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Lists of names of prokaryotic Candidatus taxa

Citation
Oren et al. (2020). International Journal of Systematic and Evolutionary Microbiology 70 (7)
Names (142)
“Vecturitrichales” “Nitrosocaldales” “Moduliflexales” “Gastranaerophilales” “Altarchaeales” “Actinomarinales” “Vecturitrichia” “Thermofontia” “Moduliflexia” “Mariprofundia” “Galacturonatibacter soehngenii” “Fukatsuia symbiotica” “Fritschea eriococci” “Fritschea bemisiae” “Fokinia solitaria” “Fokinia crypta” “Fodinibacter communicans” “Flaviluna lacus” “Finniella” “Finniella lucida” “Finniella inopinata” “Fervidibacter sacchari” “Epulonipiscium fischelsonii” “Epulonipiscioides saccharophilum” “Epulonipiscioides gigas” “Epixenosoma ejectans” “Entotheonella serta” “Entotheonella palauensis” “Entotheonella factor” “Endowatersipora glebosa” “Endoriftia persephonae” “Endonucleibacter bathymodioli” “Endolissoclinum faulkneri” “Endobugula sertula” “Endobugula glebosa” “Endecteinascidia fromenterensis” “Electrothrix marina” “Electrothrix japonica” “Electrothrix communis” “Electrothrix aarhusensis” “Electronema palustre” “Electronema nielsenii” “Ecksteinia adelgidicola” “Doolittlea endobia” “Desulfonatronobulbus propionicus” “Desulfofervidus auxilii” “Dactylopiibacterium carminicum” “Cyrtobacter comes” “Curculioniphilus buchneri” “Cryptoprodota polytropus” “Criblamydia” “Criblamydia sequanensis” “Contubernalis alkaliaceticus” “Contendibacter odensensis” “Consessor aphidicola” “Competibacter phosphatis” “Competibacter denitrificans” “Combothrix italica” “Cochliopodiiphilus cryoturris” “Clavichlamydia salmonicola” “Chryseopegocella kryptomonas” “Chlorotrichoides halophilum” “Chloroploca asiatica” “Chloranaerofilum corporosum” “Cenarchaeum symbiosum” “Catenimonas italica” “Cardinium hertigii” “Carbonibacillus altaicus” “Captivus acidiprotistae” “Calescibacterium nevadense” “Calditenuis aerorheumatis” “Caldatribacterium saccharofermentans” “Caldatribacterium californiense” “Caldarchaeum subterraneum” “Caenarcanum bioreactoricola” “Brocadia sapporonensis” “Brocadia anammoxidans” “Brevifilum fermentans” “Blochmanniella vafra” “Blochmanniella pennsylvanica” “Blochmanniella myrmotrichis” “Blochmanniella floridana” “Blochmanniella camponoti” “Bandiella euplotis” “Atelocyanobacterium thalassae” “Aquiluna rubra” “Anammoximicrobium moscoviense” “Anammoxiglobus propionicus” “Amphibiichlamydia salamandrae” “Amphibiichlamydia ranarum” “Amoebophilus asiaticus” “Amoebinatus massiliensis” “Aminicenans sakinawicola” “Altimarinus pacificus” “Altarchaeum hamiconexum” “Allospironema culicis” “Allocryptoplasma californiense” “Allobeggiatoa salina” “Aerophobus profundus” “Aenigmatarchaeum subterraneum” “Adiacens aphidicola” “Actinomarina minuta” “Actinochlamydia pangasianodontis” “Actinochlamydia clariatis” “Aciduliprofundum boonei” “Acetithermum autotrophicum” “Accumulibacter phosphatis” “Accumulibacter aalborgensis” “Promineifilum breve” “Promineifilum” Muiribacterium halophilum Ts Kapaibacterium thiocyanatum Ts Kapaibacterium Ca. Branchiomonas cystocola “Methanosuratincola” “Methanosuratincola petrocarbonis” Ca. Methanomethylicus oleisabuli Ca. Methanomethylicus mesodigestus Ca. Methanomethylicus Ca. Methanomethylicia Cloacimonas Cloacimonas acidaminivorans Ts Ca. Izemoplasma acidinucleici Ca. Sulfuritelmatomonas Ca. Sulfuritelmatobacter Ca. Sulfuripaludibacter Kryptonium thompsonii Ts Ca. Caldarchaeum Ca. Methylumidiphilus alinenensis Ca. Altiarchaeum Ca. Carsonella ruddii Ca. Carsonella Ca. Methanofastidiosum methylothiophilum Ca. Methanofastidiosum “Methanofastidiosia” “Fermentibacterales” Ca. Fermentibacteraceae Ca. Fermentibacter Ca. Fermentibacter danicus “Fermentibacteria” Ca. Allofontibacter communis Ca. Allofontibacter
Subjects
Ecology, Evolution, Behavior and Systematics General Medicine Microbiology
Abstract
We here present annotated lists of names ofCandidatustaxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status ofCandidatustaxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names ofCandidatustaxa with additions and corrections to the current lists to be published periodically in theInternational Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of theCandidatusnames if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa

Citation
Oren, Garrity (2022). International Journal of Systematic and Evolutionary Microbiology 72 (1)
Names (115)
“Nardonella hylobii” “Nardonella dryophthoridicola” “Mycoplasma haematomelis” “Treponema suis” “Typhincola belonochilicola” “Vallotia japonica” “Vallotia laricis” “Anthektikosiphon” “Aminobacteroides” “Acidifodinimicrobium” “Abditibacter” “Undinarchaeaceae” “Thiobarbaceae” “Tepidaquicellaceae” “Nanohalobiaceae” “Nanogingivalaceae” “Magnetomoraceae” “Macinerneyibacteriaceae” “Hakubellaceae” “Fermentimicrarchaeaceae” “Chazhemtonibacteriaceae” “Aminobacteroidaceae” “Adiutricaceae” “Tepidaquicellales” “Nanohalobiales” “Nanogingivalales” “Naiadarchaeales” “Methylospongiales” “Macinerneyibacteriales” “Hakubellales” “Guanabaribacteriales” “Mycoplasma erythrocervae” “Methanoflorens crillii” “Mastigocoleus perforans” “Liberibacter brunswickensis” “Ischnodemia utriculi” “Halobeggiatoa borealis” “Forterrea multitransposorum” “Fibrimonas termitidis” “Finniella dimorpha” “Euplotella sexta” “Entotheonella gemina” “Fermentimicrarchaeales” “Desulfofervidales” “Adiutricales” “Endohaliclona renieramycinifaciens” “Ehrlichia shimanensis” “Ehrlichia regneryi” “Didemniditutus mandelae” “Desulfosporosinus infrequens” “Desulfopertinax cowenii” “Cytophaga massiliensis” “Cuticulibacterium kirbyi” “Clostridium timonense” “Clostridium massiliense” “Cibionibacter quicibialis” “Brocadia braziliensis” “Borrelia fainii” “Borrelia ivorensis” “Borrelia africana” “Bartonella rudakovii” “Bartonella negevensis” “Bartonella khokhlovae” “Bartonella gerbillinarum” “Undinarchaeia” “Syntrophaliphaticia” “Nanosyncoccia” “Nanoperiodontomorbia” “Nanohalobiia” “Macinerneyibacteriia” “Desulfofervidia” “Bandiella numerosa” “Azospirillum massiliense” “Arocatia carayonii” “Aramenus sulfurataquae” “Annandiella pinicola” “Annandiella adelgistsugae” “Anaerococcus timonensis” “Anaerococcus phoceensis” “Anaerococcus massiliensis” “Anadelfobacter sociabilis” “Acidiflorens stordalenmirensis” “Theodorhartigia” “Stammera” “Rubidus” “Roseilinea” “Reconciliibacillus” “Pleuronema” “Parafinniella” “Paracaedimonas” “Ozemibacter” “Nitrobium” “Neowolbachia” “Ischnodemia” “Forterrea” “Fibrimonas” “Euplotella” “Endohaliclona” “Didemniditutus” “Cuticulibacterium” “Cibionibacter” “Changshengia” “Arocatia” “Aramenus” “Annandiella” “Acidiflorens” “Ozemibacteraceae” “Fibrimonadaceae” “Ozemibacterales” “Methanoflorentales” “Fibrimonadales” “Caenarcanales” “Ozemibacteria” “Saccharimonadia” Elulimicrobiia
Subjects
Ecology, Evolution, Behavior and Systematics General Medicine Microbiology

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Citation
Gilroy et al. (2021). PeerJ 9
Names (94)
“Mediterraneibacter excrementigallinarum” “Ruthenibacterium merdavium” “Gemmiger stercoravium” “Eisenbergiella intestinipullorum” “Merdibacter merdavium” “Enterocloster excrementipullorum” “Borkfalkia stercoripullorum” “Gemmiger stercoripullorum” “Merdibacter merdigallinarum” “Intestinimonas stercoravium” “Limosilactobacillus intestinipullorum” “Mediterraneibacter pullistercoris” “Faecalibacterium gallistercoris” “Borkfalkia excrementigallinarum” “Mediterraneibacter stercoripullorum” “Anaerotignum merdipullorum” “Fusicatenibacter merdavium” “Anaerostipes excrementavium” “Blautia pullistercoris” “Hungatella pullicola” “Borkfalkia faecipullorum” “Acetatifactor stercoripullorum” “Mediterraneibacter vanvlietii” “Eisenbergiella stercoravium” “Butyricicoccus avistercoris” “Blautia stercorigallinarum” “Acutalibacter stercorigallinarum” “Mediterraneibacter excrementavium” “Corynebacterium faecigallinarum” “Phocaeicola excrementigallinarum” “Blautia merdavium” “Anaerostipes avistercoris” “Dietzia intestinigallinarum” “Mediterraneibacter faecigallinarum” “Mediterraneibacter faecipullorum” “Dietzia intestinipullorum” “Alistipes stercoravium” “Eisenbergiella merdavium” “Ligilactobacillus avistercoris” “Eisenbergiella merdigallinarum” “Nosocomiicoccus stercorigallinarum” “Mailhella merdavium” “Fournierella excrementigallinarum” “Fournierella merdavium” “Desulfovibrio gallistercoris” “Blautia merdipullorum” “Phocaeicola faecigallinarum” “Alistipes avicola” “Bariatricus faecipullorum” “Desulfovibrio intestinavium” “Brachybacterium merdavium” “Brevibacterium intestinavium” “Agathobaculum intestinipullorum” “Limosilactobacillus excrementigallinarum” “Mediterraneibacter merdigallinarum” “Fournierella merdigallinarum” “Mediterraneibacter pullicola” “Mediterraneibacter merdipullorum” “Microbacterium stercoravium” “Collinsella stercoripullorum” “Ligilactobacillus excrementavium” “Mucispirillum faecigallinarum” “Janibacter merdipullorum” “Lactobacillus pullistercoris” “Atopostipes pullistercoris” “Gemmiger excrementavium” “Fournierella merdipullorum” “Ruania gallistercoris” “Tidjanibacter faecipullorum” “Companilactobacillus pullicola” “Rothia avicola” “Rubneribacter avistercoris” “Sphingobacterium stercorigallinarum” “Intestinimonas merdavium” “Luteimonas excrementigallinarum” “Alistipes intestinigallinarum” “Tetragenococcus pullicola” “Eisenbergiella pullistercoris” “Agathobaculum merdavium” “Evtepia faecavium” “Barnesiella excrementavium” “Acutalibacter pullistercoris” “Anaerofilum excrementigallinarum” “Evtepia faecigallinarum” “Gemmiger excrementipullorum” “Anaerobiospirillum pullistercoris” “Acinetobacter avistercoris” “Limosilactobacillus merdigallinarum” “Desulfovibrio intestinigallinarum” “Blautia stercoravium” “Barnesiella excrementigallinarum” “Gemmiger faecavium” “Alectryobacillus” “Alectryobacillus merdavium”
Subjects
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Medicine General Neuroscience
Abstract
Background The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. Conclusions Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes

Citation
Chuvochina et al. (2023). FEMS Microbiology Letters
Names (42)
“Kapaibacteriia” “Cloacimonadaceae” “Cloacimonadales” “Cloacimonadia” “Methylomirabilota” “Desulforudaceae” “Thermobaculales” “Thermobaculaceae” “Tenderiales” “Tenderiaceae” “Saccharimonadales” “Saccharimonadaceae” “Puniceispirillales” “Puniceispirillaceae” “Pseudothioglobaceae” “Promineifilales” “Promineifilaceae” “Obscuribacteraceae” “Nucleicultricaceae” “Muiribacteriia” “Muiribacteriales” “Muiribacteriaceae” “Methylomirabilia” “Methylomirabilales” “Methylomirabilaceae” “Magnetobacteriaceae” “Kapaibacteriales” “Kapaibacteriaceae” “Johnevansiales” “Johnevansiaceae” “Hepatoplasmataceae” “Hepatobacteraceae” “Bipolaricaulia” “Bipolaricaulaceae” “Bipolaricaulales” “Azobacteroidaceae” “Hydrothermaceae” “Hydrothermales” “Hydrothermia” “Binatia” “Binatales” “Binataceae”
Subjects
Genetics Microbiology Molecular Biology
Abstract
Abstract The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted in a substantial number of changes to existing classifications (https://gtdb.ecogenomic.org). In the case of union of taxa, GTDB names were applied based on the priority of publication. The division of taxa or change in rank led to the formation of new Latin names above the rank of genus that were only made publicly available via the GTDB website without associated published taxonomic descriptions. This has sometimes led to confusion in the literature and databases. A number of the provisional GTDB names were later published in other studies, while many still lack authorships. To reduce further confusion, here we propose names and descriptions for 329 GTDB-defined prokaryotic taxa, 223 of which are suitable for validation under the International Code of Nomenclature of Prokaryotes (ICNP) and 49 under the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). For the latter we designated 23 genomes as type material. An additional 57 taxa that do not currently satisfy the validation criteria of either code are proposed as Candidatus.

Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site

Citation
Vázquez-Campos et al. (2021). Frontiers in Microbiology 12
Names (30)
Ca. Micrarchaeota Ca. Methanoperedens Ca. Methanoperedenaceae “Tiddalikarchaeum anstoanum” Ca. Tiddalikarchaeaceae “Gugararchaeum adminiculabundum” Ca. Gugararchaeaceae Ca. Gugararchaeum Ca. Gugararchaeales Ca. Burarchaeum Ca. Burarchaeum australiense Ca. Anstonella stagnisolia Ca. Burarchaeaceae Ca. Anstonellaceae Ca. Burarchaeales Ca. Bilamarchaeum Ca. Anstonella Ca. Bilamarchaeum dharawalense Ca. Bilamarchaeaceae Ca. Norongarragalina Ca. Anstonellales Ca. Norongarragalina meridionalis Ca. Micrarchaeaceae Ca. Norongarragalinaceae Ca. Micrarchaeales Ca. Norongarragalinales “Tiddalikarchaeum” Ca. Micrarchaeia Ca. Tiddalikarchaeales “Nanoarchaeia”
Subjects
Microbiology Microbiology (medical)
Abstract
During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and ‘Candidatus Methanoperedenaceae’ (ANME-2D). Within the undescribed DPANN, the newly proposed orders ‘Ca. Gugararchaeales’, ‘Ca. Burarchaeales’ and ‘Ca. Anstonellales’, constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the ‘Ca. Micrarchaeota’ phylum compared to most other DPANN. The analysis of new and extant ‘Ca. Methanoperedens spp.’ MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most ‘Ca. Methanoperedens’ also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and ‘Ca. Methanoperedens’, while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.

Distribution, abundance, and ecogenomics of the Palauibacterales , a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum

Citation
Aldeguer-Riquelme et al. (2023). mSystems
Names (25)
Palauibacter ramosifaciens Palauibacter polyketidifaciens Kutchimonas denitrificans Ts Carthagonibacter metallireducens Ts Palauibacter denitrificans Palauibacter irciniicola Palauibacter australiensis Palauibacter poriticola Palauibacter rhopaloidicola Palauibacter scopulicola Palauibacter soopunensis Ts Benthicola azotiphorus Indicimonas acetifermentans Ts Benthicola marisminoris Ts Caribbeanibacter nitroreducens Ts Humimonas hydrogenitrophica Ts Kutchimonas Indicimonas Carthagonibacter Caribbeanibacter Humimonas Benthicola Palauibacter Palauibacterales Palauibacteraceae
Subjects
Biochemistry Computer Science Applications Ecology, Evolution, Behavior and Systematics Genetics Microbiology Modeling and Simulation Molecular Biology Physiology
Abstract
ABSTRACT The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales . This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N 2 O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales . Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes , as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H 2 . Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.

New globally distributed bacterial phyla within the FCB superphylum

Citation
Gong et al. (2022). Nature Communications 13 (1)
Names (24)
“Blakebacteria” “Joyebacteria” “Arandabacterum” “Blakebacterales” “Joyebacterales” “Orphanbacterota” “Blakebacteraceae” “Joyebacteraceae” “Orphanbacteria” “Blakebacterum” “Joyebacterum” “Orphanbacterales” “Blakebacterum guaymasense” “Joyebacterum haimaense” “Orphanbacteraceae” “Blakebacterota” “Arandabacterum bohaiense” “Orphanbacterum” “Arandabacteria” “Arandabacterales” “Arandabacterota” “Arandabacteraceae” “Joyebacterota” “Orphanbacterum longqiense”
Subjects
General Biochemistry, Genetics and Molecular Biology General Chemistry General Physics and Astronomy Multidisciplinary
Abstract
AbstractMicrobes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.