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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-

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Citation
Anantharaman et al. (2016). Nature Communications 7 (1)
Names
“Nealsoniibacteriota” “Niyogiibacteriota” “Portnoyibacteriota” “Raymondiibacteriota” “Ryaniibacteriota” “Schekmaniibacteriota” “Spechtiibacteriota” “Staskawicziibacteriota” “Sungiibacteriota” “Tagaibacteriota” “Tayloriibacteriota” “Terryibacteriota” “Vebleniibacteriota” “Yonathiibacteriota” “Zambryskiibacteriota” “Rifleibacteriota” “Ozemibacteria”
Abstract
AbstractThe subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth’s biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complet

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.

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,

Metagenomic Discovery of “ Candidatus Parvarchaeales”-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments

Citation
Rao et al. (2023). mSystems 8 (2)
Names
“Jingweiarchaeaceae” “Rehaiarchaeum fermentans” “Parvarchaeales” “Haiyanarchaeum thermophilum” “Jingweiarchaeum tengchongense” “Parvarchaeum tengchongense” “Haiyanarchaeum” “Jingweiarchaeum” “Haiyanarchaeaceae” “Jingweiarchaeales” “Rehaiarchaeum”
Abstract
“ Candidatus Parvarchaeales” microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments.