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The phylum Bacteroidota is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals.
Coliform bacteria are defined as either motile or non-motile Gram-negative non-spore forming bacilli that possess β-galactosidase to produce acids and gases under their optimal growth temperature of 35–37 °C. They can be aerobes or facultative aerobes, and are a commonly used indicator of low sanitary quality of foods, milk, and water. Coliforms can be found in the aquatic environment, in soil and on vegetation; they are universally present in large numbers in the feces of warm-blooded animals as they are known to inhabit the gastrointestinal system. While coliform bacteria are not normally causes of serious illness, they are easy to culture, and their presence is used to infer that other pathogenic organisms of fecal origin may be present in a sample, or that said sample is not safe to consume. Such pathogens include disease-causing bacteria, viruses, or protozoa and many multicellular parasites.
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.
Bacteroides is a genus of Gram-negative, obligate anaerobic bacteria. Bacteroides species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unusual in bacterial organisms, Bacteroides membranes contain sphingolipids. They also contain meso-diaminopimelic acid in their peptidoglycan layer.
Bacteroides fragilis is an anaerobic, Gram-negative, pleomorphic to rod-shaped bacterium. It is part of the normal microbiota of the human colon and is generally commensal, but can cause infection if displaced into the bloodstream or surrounding tissue following surgery, disease, or trauma.
Piromyces is a genus of fungi in the family Neocallimastigaceae.
Bifidobacterium longum is a Gram-positive, catalase-negative, rod-shaped bacterium present in the human gastrointestinal tract and one of the 32 species that belong to the genus Bifidobacterium. It is a microaerotolerant anaerobe and considered to be one of the earliest colonizers of the gastrointestinal tract of infants. When grown on general anaerobic medium, B. longum forms white, glossy colonies with a convex shape. B. longum is one of the most common bifidobacteria present in the gastrointestinal tracts of both children and adults. B. longum is non-pathogenic, is often added to food products, and its production of lactic acid is believed to prevent growth of pathogenic organisms.
Lentisphaerota is a phylum of bacteria closely related to Chlamydiota and Verrucomicrobiota.
Armatimonas rosea is a Gram-negative bacterium and also the first species to be characterized within the phylum Armatimonadota. The Armatimonadota were previously known as candidate phylum OP10. OP10 was composed solely of environmental 16S rRNA gene clone sequences prior to A. rosea's discovery.
Chthonomonas calidirosea is a Gram-negative bacterium and also the first representative of the new class Chthonomonadetes within the phylum Armatimonadota. The Armatimonadota were previously known as candidate phylum OP10. OP10 was composed solely of environmental 16S rRNA gene clone sequences prior to C. calidirosea's relative, Armatimonas rosea's discovery. It is now known that bacterial communities from geothermal environments, are generally constituted by, at least 5–10% of bacteria belonging to Armatimonadota.
The altered Schaedler flora (ASF) is a community of eight bacterial species: two lactobacilli, one Bacteroides, one spiral bacterium of the Flexistipes genus, and four extremely oxygen sensitive (EOS) fusiform-shaped species. The bacteria are selected for their dominance and persistence in the normal microflora of mice, and for their ability to be isolated and grown in laboratory settings. Germ-free animals, mainly mice, are colonized with ASF for the purpose of studying the gastrointestinal (GI) tract. Intestinal mutualistic bacteria play an important role in affecting gene expression of the GI tract, immune responses, nutrient absorption, and pathogen resistance. The standardized microbial cocktail enabled the controlled study of microbe and host interactions, role of microbes, pathogen effects, and intestinal immunity and disease association, such as cancer, inflammatory bowel disease, diabetes, and other inflammatory or autoimmune diseases. Also, compared to germfree animals, ASF mice have fully developed immune system, resistance to opportunistic pathogens, and normal GI function and health, and are a great representation of normal mice.
Syntrophococcus sucromutans is a Gram-negative strictly anaerobic chemoorganotrophic Bacillota. These bacteria can be found forming small chains in the habitat where it was first isolated, the rumen of cows. It is the type strain of genus Syntrophococcus and it has an uncommon one-carbon metabolic pathway, forming acetate from formate as a product of sugar oxidation.
Dehalogenimonas lykanthroporepellens is an anaerobic, Gram-negative bacteria in the phylum Chloroflexota isolated from a Superfund site in Baton Rouge, Louisiana. It is useful in bioremediation for its ability to reductively dehalogenate chlorinated alkanes.
Oscillibacter valericigenes is a species of mesophilic bacterium identified in the alimentary canal of Japanese Corbicula clams. It is Gram-negative and anaerobic, with a straight to slightly curved rod-like morphology, and is motile with petritrichous flagella. It was not observed in culture to form spores.
Lentisphera araneosa is a marine bacteria strain in the bacterial phylum Lentisphaerota. They are able to produce viscous transparent exopolymers and grow attached to each other by the polymer in a three-dimensional configuration. They are part of the natural surface bacterial population in the Atlantic and Pacific oceans. They are less than 1% of the total bacterial community. This species is gram negative, non-motile, non-pigmented, aerobic, chemoheterotrophic, and facultatively oligotrophic sphere-shaped. Its genome has been sequenced.
In microbiology, the term isolation refers to the separation of a strain from a natural, mixed population of living microbes, as present in the environment, for example in water or soil, or from living beings with skin flora, oral flora or gut flora, in order to identify the microbe(s) of interest. Historically, the laboratory techniques of isolation first developed in the field of bacteriology and parasitology, before those in virology during the 20th century.
Turicibacter is a genus in the Bacillota phylum of bacteria that has most commonly been found in the guts of animals. The genus is named after the city in which it was first isolated, Zurich, Switzerland.
Christensenella is a genus of non-spore-forming, anaerobic, and nonmotile bacteria from the family Christensenellaceae. They are also part of the order Clostridiales, the class Clostridia and the phylum Firmicutes. Phylogenetic analyzes of 16S rRNA gene sequences are used to describe this family. Due to the recent discovery of the Christensenellaceae family, it was not given importance until a few years ago. This is why very little is known about its ecology and how it may be associated with host factors and other microbiota. However, recent studies establish that members of this family, with exceptions, may be associated with a healthy phenotype for humans. The species C. minuta has been published and validated, and C. timonensis and C. massiliensis have been proposed as novel species of the genus Christensenella, all isolated from human feces.
Anaerococcus is a genus of bacteria. Its type species is Anaerococcus prevotii. These bacteria are Gram-positive and strictly anaerobic. The genus Anaerococcus was proposed in 2001. Its genome was sequenced in August 2009. The genus Anaerococcus is one of six genera classified within the group GPAC. These six genera are found in the human body as part of the commensal human microbiota.
TM7x, also known as Nanosynbacter lyticus type strain TM7x HMT 952. is a phylotype of one of the most enigmatic phyla, Candidatus Saccharibacteria, formerly candidate phylum TM7. It is the only member of the candidate phylum that has been cultivated successfully from the human oral cavity, and stably maintained in vitro. and serves as a crucial paradigm. of the newly described Candidate Phyla Radiation (CPR). The cultivated oral taxon is designated as Saccharibacteria oral taxon TM7x. TM7x has a unique lifestyle in comparison to other bacteria that are associated with humans. It is an obligate epibiont parasite, or an "epiparasite", growing on the surface of its host bacterial species Actinomyces odontolyticus subspecies actinosynbacter strain XH001, which is referred to as the "basibiont". Actinomyces species are one of the early microbial colonizers in the oral cavity. Together, they exhibit parasitic epibiont symbiosis.
References
- 1 2 van Passel, Mark (11 March 2011). "Genome Sequence of Victivallis vadensis ATCC BAA-548, an Anaerobic Bacterium from the Phylum Lentisphaerae, Isolated from the Human Gastrointestinal Tract". Journal of Bacteriology. 193 (9): 2373–2374. doi:10.1128/JB.00271-11. PMC 3133096 . PMID 21398537.
- 1 2 3 4 5 6 7 8 9 10 Zoetendal, Erwin G. (2003). "Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces". International Journal of Systematic and Evolutionary Microbiology. 53 (1): 211–215. doi: 10.1099/ijs.0.02362-0 . PMID 12656175.
- ↑ Guarner, Francisco (8 Feb 2003). "Gut flora in health and disease". The Lancet. 361 (9356): 512–519. doi:10.1016/S0140-6736(03)12489-0. PMID 12583961. S2CID 38767655 . Retrieved 11 Nov 2014.
- 1 2 3 4 5 6 7 8 Cho, Jang-Cheon (2011). Bergey's Manual of Systematic Bacteriology (2 ed.). New York: Springer Verlag. pp. 13, 785–793. ISBN 978-0-387-68572-4.
- 1 2 Cho, Jang-Cheon (2004). "Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae". Environmental Microbiology. 6 (6): 611–621. Bibcode:2004EnvMi...6..611C. doi:10.1111/j.1462-2920.2004.00614.x. PMID 15142250.
