Hugenholtz, Philip


Publications
30

Proposal of Patescibacterium danicum gen. Nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. Nov

Citation
Dutkiewicz et al. (2024). ISME Communications
Names
“Patescibacterium danicum” Ca. Patescibacteria “Patescibacteriota” “Patescibacteriia” “Patescibacteriales” “Patescibacteriaceae” “Patescibacterium”
Abstract
Abstract Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities and dependence on other prokaryotic hosts. Despite the prevalence of the name Ca. Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes (ICNP) and lacks a nomenclatural type. Here, we rectify this situation by describing two closely

Draft genome sequence of two “Candidatus Intestinicoccus colisanans” strains isolated from faeces of healthy humans

Citation
Zhou et al. (2023). BMC Research Notes 16 (1)
Names
Intestinicoccus colisanans Ts Intestinicoccus
Abstract
Abstract Objectives In order to provide a better insight into the functional capacity of the human gut microbiome, we isolated a novel bacterium, “Candidatus Intestinicoccus colisanans” gen. nov. sp. nov., and performed whole genome sequencing. This study will provide new insights into the functional potential of this bacterium and its role in modulating host health and well-being. We expect that this data resource will be useful in providing additional insight in

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
Methyloligellaceae Rhodomicrobiaceae Leptospiria Alicyclobacillia Natranaerobiia Jeotgalibacillaceae Brevinematia Amphibacillaceae Chitinimonas Chitinimonadaceae Marinicellaceae Ahniellaceae Pseudohongiellaceae Methanoculleaceae Methanofollaceae Methanosphaerulaceae Methanocellia Methanosarcinia Methanonatronarchaeia Methanoliparia Halobacteriota Exiguobacteriales Exiguobacteriaceae Salinicoccaceae Staphylococcales Gemellaceae Thermicanales Thermicanaceae Neiellaceae Oceanococcaceae Wohlfahrtiimonadaceae Thermaerobacteria Thermaerobacterales Thermaerobacteraceae Sedimentibacteraceae Proteiniboraceae Monoglobaceae Monoglobales Lutisporaceae Lutisporales Lachnospirales Christensenellales Caldicoprobacterales Caldicellulosiruptoraceae Caldicellulosiruptorales Oxobacteraceae Caloramatoraceae Acetivibrionaceae Acetivibrio Acetivibrionales Clostridiisalibacter Clostridiisalibacteraceae Caldisalinibacter Dethiosulfatibacteraceae Thermincolales Thermincolia Carboxydocellales Carboxydocellaceae Tindalliaceae Thermotaleaceae Natronincolaceae Filifactoraceae Caminicellaceae Anaerovoracaceae Peptostreptococcales Acidaminobacteraceae Mahellales Mahellaceae Thermosulfidibacterota Thermosulfidibacteria Thermosulfidibacterales Thermosulfidibacteraceae Elainellaceae Elainellales Phormidesmidaceae Phormidesmidales Hydrogenothermales Desulfurobacteriia “Paceibacteria” Vampirovibrionaceae Vampirovibrionales Vampirovibrionia Binataceae Binatales Binatia Hydrothermia Hydrothermales Hydrothermaceae Azobacteroidaceae Bipolaricaulales Bipolaricaulaceae Bipolaricaulia Hepatobacteraceae Hepatoplasmataceae Johnevansiaceae Johnevansiales Kapaibacteriaceae Kapaibacteriales Magnetobacteriaceae Methylomirabilaceae Methylomirabilales Methylomirabilia Muiribacteriaceae Muiribacteriales Muiribacteriia Nucleicultricaceae Obscuribacteraceae Promineifilaceae Promineifilales Pseudothioglobaceae Puniceispirillaceae Puniceispirillales Saccharimonadaceae Saccharimonadales Tenderiaceae Tenderiales Thermobaculaceae Thermobaculales Desulforudaceae Methylomirabilota Cloacimonadia Cloacimonadales Cloacimonadaceae Kapaibacteriia “Poriferisulfidales” Leptolyngbyaceae
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

SeqCode: a nomenclatural code for prokaryotes described from sequence data

Citation
Hedlund et al. (2022). Nature Microbiology
Names
Kryptonium mobile Kryptoniaceae Kryptoniia Kryptoniales
Abstract
AbstractMost prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is s

Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations

Citation
Ji et al. (2021). The ISME Journal 15 (9)
Names
“Eremiobacterota” “Mawsoniella” “Mawsoniella australis” “Cryoxeromicrobium” “Cryoxeromicrobium davisii” “Nyctobacter” “Nyctobacter psychrophilus” “Erabacter” “Erabacter solicola” “Hesperobacter” “Hesperobacter lustricola” “Meridianibacter” “Meridianibacter frigidus” “Aquilonibacter” “Aquilonibacter stordalenmirensis” “Tyrphobacter” “Tyrphobacter aquilonaris” “Tumulicola” “Tumulicola scandinaviensis” “Cybelea” “Cybelea septentrionalis” “Cybelea tumulisoli” “Cybelea tyrphae” “Cybelea palsarum” “Palsibacter” “Palsibacter borealis” “Hemerobacter” “Hemerobacter limicola” “Velthaea” “Velthaea versatilis” “Lustribacter” “Lustribacter caenicola” “Lustribacter telmatis” “Elarobacter” “Elarobacter winogradskyi” “Elarobacter vanleeuwenhoeki” “Elarobacter pasteuri” “Elarobacter beijerinckii” “Tityobacter” “Tityobacter terrigena” “Xenobium” “Xenobium occultum” “Bruticola” “Bruticola papionis” “Xenobium purgamenti” “Xenobiaceae” “Eremiobacterales” “Eremiobacteraceae” “Eremiobacter” “Eremiobacter antarcticus” “Eremiobacteria” “Zemelea palustris” “Zemelea” “Xenobiales” “Xenobiia”
Abstract
Abstract Candidatus phylum Eremiobacterota (formerly WPS-2) is an as-yet-uncultured bacterial clade that takes its name from Ca. Eremiobacter, an Antarctic soil aerobe proposed to be capable of a novel form of chemolithoautotrophy termed atmospheric chemosynthesis, that uses the energy derived from atmospheric H2-oxidation to fix CO2 through the Calvin-Benson-Bassham (CBB) cycle via type 1E RuBisCO. To elucidate the phylogenetic affiliation and metabolic capacities of Ca. Eremioba

Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient‐poor Antarctic soils

Citation
Montgomery et al. (2021). Environmental Microbiology 23 (8)
Names
Dormibacter Dormibacter spiritus Ts Dormibacter inghamiae Nephthysia Nephthysia bennettiae Ts Aeolococcus gillhamiae Ts Amunia Amunia macphersoniae Ts Aeolococcales Aeolococcaceae Aeolococcus “Dormibacteria” “Dormibacterota”
Abstract
SummaryCandidatus Dormibacterota is an uncultured bacterial phylum found predominantly in soil that is present in high abundances within cold desert soils. Here, we interrogate nine metagenome‐assembled genomes (MAGs), including six new MAGs derived from soil metagenomes obtained from two eastern Antarctic sites. Phylogenomic and taxonomic analyses revealed these MAGs represent four genera and five species, representing two order‐level clades within Ca. Dormibacterota. Metabolic reconstructions

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 “Jordiarchaeum” “Jordiarchaeum madagascariense” “Sifarchaeaceae” “Jordiarchaeaceae” “Sifarchaeales” “Jordiarchaeales” “Sifarchaeia” “Jordiarchaeia” “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,

Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities

Citation
Waite et al. (2020). International Journal of Systematic and Evolutionary Microbiology 70 (11)
Names
Myxococcia Polyangiia Pseudobdellovibrionaceae Bdellovibrionota Oligoflexia “Desulfofervidales” Ca. Desulfofervidaceae Ca. Desulfofervidus “Desulfofervidia” Ca. Magnetomorum “Magnetomoraceae” “Adiutricaceae” Ca. Adiutrix Myxococcota “Adiutricales”
Abstract
The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria , it rarely affiliates with other proteobacterial classes and is freque