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A motile, rod-shaped and anaerobic strain WK13T was isolated from a secondary root canal infection of a human tooth. WK13T cells were Gram-stain-negative, catalase-positive and oxidase-negative. The major fatty acids (≥ 5.0%) were C16 : 0, C18 : 0, C16 : 1  ω7c, C18 : 1  ω9c and C18 : 2  ω6,9c. The DNA G+C content was 57.94 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol, phosphatidylcholine and lysophosphatidylcholine. There were no respiratory quinones detectable. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WK13T belongs to the class Betaproteobacteria. WK13T showed a 93.6% and 93.5% 16S rRNA gene sequence similarity to the most closely related cultured species, Propionivibrio pelophilus strain DSM 12018T and Propionivibrio dicarboxylicus strain DSM 5885T, respectively. On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class Betaproteobacteria, for which we propose the name Dentiradicibacter hellwigii gen. nov., sp. nov. The type strain is WK13T (=DSM 112713T=NCTC 14938T).

Understanding the characteristics of microbes during long-term space missions is essential for safeguarding the health of astronauts and maintaining the functionality of spacecraft. In this study, a Gram-positive, aerobic, spore-forming, rod-shaped strain JL1B1071T was isolated from the surface of hardware on the China Space Station. This strain belongs to the genus Niallia, with its closest relative being Niallia circulans ATCC 4513T. The genome of JL1B1071T is 5 166 230 bp in size, with a G+C content of 35.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between JL1B1071T and N. circulans ATCC 4513T are 83.3 and 27.5%, respectively, both below the recommended thresholds for species delineation. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0. The major quinone was menaquinone-7 (MK-7). Notably, strain JL1B1071T demonstrates a unique ability to hydrolyse gelatin, suggesting that it can utilize gelatin as a substrate in nutrient-limited environments. Genomic analysis of JL1B1071T revealed two conserved signature indels in the GAF domain-containing protein and DNA ligase D protein, which are specific to the genus Niallia. Additionally, structural and functional differences in proteins BshB1 and SplA were identified, which may enhance biofilm formation, oxidative stress response and radiation damage repair, thereby aiding its survival in the space environment. Based on phenotypic, physiological and chemotaxonomic characteristics, as well as genome annotation, strain JL1B1071T was considered a novel species within the genus Niallia and is proposed to be named Niallia tiangongensis sp. nov. The type strain is JL1B1071T (=GDMCC 1.4642=KCTC 43715).

Two Gram-stain-negative, facultative anaerobic, rod-shaped and non-gliding bacteria, designated as HL-DH10T and HL-DH14, were isolated from the halophyte Suaeda japonica in a mudflat, Republic of Korea. Based on the results of 16S rRNA gene pairwise analysis, the two isolates were the members of the family Flavobacteriaceae, and Aestuariibaculum suncheonense SC17T was the most closely related to strains HL-DH10T and HL-DH14 with 96.3% and 95.4% sequence similarity, respectively. The average nt identity and digital DNA–DNA hybridization values between strains HL-DH10T and HL-DH14 and other related species were all less than 79.2% and 21.9%, respectively. The genomic DNA G+C contents of strains HL-DH10T and HL-DH14 were 32.0% and 31.5%, respectively. Cells of these strains showed optimal growth at 25 °C, pH 6.5–7.0 and 2.5–4.0% (w/v) sea salts. The major respiratory quinone was menaquinone-6. The major cellular fatty acids were iso-C15:0 (14.0–16.0%), iso-C15:1 G (10.0–12.0%), iso-C17:0 3-OH (12.4–13.9%), iso-C15:0 3-OH (11.8–14.9%) and anteiso-C15:0 (9.4–10.6%). The polar lipids consisted of phosphatidylethanolamine, an unidentified aminophospholipid, two to three unidentified aminolipids and three unidentified lipids. The comprehensive phylogenetic, genomic, phenotypic and chemotaxonomic results indicate that strains HL-DH10T and HL-DH14 are considered to represent a novel genus of Flavobacteriaceae. Hence, we propose the novel genus Thalassobellus suaedae gen. nov., sp. nov. The type strain is HL-DH10T (=KCCM 90512T=JCM 36598T).

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as HZG-20T, was isolated from a tidal flat in Zhoushan, Zhejiang Province, China. The 16S rRNA sequence similarities between strain HZG-20T and Pikeienuella piscinae RR4-56T, Coraliihabitans acroporae NNCM2T, Parvibaculum indicum P31T and Zhengella mangrovi X9-2-2T were 98.9, 91.7, 91.0 and 91.0%, respectively. Colonies of strain HZG-20T were 1.4 mm in diameter, milky white, round, smooth and convex after cultivating on marine agar at 30 °C for 48 h. Cells were catalase and oxidase-negative. Growth occurred at 15–37 ℃ (optimum, 28 ℃), pH 5.0–9.0 (optimum, pH 6.0–8.0) and with 0–8% (w/v) NaCl (optimum, 1–3%). It contained Menaquinone-8 (H2) as the sole respiratory quinone, and C16:0 (11.8–13.6%), C18:1  ω9c (6.8–13.3%) and C15:0 anteiso (10.9–27.7%) as the major cellular fatty acids. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid, one unidentified phosphoglycolipid, two unidentified glycolipids (GL1–GL2) and three unidentified lipids (L1–L3). The genome of strain HZG-20T was 3 835 886 bp in length, comprised 3746 protein-coding genes, with DNA G+C content of 67.1 mol%. The phylogenetic and phylogenomic trees indicated that strain HZG-20T formed an independent and stable clade with P. piscinae RR4-56T. However, the average nucleotide identity, digit DNA–DNA hybridization and average amino acid identity values between strain HZG-20T and P. piscinae RR4-56T, C. acroporae NNCM2T, P. indicum P31T and Z. mangrovi X9-2-2T were 81.6, 71.1, 68.7 and 69.5%; 23.0, 18.5, 17.9 and 17.5%; and 78.2, 56.8, 56.5 and 61.9%, respectively, together with distinct chemotaxonomic features, indicating strain HZG-20T should not be assigned to known genera. As a result, a novel species of a novel genus within the family Paracoccaceae, designated as Paludibacillus litoralis gen. nov., sp. nov., was proposed. The type strain is HZG-20T (MCCC 1K08468T=KCTC 82692T).

Abstract Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.

Abstract Ba.be.lo'ta. N.L. fem. n. Babela , a Candidatus genus name; L. neut. pl. n. suff. ‐ ota , ending to denote a phylum; N.L. neut. pl. n. Babelota , the Candidatus Babela phylum. Candidatus Babelota is a phylum of strictly intracellular bacteria, currently divided into two class‐level groups and at least five orders based on 16S rRNA sequence analyses. However, all known biological isolates to date belong to the same order of the Babelales, within the Babelia class. Presently, four isolates representing three families have been described and maintained in laboratory cultures through the cultivation of their hosts, which are known to be amoeboid and flagellated protists. Genomic analysis of Ca . Babelota consistently reveals a profound reduction in metabolic capabilities, suggesting a phylum‐wide, conserved parasitic lifestyle. To date, all lineages covered by genomic data indicate that parasitism is a defining trait of this phylum. Ca . Babelota exhibits a cosmopolitan environmental distribution, with sequences detected across a spectrum of habitats including soil, freshwater, and saline or hypersaline water bodies. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the phylum Candidatus Babelota is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / incertae sedis / Candidatus Babelota The phylum Candidatus Babelota can also be recovered in the Genome Taxonomy Database (GTDB) as p__Dependentiae (version v220) ** . GTDB classification: d__Bacteria / p__Dependentiae * 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

A Gram-stain-negative, non-spore-forming, rod-shaped, obligately anaerobic bacterium, designated strain BP47G, was isolated from the hindgut of a silver drummer (Kyphosus sydneyanus) fish collected from the Hauraki Gulf, New Zealand. Phylogenetic analysis based on the 16S rRNA gene sequence of the isolate indicated that it belonged to the family Oscillospiraceae in the phylum Bacillota. The gene sequence of BP47G was most similar to Oscillibacter valericigenes with 95.23% sequence identity. Isolate BP47G grew on agar medium containing mannitol and fish gut fluid as the sole carbon sources. Clear colonies of ~1 mm diameter grew within a week at 20–28 °C (optimum 28 °C) and pH 7.1–8.5 (optimum 8.5). BP47G tolerated the addition to the medium of up to 1% NaCl. Formate and butyrate were the major fermentation products. The major cellular fatty acids were C12:0, C13:0, iso-C14:0, C16:0 and C16:1 cis 7. Genomic analyses comparing BP47G with its closest relatives indicated low genomic relatedness based on the average nucleotide identity, average amino acid identity, percentage of conserved protein and in silico DNA–DNA hybridization. Supported by the phenotypic and taxonomic characteristics observed in this study, a novel genus and species Bengtsoniella intestinalis gen. nov., sp. nov. is proposed for isolate BP47G (=ICMP 24688=JCM 35770).

A hydrogenotrophic methanoarchaeon, designated strain FWC-SCC4T, was isolated from cold seep sediment of Four-Way Closure Ridge, offshore southwestern Taiwan. Strain FWC-SCC4Tutilizes H2/CO2 or formate, but not acetate, secondary alcohols, methylamines, methanol or ethanol for growth and methane production. Yeast extract is required for growth. The cell morphology is coccoid, with a diameter of 0.8–1.2 µm, and the cell envelope is composed of S-layer protein with Mr about 137.00 kDa. Cells possess multiple flagella and usually occur singly. Strain FWC-SCC4T grows at a temperature range of 20–40 °C (optimum 37 °C) and a pH range of 5.4–7.2 (optimum 7.0). The NaCl range for growth is 0–0.86 M (optimum 0.09 M). The result of phylogenetic analysis of 16S rRNA gene sequences indicates that the most closely related species are Methanoplanus limicola M3T and Methanoplanus endosymbiosus MC1T, with similarities of 95.95 and 95.63%, respectively. The G+C content of the genomic DNA is 40.3 mol%. The overall genome-relatedness indexes (OGRIs) and concatenated ribosomal protein (RBP) phylogenic analysis indicate that strain FWC-SCC4T is a novel lineage of Methanomicrobiaceae. In addition to strain FWC-SCC4T, the differences between Methanomicrobium antiquum MobHT and Methanomicrobium mobile BPT demonstrated by comparative analysis of genomic G+C content and phylogenetic analysis with non-type strain genomes are enough to support the establishment of a novel genus. In conclusion, strain FWC-SCC4T (BCRC AR10058T= NBRC 114595T) is proposed as the type strain of Methanochimaera problematica gen. nov., sp. nov., and Methanoeremita antiquus gen. nov., comb. nov. is proposed as the new name for Methanomicrobium antiquum MobHT (=DSM 21220T= NBRC 104160T).

A Gram-negative, obligatory anaerobic, chemoheterotrophic bacterium, designated strain IA91T, was isolated from sediments and formation water from deep aquifers in Japan. IA91T derives its peptidoglycan, energy and carbon from exogenous cell wall fragments, namely muropeptides, released from actively reproducing bacteria, and is dependent on other bacteria for cell wall formation, growth and even cell shape: IA91T is irregular rod-shaped but coccoids when muropeptide is absent. IA91T grew in a temperature range of 25–45 °C with optimum growth at 40 °C. IA91T utilized limited substrates, yeast extract, muropeptides and d-lactate. The major end products from yeast extract degradation were acetate, hydrogen and carbon dioxide. Co-cultivation with a hydrogen-scavenging methanogenic archaeon promoted IA91T growth. No anaerobic respiration with nitrate, nitrite, sulphate or Fe(III) was observed. The major cellular fatty acids are C16 : 0, C18 : 1 trans9, C18 : 0 and C17 : 0. The G+C content of the genomic DNA was 45.6 mol%. Phylogenetic analysis based on 16S rRNA gene and conserved protein sequences involved in replication, transcription and translation indicated that IA91T belonged to the candidate phylum Marine Group A (MG-A, SAR406 or Ca. Marinimicrobia) with no cultivated representatives. Based on the phenotypic and phylogenomic characteristics, a new genus and species, Fidelibacter multiformis gen. nov., sp. nov., is proposed for IA91T (= JCM 39387T = KCTC 25736T). In addition, a new bacterial phylum named Fidelibacterota phyl. nov. is proposed for the candidate phylum MG-A represented by F. multiformis and Fidelibacteraceae fam. nov., Fidelibacterales ord. nov. and Fidelibacteria classis nov.