| Fibrobacterota | |
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Scientific classification  | |
| Domain: | Bacteria |
| Clade: | FCB group |
| Phylum: | Fibrobacterota Garrity & Holt 2021 [1] |
| Classes | |
| Synonyms | |
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Fibrobacterota is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus Fibrobacter (the only genus of Fibrobacterota) was removed from the genus Bacteroides in 1988. [2]
Although Fibrobacterota is currently recognized as a distinct phylum, phylogenetic studies based RpoC and Gyrase B protein sequences, indicate that Fibrobacter succinogenes is closely related to the species from the phyla Bacteroidetes and Chlorobi. [3] The species from these three phyla also branch in the same position based upon conserved signature indels in a number of important proteins. [4] Lastly and most importantly, comparative genomic studies have identified two conserved signature indels (a 5-7 amino acid insert in the RpoC protein and a 13-16 amino acid insertion in serine hydroxymethyltransferase) and one signature protein (PG00081) that are uniquely shared by all of the species from these three phyla. [5] All of these results provide compelling evidence that the species from these three phyla shared a common ancestor exclusive of all other bacteria and it has been proposed that they should all recognized as part of a single “FCB”superphylum. [3] [5]
Phylogeny of Fibrobacterota.
| 16S rRNA based LTP_10_2024 [6] [7] [8] | 120 marker proteins based GTDB 09-RS220 [9] [10] [11] | ||||||||||||||||||||||||||||||||||||||||||||||||
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The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN) [12] and the National Center for Biotechnology Information (NCBI). [13]
The phylum Fibrobacterota is considered to be closely related to the CFB [Cytophaga-Flavibacterium-Bacteroidota]. [5] It contains the genus Fibrobacter, which has strains present in the guts of many mammals including cattle and pigs. [14] The two described species in this genus namely, Fibrobacter succinogenes and Fibrobacter intestinalis are important members of fibrolytic communities in mammalian guts and have received a lot of attention in recent decades due to the long-standing interest microbes capable of degrading plant fiber.
Molecular evidence based on the amplification of 16rRNA genes from various environments suggest that the phylum is much more widespread than previously thought. [15] [16] Most of the clones from mammalian environments group along with the known isolates in what has been called subphylum 1. [16] Members of subphylum 2 however, have so far been found only in the gut of termites. [16] [17] and in some litter-feeding cockroaches. [18] The predominance of subphylum 2 in cellulolytic fibre-associated bacterial communities in hindguts of wood-feeding Nasutitermes corniger suggests that they play an important role in the breakdown of plant material in higher termites. [19]
A spirochaete or spirochete is a member of the phylum Spirochaetota, which contains distinctive diderm (double-membrane) Gram-negative bacteria, most of which have long, helically coiled cells. Spirochaetes are chemoheterotrophic in nature, with lengths between 3 and 500 μm and diameters around 0.09 to at least 3 μm.
The Aquificota phylum is a diverse collection of bacteria that live in harsh environmental settings. The name Aquificota was given to this phylum based on an early genus identified within this group, Aquifex, which is able to produce water by oxidizing hydrogen. They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods. They are true bacteria as opposed to the other inhabitants of extreme environments, the Archaea.
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.
Verrucomicrobiota is a phylum of Gram-negative bacteria that contains only a few described species. The species identified have been isolated from fresh water, marine and soil environments and human faeces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes from genus Xiphinema, residing in their gametes. The verrucomicrobial bacterium Akkermansia muciniphila is a human intestinal symbiotic bacterium that is considered as a promising probiotic.
The Thermotogota are a phylum of the domain Bacteria. The phylum contains a single class, Thermotogae. The phylum Thermotogota is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria. It is the sole phylum in the kingdom Thermotogati.
Chlorobium is a genus of green sulfur bacteria. They are photolithotrophic oxidizers of sulfur and most notably utilise a noncyclic electron transport chain to reduce NAD+. Photosynthesis is achieved using a Type 1 Reaction Centre using bacteriochlorophyll (BChl) a. Two photosynthetic antenna complexes aid in light absorption: the Fenna-Matthews-Olson complex, and the chlorosomes which employ mostly BChl c, d, or e. Hydrogen sulfide is used as an electron source and carbon dioxide its carbon source.
Streptomycetaceae is a family of the class Actinomycetota, making up the monotypic order Streptomycetales. It includes the important genus Streptomyces. This was the original source of many antibiotics, namely streptomycin, the first antibiotic against tuberculosis.
The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota. Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wall twice. It has been hypothesised that a member of the PVC clade might have been the host cell in the endosymbiotic event that gave rise to the first proto-eukaryotic cell.
The order Flavobacteriales comprises several families of environmental bacteria.
Fibrobacter succinogenes is a cellulolytic bacterium species in the genus Fibrobacter. It is present in the rumen of cattle. F. succinogenes is a gram negative, rod-shaped, obligate anaerobe that is a major contributor to cellulose digestion. Since its discovery in the 1950s, it has been studied for its role in herbivore digestion and cellulose fermentation, which can be utilized in biofuel production.
The Chloroflexota are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for photosynthesis ; and anaerobic halorespirers, which uses halogenated organics as electron acceptors.
Tannerella forsythia is an anaerobic, Gram-negative bacterial species of the Bacteroidota phylum. It has been implicated in periodontal diseases and is a member of the red complex of periodontal pathogens. T. forsythia was previously named Bacteroides forsythus and Tannerella forsythensis.
The FCB group is a superphylum of bacteria named after the main member phyla Fibrobacterota, Chlorobiota, and Bacteroidota. The members are considered to form a clade due to a number of conserved signature indels.
Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.
The suffix -bacter is used in microbiology for many genera and is intended to mean "bacteria".
Candidate phylum TG3 is a candidate phylum that is closely related to the phylum Fibrobacterota based on 16S rRNA gene phylogeny. Originally thought to be composed solely of sequences from termite guts, it was later found to be more widespread in nature.
There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.
Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein.
CrAss-like phage (crassviruses) are a bacteriophage family representing the most abundant viruses in the human gut, discovered in 2014 by cross assembling reads in human fecal metagenomes. In silico comparative genomics and taxonomic analysis have found that crAss-like phages represent a highly abundant and diverse family of viruses. CrAss-like phage were predicted to infect bacteria of the Bacteroidota phylum and the prediction was later confirmed when the first crAss-like phage (crAss001) was isolated on a Bacteroidota host in 2018. Crassviruses are podoviruses, possessing short non-contractile tails and icosahedral capsids. The first 3D structure of a crassvirus was determined by cryo-EM in 2023. While the presence of crAss-like phage in the human gut is not yet associated with any specific health condition, they are generally associated with a healthy gut microbiome and likely impact significantly on the gut Bacteroidota.
Chitinispirillum is a genus of bacteria from the family of Chitinispirillaceae with one known species. Chitinispirillum alkaliphilum has been isolated from hypersaline lake sediments from the Wadi el Natrun valley in Egypt.