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Deinococcota is a phylum of bacteria with a single class, Deinococci, that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria.
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 Chlamydiota are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. Historically it was believed that all Chlamydiota had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins.
The Rhodobacteraceae are a family of Pseudomonadota in the order Rhodobacterales within the alpha subgroup. Like all Pseudomonadota, they are gram-negative. It contains chemoorganotrophs and photoheterotrophs. Many occur in aquatic habitats.
In prokaryote nomenclature, Candidatus is used to name prokaryotic taxa that are well characterized but yet-uncultured. Contemporary sequencing approaches, such as 16S ribosomal RNA sequencing or metagenomics, provide much information about the analyzed organisms and thus allow identification and characterization of individual species. However, the majority of prokaryotic species remain uncultivable and hence inaccessible for further characterization in in vitro study. The recent discoveries of a multitude of candidate taxa has led to candidate phyla radiation expanding the tree of life through the new insights in bacterial diversity.
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 was removed from the genus Bacteroides in 1988.
The Nitrosopumilales are an order of the Archaea class Nitrososphaeria.
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.
Nitrospirota is a phylum of bacteria. It includes multiple genera, such as Nitrospira, the largest. The first member of this phylum, Nitrospira marina, was discovered in 1985. The second member, Nitrospira moscoviensis, was discovered in 1995.
The phylum Elusimicrobiota, previously known as "Termite Group 1", has been shown to be widespread in different ecosystems like marine environment, sewage sludge, contaminated sites and soils, and toxic wastes. The high abundance of Elusimicrobiota representatives is only seen for the lineage of symbionts found in termites and ants.
Armatimonadota is a phylum of gram-negative bacteria.
Nanohaloarchaea is a clade of diminutive archaea with small genomes and limited metabolic capabilities, belonging to the DPANN archaea. They are ubiquitous in hypersaline habitats, which they share with the extremely halophilic haloarchaea.
The "Aigarchaeota" are a proposed archaeal phylum of which the main representative is Caldiarchaeum subterraneum. It is not yet clear if this represents a new phylum or a Nitrososphaerota order, since the genome of Caldiarchaeum subterraneum encodes several Nitrososphaerota-like features. The name "Aigarchaeota" comes from the Greek αυγή, avgí, meaning "dawn" or "aurora", for the intermediate features of hyperthermophilic and mesophilic life during the evolution of its lineage.
Melainabacteria is a class of bacteria within the phylum Cyanobacteriota. Vampirovibrio chlorellavorus is the only species of class Melainabacteria that has been grown in cell culture. Candidatus species of Melainabacteria have been discovered through DNA and RNA sequence analysis of samples from soil, the human gut and various aquatic habitats such as groundwater. Melainabacteria was originally designated a phylum when its DNA was discovered in 2013, then in 2014 was demoted to a class. By analyzing genomes of Melainabacteria, predictions are possible about their cell structure and metabolic abilities. The deduced structure of the bacterial cell is similar to cyanobacteria in being surrounded by two membranes. It differs from cyanobacteria in its predicted ability to move by flagella, though some members appear to lack flagella. It is predicted that Melainabacteria are not able to perform photosynthesis, but obtain energy by fermentation. Class Melainabacteria is also known as class Vampirovibrionophyceae.
Parvarchaeota is a phylum of archaea belonging to the DPANN archaea. They have been discovered in acid mine drainage waters and later in marine sediments. The cells of these organisms are extremely small consistent with small genomes. Metagenomic techniques allow obtaining genomic sequences from non-cultured organisms, which were applied to determine this phylum.
The candidate phyla radiation is a large evolutionary radiation of bacterial lineages whose members are mostly uncultivated and only known from metagenomics and single cell sequencing. They have been described as nanobacteria or ultra-small bacteria due to their reduced size (nanometric) compared to other bacteria.
The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to resolving paraphyletic groups, this method also reassigns taxonomic ranks algorithmically, updating names in both cases. Information for archaea was added in 2020, along with a species classification based on average nucleotide identity. Each update incorporates new genomes as well as automated and manual curation of the taxonomy.
Methanobacteriota is a proposed phylum in the domain Archaea.
References
- ↑ J.P. Euzéby. "Bacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.
- ↑ Sayers; et al. "Bacteria". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
- ↑ All-Species Living Tree Project. "16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database . Retrieved 2020-08-20.
- ↑ Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004. bioRxiv 10.1101/256800 . doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
- ↑ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964 . doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.
- ↑ Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics. 36 (6): 1925–1927. doi: 10.1093/bioinformatics/btz848 . PMC 7703759 . PMID 31730192.
- ↑ Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco; Beracochea, Martin; Shi, Zhou Jason; Pollard, Katherine S.; Sakharova, Ekaterina; Parks, Donovan H.; Hugenholtz, Philip; Segata, Nicola; Kyrpides, Nikos C.; Finn, Robert D. (20 July 2020). "A unified catalog of 204,938 reference genomes from the human gut microbiome". Nature Biotechnology. 39 (1): 105–114. doi: 10.1038/s41587-020-0603-3 . PMC 7801254 . PMID 32690973.
- ↑ Nayfach, Stephen; et al. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. 39 (4): 499–509. doi: 10.1038/s41587-020-0718-6 . PMC 8041624 . PMID 33169036.
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