Three previously uncharacterized bacterial species, designated strains BD586, BD613 and BD626, isolated from human clinical specimens, were identified at Mayo Clinic, Rochester, Minnesota, USA. Initial identification efforts using matrix-assisted laser desorption ionization-time-of-flight MS and partial 16S rRNA gene sequencing proved inconclusive. Comprehensive analysis involving phenotypic characterization, biochemical assays and whole-genome sequencing was undertaken. The isolates were Gram-negative, motile, facultatively anaerobic rods, occurring singly, in pairs and in short chains; BD613 additionally formed small aggregates. The isolates tested positive for catalase and negative for oxidase. Their colonies appeared smooth, white, opaque and non-haemolytic. Growth was observed at 35 °C under aerobic, anaerobic and CO₂-enriched conditions, as well as in media with NaCl concentrations up to 10% and at pH 7-9. Phylogenetic relationships were inferred from core gene alignments, average nucleotide identity and digital DNA-DNA hybridization comparisons. Results confirmed the placement of BD586, BD613 and BD626 within the recently established genus, while also indicating their novelty as distinct species. The major cellular fatty acids were C and C cyclo. Based on these findings, a formal description of three new species, sp. nov. (type strain BD586=TSD 474, =NCTC 15089, =DSM 119465), sp. nov. (type strain BD613=TSD 475, =NCTC 15090, =DSM 119466) and sp. nov. (type strain BD626=TSD 476, =NCTC 15091, =DSM 119479), is proposed, and the genus description of is emended to refine its genomic, morphological and chemotaxonomic boundaries.

In the present study, genome-based metrics, phylogenetic and pangenomic analyses were used to investigate the relationship between three closely related species within the genus (, and ). While 16S rRNA gene comparison revealed high similarity, overall genomic relatedness indices, including digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI), exceeded the species delineation thresholds (ANI: 95-96 %, dDDH: 70%), indicating an even closer genetic relationship. Additionally, the phylogenomic analysis, along with pan-genome analysis, further supported the close relationship, placing the three species in a well-supported branch with a significant proportion of 3,809 shared core genes. Based on the combined evidence from genomic and phenotypic comparison, we propose reclassifying Daroonpunt 2016 and Khelaifia 2023 as later heterotypic synonyms of (Garabito 1997) Heyrman 2003. This study underscores the effectiveness of genome-based methods for accurate and reliable bacterial classification.

A marine bacterium capable of degrading alginate, designated as strain TSD2052, was isolated from a tidal flat sediment sample collected in Taean County, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TSD2052 belonged to the genus showing 96.2-97.8% sequence similarity. The whole genome of strain TSD2052 was 4.62 Mb, with a DNA G+C content of 44.3 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain TSD2052 and all genome-sequenced species of the genus were below 76.7%, 81.7% and 20.6%, respectively, indicating values lower than the standard cut-off for species delineation. Growth was observed at 10-35 °C (optimum 25 °C), pH 6-10 (optimum pH 8) and 1-5% (w/v) NaCl (optimum 3%). The major fatty acids (>10%) were C, C, summed feature 3 (C 6 and/or Cω) and summed feature 8 (C 6 and/or Cω). The respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and four unidentified lipids. Based on the results of phenotypic characterization, phylogenetic analysis and genome-based comparisons, strain TSD2052 represents a novel species in the genus , for which we propose the name sp. nov. (=KCTC 92288=JCM 35392).

During a survey of fungi in the Furna Nova cave of the Brazilian dry forest (Caatinga), two specimens of (URM 9081 and URM 9082) were isolated. Based on morphological and molecular data (ITS and LSU rDNA regions), a new species that is closely related to is delimited. The isolates form light grey to dark brown colonies and reverse yellowish. Dimorphic, short and tall sporangiophores are formed. Short sporangiophores are circinate, unbranched or sympodially branched, while the tall ones are erect, unbranched or simply branched, with some showing a swelling below apophyses. Sporangia of tall sporangiophores are deliquescent-walled, while the ones of short sporangiophores are persistent-walled. Sporangiospores are hyaline and elliptical, some with rounded ends. Zygosporangia are homothallic, yellow to brown, ornamented-walled, and suspensors are opposed and unequal in shape and size. This study contributes to the knowledge of species in Brazilian caves.

Members of the genus and six closely related genera were classified based on their genomic data, including the aa identity value threshold and the position on the phylogenomic trees and 16S rRNA gene phylogenetic trees. We suggested that , and should be reclassified as the genus on their genome-based classification. However, the phenotypic data of these three genera remains unclear and requires more closely related strains of these genera to confirm their taxonomic position in the future. The diaminopimelic acid (DAP) of was -DAP or -DAP and 3-DAP, while Nucisporomicrobium contained -DAP. The genus contains l-lysine, and contains DAP and 3-DAP. and these three genera contained MK-9(H) or MK-9(H) being the major menaquinones. The major fatty acids of these genera were - and -branched, and their polar lipids comprised phosphatidylethanolamine. Moreover, subsp. was reclassified as comb. nov. In addition, an endophytic actinobacterium, strain RD1, isolated from the leaf sample of a Jasmine rice plant () in Thailand has been classified. This strain is an aerobic actinobacterium with well-developed substrate mycelia. Aerial mycelia rarely produce poly-sporous-tubular sporangia, and spores are motile. Strain RD1 shared 98.9% of 16S rRNA gene similarity with NEAU-24. TISTR 2343 shared the highest digital DNA-DNA hybridization, average nucleotide identity blast and average nucleotide identity MUMmer, with values of 40.9%, 89.8% and 91.2%, respectively. The genotypic and chemotaxonomic data confirmed that strain RD1 belonged to the genus and was recognized as a novel species named sp. nov. The type strain is RD1 (=TBRC 17751=NRRL B-65688). Genome mining of strain RD1 revealed the biosynthetic genes encoding proteins related to antibiotic production and plant growth promotion.

The genus is widely distributed in nature. A key step in the evolutionary trajectory of is the diversification of species that are well adapted to human-made environments, particularly hospitals, including those capable of causing infection outbreaks. The temporal dynamics, routes and mechanisms of such nosocomial adaptations remain to be elucidated. This review provides a comprehensive description of 162 isolates collected between 1910 and 1970 under various taxonomic names, which may facilitate a more detailed exploration of the pathogenic and nosocomial shifts of . Genomic analysis of these isolates can help reveal the earliest traits of antimicrobial resistance and detect initial genetic events, thereby allowing hypotheses on driving factors that may have preceded the extensive use of modern antimicrobials. Through comparison with contemporary isolates, the evolutionary events and ecological processes that have shaped the phylogeny of today's highly successful strains can be mapped, and their arsenals of antimicrobial resistance determinants and virulence factors can be tracked chronologically.

Novel Gram-stain-negative, non-spore-forming, non-motile rods, designated HTMS2 and HTMS3, were isolated from a biofilm on the membrane of a municipal sewage treatment membrane bioreactor in Nagaoka, Japan. Phylogenetic analysis of 16S rRNA genes placed them in the family , most closely related to A2P5 (94.14% similarity). Genome sequencing (2.52 Mb, 48.2% G+C) and phylogenomic analysis affiliated them with the uncultured genus lineage CTSOIL-112 in the Genome Taxonomy Database. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values to related taxa were below species thresholds (ANI ≤77.0%, dDDH ≤54.9%). In addition, average amino acid identity values to related taxa were ≤68.6%. Both strains are catalase- and oxidase-positive, reduced nitrate and utilized various carbohydrates but not -acetyl-glucosamine; they differed in sorbitol assimilation. The major respiratory quinone is Q-8, and the predominant fatty acids are summed feature 3 (C_16:1 ω7c/ω6c), summed feature 8 (C_18:1 ω7c/ω6c) and C_16:0. Genomic data supported a non-motile, Gram-stain-negative phenotype. Polyphasic analysis indicates that these strains represent a novel genus and species, gen. nov., sp. nov. (type strain HTMS3=NBRC 117344=LMG 34133).

The bacterial order has recently undergone major taxonomic revisions, with several new families and genera described. Within this framework, the rare genus and the newly proposed genus occupy closely related positions. The present study provides a comprehensive phylogenomic, phenotypic and functional assessment of LAM2020 and H11S18 to clarify their taxonomic relationship. Genomic relatedness indices revealed high similarity between the two type strains, with average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values exceeding established species delineation thresholds. Phylogenetic analyses based on 16S rRNA, whole genomes and core gene sets consistently placed the two strains in a robustly supported monophyletic clade. These findings were further supported by shared metabolic and phenotypic traits. Taken together, the evidence demonstrates that and represent members of the same biological species. Accordingly, and in line with Rule 42 of the International Code of Nomenclature of Prokaryotes, we propose the reclassification of Li 2024 as a later heterotypic synonym of Maddock 2023. Furthermore, we propose two subspecies within this species: subsp. comb. nov. and subsp. comb. nov.

The species epithet Huang . 2023 is illegitimate under Rule 51b (5) of the International Code of Nomenclature of Prokaryotes, as it is a later homonym of Hu . 2023. The type strains of these two species share average nucleotide identity (84.7%; <95 %) and digital DNA-DNA hybridization (21%; <70 %) values below the recommended species delineation thresholds, substantiating their positions as two distinct species. Herein, the replacement name is proposed, preserving the original meaning related to the isolation of the type strain from mangrove sediments.

Two Gram-stain-negative, facultatively anaerobic, non-motile and rod-shaped bacterial strains, designated 2201CG32-9 and 2304DJ12-6, were isolated from marine sponges collected in the Republic of Korea. Both strains exhibited catalase and oxidase activities but tested negative for nitrate reduction and indole production. Strain 2201CG32-9 showed optimal growth at 30 °C and pH 7.0-8.0 in the presence of 3% (w/v) NaCl, whereas strain 2304DJ12-6 grew optimally at 25 °C, pH 8.0 and 3% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene and phylogenomic analysis of genome sequences indicated that strains 2201CG32-9 and 2304DJ12-6 represented novel species within the genus . Based on whole-genome phylogenomic analysis, the two strains were most closely related to OS29 and ATCC 700307, respectively. The average nucleotide identity values of these strains were found to be <75.9%, and their digital DNA-DNA hybridization values were <22.5%. The DNA G+C contents of strains 2201CG32-9 and 2304DJ12-6 were 56.5 and 53.5 mol%, respectively. In both strains, ubiquinone-8 was identified as the predominant respiratory quinone, and the major cellular fatty acids (>5.0%) were C, iso-C 3-OH, iso-C, iso-C, summed feature 8 and summed feature 9. As for polar lipids, both strains comprised phosphatidylglycerol, phosphatidylethanolamine and phosphoglycolipid as common major polar lipids. Strains 2201CG32-9 and 2304DJ12-6 are classified as two novel species of the genus based on a polyphasic taxonomic approach, for which the names sp. nov. (2201CG32-9=KACC 23829=JCM 37223) and sp. nov. (2304DJ12-6=KACC 23832=MCCC 1K09533) are proposed, respectively.

' Ferrigenium straubiae' strain KS (KCTC 25982, DSM 118991) is a neutrophilic, Fe(II)-oxidizing bacterium representing up to 98% of the community in culture KS, the most extensively studied mixed culture known for autotrophic nitrate-reducing Fe(II) oxidation. The phylogeny and genome of this bacterium were previously analysed and identified as ' Ferrigenium straubiae'. In this study, we report the first-time successful isolation of ' Ferrigenium straubiae' strain KS and its experimental physiological characterization. The bacterium was identified as a non-stalk-forming, rod-shaped and non-halophilic strain with a Gram-negative classification. We characterized its physiology when grown in agarose-stabilized Fe(II)-O gradient tubes where Fe(II) stemming from FeS functions as the electron donor and O as the electron acceptor. It showed growth at temperatures of 20-30 °C (optimal at 25°C) and at pH levels of 6.0-7.5 (optimal at pH 6.5-7.0). The doubling time at 20 °C and pH 6.5 was 16 h. We further optimized the gradient tubes for sustainable culture maintenance using modified Wolfe's mineral medium (MWMM; 1 g l NHCl) supplemented with 7-vitamin solution, SL-10 trace elements, selenite-tungstate solution and selenite-molybdate-nickel-copper-arsenic-vanadium solution (final concentrations of 10 µM Se, 10 µM Mo, 0.1 µM Ni, 0.1 µM Cu, 0.1 µM As and 5 nM V). We also evaluated several Fe(II) sources (with O as electron acceptor), as well as both inorganic and organic substrates for their influence on growth. Although a known member of the denitrifying community in culture KS, the isolated strain ' Ferrigenium straubiae' KS exhibited exclusively microaerobic and autotrophic growth in agarose-stabilized Fe(II)-O gradients, utilizing Fe(II) from FeS as the electron donor.

A strain, namely Oc8, was isolated from a root nodule of in Uruguay. This strain induced effective nodules in roots of , , and . Oc8 belongs to the genus according to the results of the 16S rRNA gene sequence analysis, and it forms an independent lineage within a cluster encompassing 13 described species of this genus. From them, the type strains closest related to the strain Oc8 with more than 99.5% similarity in 16S rRNA gene sequence were those of , , and (99.71%, 99.65%, 99.60% and 99.57%, respectively). A genome-based phylogeny showed that JCM 19881, CTAW11 and CTAW71 were the closest type strains to the strain Oc8. Values lower than the species cutoff of 95% and 70% were found after average nucleotide identity and digital DNA-DNA hybridization calculation between the genome of the strain Oc8 and those available genomes of the closest related species. These results, together with those of the symbiotic gene analysis, support the affiliation of this strain to the symbiovar cyanophyllae of a new species of for which the name sp. nov. is proposed. The type strain is Oc8 (=LMG 33261=CECT 30885).

Two strains of -like fungi were isolated from the dorsal region of a live bat (, nectarivore species) captured inside Gruta do Arnoud, a cave in the Caatinga biome of northeastern Brazil. These isolates presented unique morphological features, and achieving a consensus identification at the species level proved to be challenging. Phylogenetic analysis, based on nucleotide sequences from the internal transcribed spacer, large subunit ribosomal RNA gene, translation elongation factor 1-alpha () and beta-tubulin () genes, confirmed that these fungi represent previously undescribed species within the genus . The new species is named URM 9260. Phylogenetically, they grouped in a clade closely related to , and , but distinct differences were observed. Morphologically, the new species could be differentiated by their distinctive characteristics, such as reduced growth on oatmeal agar medium, reaching 15 mm after 14 days at 25 °C. Microscopically, it differs in the size of the conidiophores, which are shorter and broader compared to and . Additionally, it presents globose to subglobose conidia with diameters larger than those observed in closely related species. The use of a four-marker combination was an efficient approach to support the taxonomic novelty. This discovery enhances the understanding of diversity, particularly within cave ecosystems, and emphasizes the potential for discovering new fungal species in such specialized environments.

Earlier studies on the genus showed that pairs of strains having over 0.02 or 0.04 genetic distance are likely to be different species. However, in this work, it was found that a genetic distance of 0.012 or a genetic distance of 0.019 or a genetic distance of 0.013 can be acted as a threshold for describing species. In light of this relationship, a novel actinobacterial strain cg13 from the rhizosphere soil of was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis revealed that strain cg13 exhibited the highest similarities to IMSNU 22139 and JCM 13279. Phylogenetic analysis of 16S rRNA gene and whole-genome sequences indicated that strain cg13 was closely related to them. But the average nucleotide identity based on MUMmer (ANIm) and digital DNA-DNA hybridization (dDDH) values between genomes of strain cg13 and these two strains were below the thresholds for delineating species, suggesting that strain cg13 may be a new species. Significant differences in phenotypic and chemotaxonomic characteristics between strain cg13 and them further provided some useful information for strain cg13 as an independent species. Furthermore, ANIm and dDDH between genomes of strain cg13 and those strains (except SE(8)3), which had more than 98.65% 16S rRNA gene sequence similarities to strain cg13, were far below the thresholds for delineating species. Although the genomic correlation between strain cg13 and SE(8)3 cannot be evaluated due to unavailable genomic data of SE(8)3, the genetic distances between them were much above the maximum range of 0.012, 0.019 and 0.013 recommended above for delineating an species. Based on all these results, strain cg13 represents a novel species, for which the name sp. nov. is proposed. The type strain is cg13=MCCC 1K09229=KCTC 59393.

An aerobic methanotroph was isolated from a biofilm of coal mine Gruve 7 (Svalbard) and designated strain G7. Cells of strain G7 were Gram-stain-negative, pink-pigmented and motile rods. Strain G7 could grow at pH 6.8 and at temperatures ranging from 4 to 21 °C. The genome size was 4.00 Mb with a (digital) DNA G+C content of 47.7 mol%. Strain G7 represents a member of the family of the class . It displayed 94.6-99.7% 16S rRNA gene sequence similarity to the type strains of the genus . Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) confirmed that strain G7 represents a novel species. It showed 16S rRNA gene identity of 99.7%, 91.8% ANI and 46% dDDH to the closest type strain, LS7-T4A, with ANI and dDDH being much lower than the typically used 95 and 70% cutoffs, respectively, to delineate different species. For methane activation, strain G7 carries genes encoding particulate methane monooxygenase (pmoCAB). Also, genes of the methane utilization pathways, i.e. oxidation of methane to carbon dioxide and assimilation of methane-carbon to biomass, were encoded in the genome. Strikingly, compared to all other spp. strains, strain G7 did not have nitrogenase genes for nitrogen fixation. Strain G7 also possessed genes for ectoine production, which was not observed in the genomes of its closest relatives. Based on phenotypic, genetic and phylogenetic data, strain G7 represents a novel species within the genus for which the name sp. nov. is proposed, with strain G7 (DSM: 117899; LMG: 33632) as the type strain.

A Gram-stain-negative, strictly aerobic and motile bacterium, designated as FT89, was isolated from mangrove sediment in Shenzhen, China. Phylogenetic analysis of strain FT89 was mostly related to , with 16S rRNA gene similarity of 99.66%. The genome size of strain FT89 was 5,065,293 bp and the calculated G+C molar content was 65.90mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) value towards yielded 93.86% ANI and 53.2% dDDH. Although the 16S rRNA gene similarity is above 98.7%, the ANI and dDDH values are below the established species delineation thresholds (ANI <95% and dDDH <70%). Here, we confirm that strain FT89 represents a novel species. Phenotypic characterization revealed that cells of strain FT89 were ovoid to rod shaped, measuring 0.3-0.7 µm in width and 0.9-3.2 µm in length. Strain FT89 grew at 20-40 °C (optimum 35 °C) at pH 5.5-9.0 (optimum pH 6.0-7.0) with 0-9% (w/v) NaCl (optimum 1-2%). The cells of strain FT89 contained Q-10, and the major cellular fatty acids were composed of C cyclo 8 (41.7%) and summed feature 8 (C 7 and/or C 6) (32.4%). Based on phylogenetic, phenotypic and chemotaxonomic analysis, strain FT89 should represent a novel species of the genus , for which the proposed name is FT89 (=MCCC 1K08485=KCTC 8079).

A thermophilic, strictly anaerobic, Gram-stain-negative and ferric iron-reducing bacterium, designated as DY30410, was isolated from a hydrothermal sulphide sample collected from the Southwest Indian Ocean Ridge during the cruise DY30 of R/V . Cells of strain DY30410 were rod-shaped with rounded ends and motile with one or more laterally inserted flagellum (flagella). Strain DY30410 grew optimally at pH 6.5-7.0, 50 °C, with salinity (sea salts) of 35-45 g l. Ferric oxyhydroxide, ferric chloride, thiosulphate and elemental sulphur can be used as electron acceptors. Glucose and starch are used for growth. Elemental sulphur or yeast extract is not necessary. The principal fatty acids of strain DY30410 were iso-C, C, 3OH-iso-C and anteiso-C. No respiratory quinone was detected. Phylogenetically, strain DY30410 branched within the family with DY22619 being its closest phylogenetic relative (98.4% similarity), followed by the type species MV1087 (97.2%). Strain DY30410 has a draft genome size of 2.57 Mbp and has 2,852 predicted coding sequences. The genome DNA G+C content of strain DY30410 was 29.2 mol%. The DNA-DNA hybridization between strain DY30410 and its closest relatives, DY22619 or MV1087, was all 45.5%. The average nucleotide identity values between strain DY30410 and DY22619 and MV1087 were 91.9 and 91.3%, respectively. Phylogenomic analysis also showed that strain DY30410 branched within the family with DY22619 and MV1087 being its closest relatives. On the basis of phenotypic, phylogenetic and chemotaxonomic characteristics, we propose a representative of a new species in the genus , for which the name sp. nov. is proposed. The type strain is DY30410 (=KCTC 25912=MCCC 1A01531).

is a genus of moderately halophilic bacteria within the class , commonly isolated from diverse saline environments. Traditional phenotypic methods have proven insufficient to resolve taxonomic boundaries among closely related species in this genus. With the advent of whole-genome sequencing, genome-based analyses have become essential for accurate species and subspecies delineation. This study used comprehensive phenotypic and genomic comparisons to investigate the taxonomic relationship between YIM 95161 and MK-B5. Phylogenomic analyses based on core gene alignments revealed that YIM 95161 and MK-B5 form a robust monophyletic clade, consistent with high average nucleotide identity (>96%) and digital DNA-DNA hybridization values (>70%), confirming their membership within the same species. However, notable and consistent differences in growth physiology, enzymatic activity, fatty acid composition and genomic G+C content (69.5 mol% vs. 63.4-63.6 mol%) support the recognition of two distinct subspecies. Carbohydrate-active enzyme (CAZyme) repertoires also revealed divergence in CAZyme profiles, aligning with ecological differentiation. Therefore, we propose that YIM 95161 be reclassified as subsp. subsp. nov., while MK-B5ᵀ be retained as subsp. subsp. nov. This refined classification highlights the value of integrated genomic and phenotypic approaches in resolving intraspecific structure and improving taxonomic resolution within halophilic bacterial genera.