the host. Intestinal bacteria also play a role in synthesizing certain B vitamins and vitamin K as well as metabolizing bile acids, sterols, and xenobiotics. 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. Dysregulation of the gut flora has been correlated with a host of inflammatory and autoimmune conditions.
The composition of human gut microbiota changes over time, when the diet changes, and as overall health changes. 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. 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.
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. Fungi, protists, archaea, and viruses are also present in the gut flora, but less is known about their activities.Many species in the gut have not been studied outside of their hosts because they cannot be cultured. While there are a small number of core microbial species shared by most individuals, populations of microbes can vary widely. Within an individual, their microbial populations stay fairly constant over time, with some alterations occurring due to changes in lifestyle, diet and age. The Human Microbiome Project has set out to better describe the microbiota of the human gut and other body locations.
The four dominant bacterial phyla in the human gut are Bacillota, Bacteroidota, Actinomycetota, and Pseudomonadota. Most bacteria belong to the genera Bacteroides, Clostridium, Faecalibacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, and Bifidobacterium. Other genera, such as Escherichia and Lactobacillus, are present to a lesser extent. 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.
Fungal genera that have been detected in the gut include Candida, Saccharomyces, Aspergillus, Penicillium, Rhodotorula, Trametes, Pleospora, Sclerotinia, Bullera, and Galactomyces, among others. 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.
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.
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. There are indications that long-term diet influences enterotype. Three human enterotypes have been proposed, but their value has been questioned.Composition
Bacteria
Stomach
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. The interaction between the pre-existing gastric microbiota with the introduction of H. pylori may influence disease progression. When there is a presence of H. pylori it becomes the dominant species of the microbiota.Intestines
The small intestine contains a trace amount of microorganisms due to the proximity and influence of the stomach. Gram-positive cocci and rod-shaped bacteria are the predominant microorganisms found in the small intestine. However, in the distal portion of the small intestine alkaline conditions support gram-negative bacteria of the Enterobacteriaceae. The bacterial flora of the small intestine aid in a wide range of intestinal functions. The bacterial flora provide regulatory signals that enable the development and utility of the gut. Overgrowth of bacteria in the small intestine can lead to intestinal failure. In addition the large intestine contains the largest bacterial ecosystem in the human body. About 99% of the large intestine and feces flora are made up of obligate anaerobes such as Bacteroides and Bifidobacterium. Factors that disrupt the microorganism population of the large intestine include antibiotics, stress, and parasites.Bacteria make up most of the flora in the colon and account for 60% of fecal nitrogen. This fact makes feces an ideal source of gut flora for any tests and experiments by extracting the nucleic acid from fecal specimens, and bacterial 16S rRNA gene sequences are generated with bacterial primers. This form of testing is also often preferable to more invasive techniques, such as biopsies.
Five phyla dominate the intestinal microbiota: Bacteroidota, Bacillota, Actinomycetota, Pseudomonadota, and Verrucomicrobiotawith Bacteroidota and Bacillota constituting 90% of the composition. Somewhere between 300 and 1000 different species live in the gut, with most estimates at about 500. However, it is probable that 99% of the bacteria come from about 30 or 40 species, with Faecalibacterium prausnitzii being the most common species in healthy adults.
Research suggests that the relationship between gut flora and humans is not merely commensal, but rather is a mutualistic, symbiotic relationship. Though people can survive with no gut flora, the microorganisms perform a host of useful functions, such as fermenting unused energy substrates, training the immune system via end products of metabolism like propionate and acetate, preventing growth of harmful species, regulating the development of the gut, producing vitamins for the host, and producing hormones to direct the host to store fats. Extensive modification and imbalances of the gut microbiota and its microbiome or gene collection are associated with obesity. However, in certain conditions, some species are thought to be capable of causing disease by causing infection or increasing cancer risk for the host.
Fungi
also make up a part of the gut flora, but less is known about their activities.Due to the prevalence of fungi in the natural environment, determining which genera and species are permanent members of the gut mycobiome is difficult. Research is underway as to whether Penicillium is a permanent or transient member of the gut flora, obtained from dietary sources such as cheese, though several species in the genus are known to survive at temperatures around 37 °C, about the same as the core body temperature. Saccharomyces cerevisiae, brewer's yeast, is known to reach the intestines after being ingested and can be responsible for the condition auto-brewery syndrome in cases where it is overabundant, while Candida albicans is likely a permanent member, and is believed to be acquired at birth through vertical transmission.