question: Where does the bacteria in the human gut originate from and how can our gut sustain bacterial life?
comment: Our gut flora comes from the food and liquids we ingest. They are bacteria that survive the stomach acid. The bacteria assist our digestive system by helping break down certain things. The bacteria survive in our gut because it is a warm environment with lots of food
passages: Over 99% of the bacteria in the gut are anaerobes, but in the cecum, aerobic bacteria reach high densities. It is estimated that these gut flora have around a hundred times as many genes in total as there are in the human genome.
   BULLET::::- "Lactobacillus rhamnosus"
  
  BULLET::::- "Propionibacterium freudenreichii"
  
  BULLET::::- "Bifidobacterium breve"
  
  BULLET::::- "Lactobacillus reuteri"
  
  BULLET::::- "Lactobacillus salivarius"
  
  BULLET::::- "Bifidobacterium infantis"
  
  BULLET::::- "Streptococcus thermophilus"
  
  Section::::Alterations in flora balance.:Research.
  
  Tests for whether non-antibiotic drugs may impact human gut-associated bacteria were performed by "in vitro" analysis on more than 1000 marketed drugs against 40 gut bacterial strains, demonstrating that 24% of the drugs inhibited the growth of at least one of the bacterial strains.
  
  Section::::Role in disease.
   In humans, the gut microbiota has the largest numbers of bacteria and the greatest number of species compared to other areas of the body. In humans, the gut flora is established at one to two years after birth, by which time the intestinal epithelium and the intestinal mucosal barrier that it secretes have co-developed in a way that is tolerant to, and even supportive of, the gut flora and that also provides a barrier to pathogenic organisms.
   Human gastrointestinal microbiota
  
  Human gastrointestinal microbiota, also known as gut flora or gut microbiota, are the microorganisms that live in the digestive tracts of humans. Many non-human animals, including insects, are hosts to numerous microorganisms that reside in the gastrointestinal tract as well. The human gastrointestinal metagenome is the aggregate of all the genomes of gut microbiota. The gut is one niche that human microbiota inhabit.
  
  Section::::Overview.
   The relationship between some gut flora and humans is not merely commensal (a non-harmful coexistence), but rather a mutualistic relationship. 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. Intestinal bacteria also play a role in synthesizing vitamin B 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, and dysregulation of the gut flora has been correlated with a host of inflammatory and autoimmune conditions.
   During the first year of life, the composition of the gut flora is generally simple and changes a great deal with time and is not the same across individuals. The initial bacterial population are generally facultative anaerobic organisms; investigators believe that these initial colonizers decrease the oxygen concentration in the gut, which in turn allows obligately anaerobic bacteria like "Bacteroides", "Actinobacteria", and "Firmicutes" to become established and thrive. Breast-fed babies become dominated by bifidobacteria, possibly due to the contents of bifidobacterial growth factors in breast milk, and by the fact that breast milk carries prebiotic components, allowing for healthy bacterial growth. In contrast, the microbiota of formula-fed infants is more diverse, with high numbers of "Enterobacteriaceae", enterococci, bifidobacteria, "Bacteroides", and clostridia.
   Gut microbiome composition depends on the geographic origin of populations. Variations in a trade-off of "Prevotella", the representation of the urease gene, and the representation of genes encoding glutamate synthase/degradation or other enzymes involved in amino acids degradation or vitamin biosynthesis show significant differences between populations from the US, Malawi or Amerindian origin.
   On a smaller scale, it has been shown that sharing numerous common environmental exposures in a family is a strong determinant of individual microbiome composition. This effect has no genetic influence and it is consistently observed in culturally different populations.
  
  Section::::Acquisition in human infants.
  
  The establishment of a gut flora is crucial to the health of an adult, as well the functioning of the gastrointestinal tract. In humans, a gut flora similar to an adult's is formed within one to two years of birth.
   Section::::Composition of the microbiome.
  
  Section::::Composition of the microbiome.:Individual Microbiomes.
  
  Section::::Composition of the microbiome.:Individual Microbiomes.:Gut.
  
  Within the intestines, the majority of microbes can be found in the large intestine, where the pH is higher and more conducive to survival. These bacteria are often more efficient than our own digestive enzymes, and function to digest protein and carbohydrates. The results of over 690 human microbiomes have shown that the majority of bacteria of the gut microbiome belongs to four phyla: Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria.
  
  Section::::Composition of the microbiome.:Individual Microbiomes.:Vagina.
   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. The colon, in contrast, contains a densely-populated microbial ecosystem with up to 10 cells per gram of intestinal content. These bacteria represent between 300 and 1000 different species. However, 99% of the bacteria come from about 30 or 40 species. As a consequence of their abundance in the intestine, bacteria also make up to 60% of the dry mass of feces. Fungi, protists, archaea, and viruses are also present in the gut flora, but less is known about their activities.
   Bacteria make up most of the flora in the colon and 60% of the dry mass of feces. 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. 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. Fungi and protists also make up a part of the gut flora, but less is known about their activities. The virome is mostly bacteriophages.
   Many species in the gut have not been studied outside of their hosts because most cannot be cultured. While there are a small number of core species of microbes shared by most individuals, populations of microbes can vary widely among different individuals. Within an individual, microbe populations stay fairly constant over time, even though some alterations may occur with changes in lifestyle, diet and age. The Human Microbiome Project has set out to better describe the microflora of the human gut and other body locations.
   Other strains of L. mucosae have been isolated from human feces, referred to as ME-340, human intestine and vagina, the intestines of dogs, calves, and horses, and the stomach mucosa of breast-fed lamb, strain D.
  
  Section::::Special Functions.
   Anaerobic gram-positive cocci are part of the normal gastrointestinal microbiota. They are isolated in approximately 20% of specimens from intra-abdominal infections, such as peritonitis. Found in abscesses of the liver, spleen, and abdomen. Like in upper respiratory tract and dental infections, anaerobic gram-positive cocci are recovered mixed with other bacteria. In this case they are mixed with organisms of intestinal origin such as E coli, bacteroides fragilis group, and clostridium species.
  
  Section::::Infections.:Infection types.:Female pelvic infections.
   The value of classifying by enterotype has been challenged. Subsequent studies have ruled out existence of a "Ruminococcus" enterotype.
  
  In a study of gut bacteria of children in Burkina Faso (in Africa), "Prevotella" made up 53% of the gut bacteria, but were absent in age-matched European children. 
  
  Studies also indicate that long-term diet is strongly associated with the gut microbiome composition—those who eat plenty of protein and animal fats typical of Western diet have predominantly "Bacteroides" bacteria, while for those who consume more carbohydrates, especially fibre, the "Prevotella" species dominate.
   BULLET::::- Microbiome br There has been increased attention to the role of bacteria and the microbiome in overall health and disease. There is evidence for a group of microorganisms which play a role in the brain-gut axis. Studies have revealed that the bacterial composition of the gastrointestinal tract in IBS patient differs from healthy individuals (e.g., increased Firmicutes and reduced Bacteroidetes and Bifidobacteria) However, further research is needed to determine the role of the microbiome in FGIDs.
   In humans, the composition of the gastrointestinal microbiome is established during birth. Birth by Cesarean section or vaginal delivery also influences the gut's microbial composition. Babies born through the vaginal canal have non-pathogenic, beneficial gut microbiota similar to those found in the mother. However, the gut microbiota of babies delivered by C-section harbors more pathogenic bacteria such as Escherichia coli and Staphylococcus and it takes longer to develop non-pathogenic, beneficial gut microbiota.
   The relationship between some gut flora and humans is not merely commensal (a non-harmful coexistence), but rather a mutualistic relationship. 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. Intestinal bacteria also play a role in synthesizing vitamin B 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, and dysregulation of the gut flora has been correlated with a host of inflammatory and autoimmune conditions.
   The traditional view of the gastrointestinal tract of a normal fetus is that it is sterile, although this view has been challenged in the past few years. Multiple lines of evidence have begun to emerge that suggest there may be bacteria in the intrauterine environment. In humans, research has shown that microbial colonization may occur in the fetus with one study showing "Lactobacillus" and "Bifidobacterium" species were present in placental biopsies. Several rodent studies have demonstrated the presence of bacteria in the amniotic fluid and placenta, as well as in the meconium of babies born by sterile cesarean section. In another study, researchers administered a culture of bacteria orally to a pregnant dam, and detected the bacteria in the offspring, likely resulting from transmission between the digestive tract and amniotic fluid via the blood stream. However, researchers caution that the source of these intrauterine bacteria, whether they are alive, and their role, is not yet understood.
   BULLET::::- "Atlantibacter" (2016)
  
  BULLET::::- "Averyella" (2005)
  
  BULLET::::- "Chania" (2016)
  
  BULLET::::- "Grimontella" (2003)
  
  BULLET::::- "Guhaiyinggella" (1995)
  
  BULLET::::- "Margalefia" (2004)
  
  BULLET::::- "Tiedjeia" (2005)
  
  Section::::Identification.
  
  To identify different genera of Enterobacteriaceae, a microbiologist may run a series of tests in the lab. These include:
  
  BULLET::::- Phenol red
  
  BULLET::::- Tryptone broth
  
  BULLET::::- Phenylalanine agar for detection of production of deaminase, which converts phenylalanine to phenylpyruvic acid
  
  BULLET::::- Methyl red or Voges-Proskauer tests depend on the digestion of glucose. The methyl red tests for acid endproducts. The Voges Proskauer tests for the production of acetylmethylcarbinol.
   Bacteria in the digestive tract can contribute to and be affected by disease in various ways. The presence or overabundance of some kinds of bacteria may contribute to inflammatory disorders such as inflammatory bowel disease. Additionally, metabolites from certain members of the gut flora may influence host signalling pathways, contributing to disorders such as obesity and colon cancer. Alternatively, in the event of a breakdown of the gut epithelium, the intrusion of gut flora components into other host compartments can lead to sepsis.
  
  Section::::Role in disease.:Ulcers.
   The type of bacteria involved in bacteremia is greatly influenced by the infection's portal of entry and the underlying disease. The isolation of "B. fragilis" group and "Clostridium" spp. is often associated with a gastrointestinal source, pigmented "Prevotella" and "Porphyromonas" spp. and "Fusobacterium" spp.with oropharynx and pulmonary sites, "Fusobacterium" spp. with the female genital tract locations," P. acnes" with a foreign body, and "Peptostreptococcus" spp. with all infection sources, but mostly with oropharyngeal, pulmonary and female genital tract locations. The association of these organisms is related to the origin of the initial infection and the endogenous bacterial ﬂora at that site.
   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.
  
  Industralization 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.
  
  Section::::Classifications.:Enterotype.
   In 1972, "Ruminococcus bromii" was reportedly found in the human gut, which was the first of several species discovered.
  
  One study found that "R. albus", "R. callidus", and "R. bromii" are less abundant in people with inflammatory bowel disease. Ruminococcus is also less abdundant in Parkinson's disease. They may play a role in plant cell wall breakdown in the colon.
  
  Section::::Species.
  
  BULLET::::- "Ruminococcus albus"
  
  BULLET::::- "Ruminococcus bromii"
  
  BULLET::::- "Ruminococcus callidus"
  
  BULLET::::- "Ruminococcus flavefaciens"
  
  Species belonging to the Lachnospiraceae family and therefore in need of reclassification:
  
  BULLET::::- "Ruminococcus gauvreauii"
  
  BULLET::::- "Ruminococcus gnavus"
  
  BULLET::::- "Ruminococcus lactaris"
  
  BULLET::::- "Ruminococcus obeum"
  
  BULLET::::- "Ruminococcus torques"
   In humans, the gut microbiota has the largest numbers of bacteria and the greatest number of species compared to other areas of the body. In humans the gut flora is established at one to two years after birth, and by that time the intestinal epithelium and the intestinal mucosal barrier that it secretes have co-developed in a way that is tolerant to, and even supportive of, the gut flora and that also provides a barrier to pathogenic organisms.
  