International Journal of Systematic and Evolutionary Microbiology

A Gram-positive, aerobic, non-motile coccoid bacterium, designated strain ZF39T, was isolated from a farm in Quandian Village, Zhengzhou City, Henan Province, China, and subjected to taxonomic characterization. Optimal growth occurred at 32 ℃, pH 7.0 and 0–1% NaCl (w/v). Mannose and glucose were identified as the sugar components in the whole-cell hydrolysates. The strain’s peptidoglycan type was classified as A3γ (ll-Dpm-Gly), and MK-9(H4) was identified as the predominant respiratory quinone. Aminoglycolipid, aminophospholipid, glycolipids, phosphatidylglycerol and phospholipid were detected as the major polar lipids. The predominant cellular fatty acids were anteiso-C15 : 0 (48.7%) and iso-C15 : 0 (20.2%). Phylogenetic analysis based on 16S rRNA gene sequences placed strain ZF39T within the family Propionibacteriaceae. The strain formed a distinct genetic lineage adjacent to the genus Desertihabitans, with 16S rRNA gene sequence similarities of 94.70% to Desertihabitans aurantiacus CPCC 204711T and 94.56% to Desertihabitans brevis KCTC 49116T. The genomic G+C content was 67.7 mol%. Genome comparisons revealed that the average nucleotide identity values between strain ZF39T and D. aurantiacus CPCC 204711T, D. brevis KCTC 49116T, Granulicoccus phenolivorans DSM 17626T were 72.50%, 71.98% and 72.36%, respectively. Moreover, phylogenetic analysis and phenotypic characterization supported the classification of strain ZF39T as a novel species of a new genus within the family Propionibacteriaceae. The name Ammonicoccus fulvus gen. nov., sp. nov. is proposed, with ZF39T (=CGMCC 1.60047T=KCTC 59250T=MCCC 1K08851T) as the type strain.

Bacterial strain SL12-8T was characterized and isolated from the skin microbiota of Pelophylax perezi, the Perez’s frog. Strain SL12-8T stained Gram-negative and formed rod-shaped cells that grew optimally at 25 °C and pH 7.0–7.5. The G+C content of the DNA was 66.2 mol%. Ubiquinone 8 was the respiratory quinone identified in the studied strain and the most closely related taxon. The major fatty acids were summed in feature 3 and summed in feature 8 and C16:0, representing 84% of the total fatty acids. Phylogenetic analyses based on the 16S rRNA gene sequence placed strain SL12-8T within the order Burkholderiales in a distinct lineage. The 16S rRNA gene sequence similarities of strain SL12-8T to that of Rubrivivax albus, Scleromatobacter humisilvae, Piscinibacter aquaticus, Azohydromonas caseinilytica and Aquincola agrisoli were 94.41, 94.08, 93.72, 93.72 and 93.64%, respectively. The draft genome sequence of strain SL12-8T comprises 3,115,197 bases with a 313-fold mapped genome coverage. The assembled genome consists of 53 large contigs with more than 500 bp, and the genome encodes 2,814 putative coding sequences. The analysis of the available genomes from the closest genera showed 124 core genes that reveal a novel genus-level clade including the strain SL12-8T. Analysis of the SL12-8T genome revealed the presence of the beta-lactone and terpene biosynthetic gene clusters. The phylogenomic, phylogenetic, phenotypic and chemotaxonomic data showed that strain SL12-8T (=UCCCB 131T=CECT 30762T) represents the type of a novel species and genus, for which we propose the name Amphibiibacter pelophylacis gen. nov., sp. nov.

The strain TOYAMA8T is a deep-sea alkaliphilic cellulolytic bacterium isolated from a slurry-adhered epiphytic site of Megalodicopia hians. Cells of this strain are Gram-negative, aerobic, curved rods or spirilla, motile with monopolar flagella, and grow on cellulose as the sole carbon source. Compared to other closely related species, this bacterium is characterized by a large number of cellulase genes. Strain TOYAMA8T showed alkaliphilic growth within the pH range 7.5–9.0. The major cellular fatty acids were C18 : 1 ω7, C14 : 0, C16 : 0 and C16 : 1 ω7. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipids and aminolipids. A major respiratory lipoquinone was Q-9. Phylogenomic analysis using the 16S rRNA gene and whole-genome sequence data showed that the strain is related to the families Gynuellaceae, Saccharospirillaceae and Natronospirillaceae. The values of 16S rRNA gene sequence similarity, amino acid identity and percentage of conserved proteins between the strain TOYAMA8T and related species were low, with maximum values of 90.6, 48.1 and 34.6%, respectively. These results, together with differences in phenotypic and biochemical characteristics, indicate that the new isolate TOYAMA8T represents a novel genus and species, for which the name Marinicellulosiphila megalodicopiae gen. nov., sp. nov., is proposed. The type strain is TOYAMA8T (JCM 31119T=DSM 114864T).

Phylogenetic analysis of the genus Aureimonas, utilizing both 16S rRNA gene sequences and comprehensive whole-genome data, revealed its polyphyletic nature, necessitating a revision to accommodate phylogenetically distinct species. Based on established threshold values for genus demarcation – specifically, 16S rRNA gene similarity, Average Amino Acid Identity and Percentage of Conserved Proteins – a notably substantial divergence was observed within the genus Aureimonas, and the division of Aureimonas into four distinct genera is strongly supported. To address this, we propose the establishment of four new genera: Dennerimonas gen. nov., Mesocryomonas gen. nov., Rathsackimonas gen. nov. and Plantimonas gen. nov. These classifications accommodate species that are significantly divergent from the type species of Aureimonas, thereby more accurately reflecting their distinct evolutionary lineages. Additionally, Aureimonas glaciistagni is proposed to be reclassified within the genus Jiella as Jiella glaciistagni comb. nov. based on phylogenetic evidence indicating a closer evolutionary relationship to Jiella species than to other members of Aureimonas. Our analysis, which included assessments of 16S rRNA gene similarity, Average Nucleotide Identity, and digital DNA–DNA hybridization values exceeding species delineation thresholds, further supports the reclassification of Jeongeupella Jiang et al. 2024 as a later heterotypic synonym of Antarcticirhabdus Du et al. 2023.

An anaerobic isolate, designated me31T, was isolated from pit mud in Yibin, Sichuan Province, PR China. Phylogenetic results based on 16S rRNA gene sequence showed that strain me31T belongs to the family Dysgonomonadaceae, and the most closely related isolated relatives were Seramator thermalis SYSU GA16112T (93.65%) and Proteiniphilum propionicum JNU-WLY501T (93.22%). The DNA G+C content was 44.26 mol%. The ANI and AAI values between strain me31T and the closely related strains were 69.25–71.18% and 69.59–71.15%, respectively. Cells of strain me31T were Gram-stain-negative, rod-shaped and non-motile. Growth of strain me31T was observed at 25–37 °C, pH 6.0–8.0 and a salt tolerance range of 0–1.0% (w/v). The predominant respiratory quinone was MK-9. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and C17 : 0 2OH. The polar lipids of strain me31T were found to consist of phosphatidylethanolamine, three unidentified phospholipids, three unidentified phosphoglycolipids, one unidentified phosphoglycolipid, one unidentified lipid, two unidentified glycolipids and one aminophosphoglycolipid. According to the results of morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic analysis, strain me31T represents a novel species of a novel genus of the family Dysgonomonadaceae, for which the name Limibacterium fermenti gen. nov., sp. nov. is proposed. The type strain is me31T (=GDMCC 1.4237T=KCTC 25756T=WMCC 10035T).

A taxonomic study was conducted on four bacterial strains isolated from the soil of a coking plant. Phylogenetic analysis showed that the four strains belonged to three families: Comamonadaceae, Micrococcaceae and Roseiarcaceae. Identification of the 16S rRNA gene exhibited that their sequence similarities were between 94.96 and 98.98% when compared to known and validly nominated species. Their genomes ranged from 3.4 to 7.2 Mb, with DNA G+C molar contents varying from 62.3 to 67.2%. The average nucleotide identities ranged from 71.4 to 92.3%, and digital DNA–DNA hybridization values were 19.7–47.0% when comparing them with closely related type species, supporting the classification of these four strains. Functional analysis demonstrated that strain H3Y2-7T was robustly resistant to chromate (VI) and arsenite (III) and was able to grow on aromatic compounds including naphthalene as carbon sources even in the presence of chromate (VI). These features reflect its ability to treat combined pollutants and adapt to a polluted environment. Based on the analysis of polyphasic taxonomy, we propose the four bacterial strains representing novel species, namely Curvibacter soli sp. nov. (type strain H39-3-26T=JCM 36178T=CGMCC 1.61344T), Extensimonas soli sp. nov. (type strain H3M7-6T=JCM 36176T=CGMCC 1.61336T), Pseudarthrobacter naphthalenicus sp. nov. (type strain H3Y2-7T=JCM 36482T=CGMCC 1.61323T) and Terripilifer ovatus gen. nov., sp. nov. (type strain H3SJ34-1T=JCM 36465T=CGMCC 1.61333T).

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).

Opinion 131 addresses a Request for an Opinion asking the Judicial Commission to conserve the genus name Proteus Hauser 1885 (Approved Lists 1980) over its earlier homonym, the protozoan genus name Proteus Müller 1786. The Judicial Commission agrees that the later homonym is illegitimate and that the replacement of the prokaryotic name Proteus would be undesirable. It is also concluded that Proteus Müller 1786 is an objectively invalid name under the International Code of Zoological Nomenclature. Judicial Opinions 9, 12 and 130 serve as precedents for the conservation of Proteus Hauser 1885 (Approved Lists 1980) over Proteus Müller 1786. This action is taken here and makes the prokaryotic name Proteus legitimate.

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).

In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly characterized, leaving a major knowledge gap in microbial ecology. We recently discovered a novel cross-domain symbiosis between Ca. Patescibacteria and Archaea in highly purified enrichment cultures and proposed Candidatus taxa for the characterized species, including Ca. Minisyncoccus archaeophilus and the corresponding family Ca. Minisyncoccaceae. In this study, we report the isolation of this bacterium, designated strain PMX.108T, in a two-strain co-culture with a host archaeon, Methanospirillum hungatei strain DSM 864T (JF-1T), and hereby describe it as the first representative species of Ca. Patescibacteria. Strain PMX.108T was isolated from mesophilic methanogenic sludge in an anaerobic laboratory-scale bioreactor treating synthetic purified terephthalate- and dimethyl terephthalate-manufacturing wastewater. The strain could not grow axenically and is obligately anaerobic and parasitic, strictly depending on M. hungatei as a host. The genome was comparatively large (1.54 Mbp) compared to other members of the clade, lacked some genes involved in the biosynthesis pathway and encoded type IV pili-related genes associated with the parasitic lifestyle of ultrasmall microbes. The G+C content of the genomic DNA was 36.6 mol%. Here, we report the phenotypic and genomic properties of strain PMX.108T; we propose Minisyncoccus archaeiphilus gen. nov., sp. nov. to accommodate this strain. The type strain of the species is PMX.108T (=JCM 39522T). We also propose the associated family, order, class and phylum as Minisyncoccaceae fam. nov. Minisyncoccales nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. within the bacterial kingdom Bacillati.