Oren, Aharon

After the International Committee on Systematics of Prokaryotes (ICSP) had voted to include the rank of phylum in the rules of the International Code of Nomenclature of Prokaryotes (ICNP), and following publication of the decision in the IJSEM, we here present names and formal descriptions of 42 phyla to effect valid publication of their names, based on genera as the nomenclatural types.

Abstract Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood–Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b–3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H2-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.

Abstract Na.no.ha.lo'bi.um. Gr. masc. n. nanos a dwarf; Gr. masc. n. hals , halos salt; Gr. masc. n. bios life; N.L. neut. n. Nanohalobium small organism living in salt. The genus Candidatus Nanohalobium was established based on a genome sequence found after the enrichment, cultivation, and characterization of a binary association with its chitinolytic host, obtained from a crystallizer pond brine collected in the marine solar saltern Saline della Laguna of Trapani, Italy. Ca . Nanohalobium is phylogenetically affiliated with members of the Ca . Nanohaloarchaeota ( Candidatus Haloredivivus, Candidatus Nanosalina, and Candidatus Nanosalinicola) of the archaeal DPANN superphylum. Cultivation experiments and analysis of the 0.97 Mb genome of Ca . Nanohalobium constans LC1Nh revealed that the organism has an organoheterotrophic, sugar‐fermenting lifestyle, lacking key anabolic machinery and any respiratory complexes. Additionally, the cultivation experiments revealed a remarkable mutualism of a nanohaloarchaeon–haloarchaeon association, namely the nanohaloarchaeon's ability to hydrolyze glycogen and starch to glucose, enabling the growth of Halomicrobium sp. LC1Hm in the absence of chitin. The low‐median isoelectric point for the predicted proteins suggests a “salt‐in” strategy used by the nanohaloarchaeon for osmotic balance. 16S rRNA gene sequences affiliated with Ca . Nanohalobium were recovered from other saltern ponds and hypersaline lakes worldwide. DNA G + C content (mol%) : 43.2 (genome). Type species : Candidatus Nanohalobium constans , La Cono et al. 2020. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanohalobium is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / Candidatus Nanohalobiia / Candidatus Nanohalobiales / Candidatus Nanohalobiaceae / Candidatus Nanohalobium The genus Candidatus Nanohalobium can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nanohalobium (version v220) ** . GTDB classification: d__Archaea / p__Nanohaloarchaeota / c__Nanosalinia / o__Nanosalinales / f__Nanosalinaceae / g__Nanohalobium * 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

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.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.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