Oren, Aharon

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.

Abstract Na.no.pe.trae'us. Gr. masc. n. nanos a dwarf; L. masc. adj. petraeus (from Gr. masc. adj. petraios ) living on or among the rocks; N.L. masc. n. Nanopetraeus small organism growing inside rocks. The originally proposed name Nanopetramus was corrected to Nanopetraeus . The genus Candidatus Nanopetraeus corrig. (originally named Candidatus Nanopetramus) was established based on a genome sequence found in the metagenome of halite endoliths sampled at Salar Grande in the northern Atacama Desert, Chile. A species name was not proposed. Candidatus Nanopetraeus is phylogenetically affiliated with members of the Ca . Nanohaloarchaeota branch ( Candidatus Haloredivivus, Candidatus Nanosalina, and Candidatus Nanosalinicola corrig.) of the archaeal DPANN superphylum. Analysis of the 1.1 Mb genome of Ca . Nanopetraeus SG9 with 46.4% DNA G + C suggests that the organism has a photoheterotrophic lifestyle, based on the presence of archaeal genes for carbohydrate metabolism and rhodopsin biosynthesis. The low median isoelectric point for the predicted proteins suggests a “salt‐in” strategy for osmotic balance. 16S rRNA gene sequences affiliated with Ca . Nanopetraeus were recovered from saltern ponds and hypersaline lakes worldwide. DNA G + C content (mol%) : 46.4 (metagenome‐assembled genome sequence). Type species : Not assigned. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanopetraeus is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / incertae sedis / incertae sedis / incertae sedis / Candidatus Nanopetraeus Candidatus Nanopetraeus could not be recovered in GTDB ** . * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Ha.lo.bo'num. Gr. masc. n. hals , halos salt; L. masc. adj. bonus good; N.L. neut. n. Halobonum a good salt organism. The genus Candidatus Halobonum with a single proposed species Candidatus Halobonum tyrrellense corrig. consists of extremely halophilic members of the haloarchaeal family Halorubraceae most closely related to the genus Halobaculum . The only isolate known was obtained from hypersaline surface waters of Lake Tyrrell, Victoria, Australia. In spite of the fact that a pure culture was isolated, Ca . Halobonum and Ca . Halobonum tyrrellense were described as Candidatus taxa. No cultures are currently available. Ca . Halobonum tyrrellense strain G22 was isolated on medium containing 235 g/l salt and with glycerol as the sole carbon source. Few phenotypic properties were reported. The genome size was estimated at 3,675,087 bp, with a DNA G + C content of 70.1 mol %. A putative sensory rhodopsin and a high number of ABC transporters and carbon metabolism genes were identified in the draft genome. 16S rRNA gene sequences affiliated with Ca . Halobonum were recovered from a hypersaline, ephemeral playa at the White Sands National Monument, New Mexico, USA, and from Chinese salt lakes and salterns. DNA G + C content (mol %) : 70.1 (genome sequence). Type species : Candidatus Halobonum tyrrellense. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Halobonum is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Halobacteria / Halobacteriales / Haloferacaceae / Candidatus Halobonum The genus Candidatus Halobonum can also be recovered in the Genome Taxonomy Database (GTDB) as g__Halobaculum (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Halobacteria / o__Halobacteriales / f__Haloferacaceae / g__Halobaculum * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Ha.lo.re.di.vi'vus. Gr. masc. n. hals , halos salt; L. masc. adj. redivivus renewed, renovated; N.L. masc. n. Haloredivivus a reconstructed salty organism. The genus Candidatus Haloredivivus was established based on a sequence of a single‐cell‐amplified genome recovered from a solar saltern pond of intermediate salinity in Spain. Ca . Haloredivivus is phylogenetically affiliated with members of the Candidatus Nanohaloarchaeota branch ( Candidatus Nanosalina, Candidatus Nanosalinicola corrig., and Candidatus Nanopetraeus corrig.) of the archaeal DPANN superphylum. Analysis of the ∼1.2 Mb genome of Ca . Haloredivivus with 42.1% G + C suggests that the organism leads a photoheterotrophic lifestyle and may be able to degrade different polysaccharides. The low median isoelectric point for the predicted proteins suggests a “salt‐in” strategy for osmotic balance. Gene sequences affiliated with Ca . Haloredivivus were recovered from a salt lake in Romania and from soda lakes in Siberia. DNA G + C content (mol%) : 42.0–42.1 (genome sequence). Type species : Not assigned. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Haloredivivus is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / Candidatus Nanohaloarchaea / incertae sedis / incertae sedis / Candidatus Haloredivivus Candidatus Haloredivivus could not be recovered in GTDB ** . * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Na.no.sa.li'na. Gr. masc. n. nanos dwarf; N.L. masc. adj. salinus salty; N.L. fem. n. Nanosalina a dwarf‐size salty organism. The genus Candidatus Nanosalina was established based on a sequence from a metagenome recovered from the hypersaline Lake Tyrrell in Victoria, Australia. Ca . Nanosalina is phylogenetically affiliated with members of the Candidatus Nanohaloarchaeota branch ( Candidatus Nanosalinicola corrig., Candidatus Nanopetraeus corrig., and Candidatus Haloredivivus) of the archaeal DPANN superphylum. On the basis of fluorescence in situ hybridization, cells are ∼0.6 μm in diameter. Analysis of the ∼1.23 Mb genome of Ca . Nanosalina J07AB43 with 43.5% DNA G + C suggests that the organism possesses an aerobic, photoheterotrophic lifestyle. The high proportion of acidic amino acids of the predicted proteins suggests a “salt‐in” strategy for osmotic balance. Gene sequences affiliated with Ca . Nanosalina have been recovered from coastal salterns in Australia and California, USA. DNA G + C content (mol%) : 43.5 (genome sequence). Type species : Not assigned. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanosalina is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / Candidatus Nanohaloarchaea / Candidatus Nanosalinales / Candidatus Nanosalinaceae / Candidatus Nanosalina Candidatus Nanosalina could not be recovered in GTDB ** . * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Na.no.sa.li.ni'co.la. Gr. masc. n. nanos dwarf; L. fem. pl. n. salinae saltworks; L. suff. –cola (from L. masc. or fem. n. incola ) inhabitant, dweller; N.L. masc. n. Nanosalinicola a dwarf‐sized organism inhabiting saltworks. The genus Candidatus Nanosalinicola corrig., originally described as Candidatus Nanosalinarum, was established based on a sequence from a metagenome recovered from the hypersaline Lake Tyrrell in Victoria, Australia. Ca . Nanosalinicola is phylogenetically affiliated with members of the Candidatus Nanohaloarchaeota branch ( Candidatus Nanosalina, Candidatus Nanopetraeus corrig., and Candidatus Haloredivivus) of the archaeal DPANN superphylum. On the basis of fluorescence in situ hybridization, cells are ∼0.6 μm in diameter. Analysis of the ∼1.22 Mb genome of Ca . Nanosalinicola J07AB56 with 56% DNA G + C suggests that the organism is an aerobic photoheterotroph. The high proportion of acidic amino acids of the predicted proteins suggests a “salt‐in” strategy for osmotic balance. Gene sequences affiliated with Ca . Nanosalinicola have also been recovered from coastal salterns in Australia and California, USA. DNA G + C content (mol%) : 56 (genome sequence). Type species : Not assigned. Genome sequence : AEIX00000000. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanosalinicola is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / Candidatus Nanohaloarchaea / incertae sedis / incertae sedis / Candidatus Nanosalinicola Candidatus Nanosalinicola could not be recovered in GTDB ** . * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

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.