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Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake

Citation
Williams et al. (2021). Frontiers in Microbiology 12
Names
Cloacimonadota “Aadella gelida” “Aceula” “Aceula lacicola” “Aceula meridiana” “Gorgyraea” “Gorgyraea atricola” “Gygaella” “Gygaella obscura” “Kaelpia” “Kaelpia aquatica” “Kaelpia imicola” “Saelkia” “Saelkia tenebricola” “Tantalella” “Tantalella remota” “Zapsychrus” “Zapsychrus exili” “Aadella” “Susulua” “Susulua stagnicola”
Abstract
The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial “dark matter” taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hil

Global diversity of enterococci and description of 18 previously unknown species

Citation
Schwartzman et al. (2024). Proceedings of the National Academy of Sciences 121 (10)
Names
Enterococcus mansonii Enterococcus ikei Enterococcus myersii Enterococcus leclercqii Enterococcus ferrettii Enterococcus wittei Enterococcus courvalinii Enterococcus palustris Enterococcus dunnyi Enterococcus huntleyi Enterococcus mangumiae Enterococcus moelleringii Enterococcus murrayae Enterococcus testudinis Enterococcus lowellii Enterococcus willemsii Enterococcus lemimoniae Enterococcus clewellii Vagococcus giribetii
Abstract
Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug-resistant hospital-

Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus “CandidatusAccumulibacter”

Citation
Petriglieri et al. (2022). mSystems 7 (3)
Names
“Accumulibacter” “Accumulibacter adiacens” “Accumulibacter meliphilus” “Accumulibacter propinquus” “Accumulibacter contiguus” “Accumulibacter vicinus” “Accumulibacter cognatus” “Accumulibacter affinis” “Accumulibacter proximus” “Accumulibacter necessarius” “Accumulibacter iunctus” “Accumulibacter similis” “Accumulibacter conexus” “Propionivibrio dominans” “Accumulibacter adjunctus” “Proximibacter danicus” “Proximibacter”
Abstract
“CandidatusAccumulibacter” is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages.

Filling the gaps: missing taxon names at the ranks of class, order and family

Citation
Göker (2022). International Journal of Systematic and Evolutionary Microbiology 72 (12)
Names
Kitasatosporales Nitrospiraceae Pseudobdellovibrionaceae Hydrogenophilia Bryobacterales Terriglobia Terriglobales Acidobacteriaceae Nitrospinales Nitrospinia Kiritimatiellia Chlorobiia Calditrichia Nitrospiria “Nitrobium” Nitrospirales Paracoccaceae
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) recently underwent some major modifications regarding the higher taxonomic ranks. On the one hand, the phylum category was introduced into the ICNP, which rapidly led to the valid publication of more than forty names of phyla. On the other hand, a decision on the retroactivity of Rule 8 regarding the names of classes was made, which removed most of the nomenclatural uncertainty that had affected those names during the last decade. Howe

Genomic delineation and description of species and within-species lineages in the genus Pantoea

Citation
Crosby et al. (2023). Frontiers in Microbiology 14
Names
Pantoea alvi Pantoea multigeneris Pantoea floridensis Pantoea haifensis Pantoea varia Pantoea rara Pantoea gossypiicola Pantoea bituminis Pantoea deserta Pantoea formicae Pantoea soli Pantoea astica Pantoea borealis Pantoea superficialis Pantoea symbiotica Pantoea communis
Abstract
As the name of the genus Pantoea (“of all sorts and sources”) suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions

An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea

Citation
Buessecker et al. (2022). Nature Communications 13 (1)
Names
Wolframiiraptor gerlachensis Ts Wolframiiraptor Wolframiiraptoraceae Benthortus lauensis Ts Geocrenenecus dongiae Ts Geocrenenecus arthurdayi Geocrenenecus huangii Terraquivivens ruidianensis Terraquivivens tengchongensis Terraquivivens yellowstonensis Benthortus Geocrenenecus Terraquivivens Terraquivivens tikiterensis Ts Wolframiiraptor sinensis Wolframiiraptor allenii
Abstract
AbstractTrace metals have been an important ingredient for life throughout Earth’s history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredox

Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages

Citation
Sun et al. (2021). ISME Communications 1 (1)
Names
Ca. Borrarchaeum weybense “Jordarchaeum” “Jordarchaeum madagascariense” “Sifarchaeaceae” “Jordarchaeaceae” “Sifarchaeales” “Jordarchaeales” “Sifarchaeia” “Jordarchaeia” Ca. Borrarchaeaceae Ca. Borrarchaeum “Sifarchaeum” Ca. Sifarchaeum marinoarchaea Ca. Sifarchaeum subterraneus “Sifarchaeota”
Abstract
AbstractAsgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface,