Strain 246TCP1[T], isolated from a strictly anaerobic 2,4,6-trichlorophenol-dehalogenating enrichment culture originating from contaminated groundwater, was assigned to the genus Sporomusa based on 16S rRNA gene phylogeny. Although members of the genus Sporomusa are recognized for autotrophic carbon fixation, the ecophysiological adaptations of environmental isolates remain poorly characterized. In this study, strain 246TCP1[T] was comprehensively characterized using phenotypic, genomic, and phylogenomic approaches. Strain 246TCP1[T] rapidly fermented DL-lactate in the absence of exogenous yeast extract, producing acetate at a rate of 8.21 ± 2.01 mM/day and accumulating hydrogen up to 42.09 ± 8.10 μM. Genomic analysis revealed a diverse hydrogenase repertoire, a complete Wood-Ljungdahl pathway, and a lactate utilization pathway, consistent with its metabolic potential as a versatile fermentative acetogen. The genome further encodes an Acg-family FMN-binding oxidoreductase potentially involved in redox buffering against transient oxidative stress, alongside a truncated dihydropyrimidinase-mediated salvage pathway putatively contributing to necromass recycling. Phylogenomic analysis based on single-copy marker proteins demonstrated that strain 246TCP1[T] forms a distinct lineage within the genus Sporomusa. Average nucleotide identity and digital DNA-DNA hybridization values between strain 246TCP1[T] and its closest type strain, S. ovata An4, were 94.9% and 63.4%, respectively, both below the accepted species delineation thresholds. Based on the polyphasic taxonomic evidence, strain 246TCP1[T] represents a novel species of the genus Sporomusa, for which the name Sporomusa lactatifermentans sp. nov. is proposed. The type strain is 246TCP1[T] (= GDMCC 1.6958[T]).

Understudied bacterial genera present a dynamic phylogenetic landscape and opportunities for discovering new taxa as more strains are isolated and genomic data is added. Here, through phylogenomic analysis, we describe three novel species of the globally distributed cosmopolitan marine bacterial genus Microbulbifer. This genus is ubiquitous in marine microbiomes and is a validated source of biodegradation enzymes as well as high value small molecule natural products. Average nucleotide identity (ANI) to the closest known species, Microbulbifer variabilis ATCC 700307[T], was less than 88.4% for all three novel species. Isolates of the three novel species, designated as PAAF003[Ts] (T = type genome), ZKSA006[Ts], and SSSA003[Ts] were imaged to reveal their morphological characteristics. Based on phylogenetic data, strains PAAF003[Ts], ZKSA006[Ts], and SSSA003[Ts] represent three new species of the genus Microbulbifer, for which the names Microbulbifer maximicatervae sp. nov., Microbulbifer regidiadema sp. nov., and Microbulbifer mixtoriginis sp. nov. are proposed, respectively, under the SeqCode. We also reconstructed a robust phylogeny of available Microbulbifer genomes, which should facilitate future isolation and strain description studies.

Rule 30 of the International Code of Nomenclature of Prokaryotes (ICNP) requires deposition of type strains in two publicly accessible culture collections in different countries as a condition of valid publication of the name, a requirement that structurally conflicts with access and benefit-sharing (ABS) legislation in biodiversity-rich nations. India's Biological Diversity Act, 2002 (amended 2023) exemplifies this conflict: researchers seeking to export isolates to satisfy Rule 30 must obtain National Biodiversity Authority approval, which routinely imposes use restrictions incompatible with the Code's unrestricted-access requirement. This review examines three pathways now available to researchers facing this constraint, traditional ICNP valid publication, the newly regulated Candidatus pro-status system under ICNP Section 10 (effective 2025), and the independent genome-based SeqCode, and evaluates their relative suitability for Indian microbial taxonomy. We find that while the policy-level mechanism connecting biodiversity law to nomenclatural non-compliance is well documented, case-level attribution for specific published Indian taxa remains largely unverified in the public record, a gap we identify and propose steps to close. We conclude with pathway-specific implementation recommendations for Indian repositories, researchers, and policy bodies, and note that the dual-code editorial policy of Systematic and Applied Microbiology, and a few other journals offers a comparatively low-friction venue for taxa affected by this conflict.

Insects host diverse and distinctive communities of gut mutualistic bacteria, including lactic acid bacteria of the Lactobacillus genus. Recently, most research in the insect microbial taxonomy has focused on identifying novel Lactobacillaceae species in managed insects such as Apis mellifera and few species of Bombus spp. from North America, Europe, and China. However, the gut microbiota of wild insects remains largely unexplored. Yet, insects represent the largest animal class and a vast, untouched source of novel microbial symbionts, especially in wild populations. This study focuses on the isolation and characterization of novel Lactobacillaceae strains from wild and solitary insects, such as the carpenter bee (Xylocopa violacea), the strawberry seed beetle (Harpalus rufipes), and the giant honeybee (Apis dorsata). Full-genome sequencing and annotation, including investigation of distinctive functional traits, were performed for these strains, along with phenotypic characterization of sugar fermentation, enzymatic activity, cellular fatty acid profiles and G + C content. Phylogenetic relationships were determined using 16S rRNA gene sequences and core genome computation, which confirmed the classification of novel taxa within the Lactobacillus genus. From the aforementioned insect species, three novel Lactobacillus species were isolated and characterized: Lactobacillus xylocopae XV31L (= DSM 120036[T] = MSCL 1776[T]) and Lactobacillus pollinatoris XV13L (= DSM 104957 [T] = LMG 30141[T]) from X. violacea, and CA30L (= DSM 119968[R] = MSCL 1777[R]) from H. rufipes, and Lactobacillus apisdorsatae C449L (= VTT E-263657 [T] = MSCL 1775[T] = NCCB 101125[T]) from A. dorsata.

The deep-sea biosphere hosts distinctive microbial communities with specialized adaptive traits, yet the mechanisms underpinning their physiological survival remain largely obscure. In this study a novel Gram-stain-positive, aerobic bacterium, designated strain SKLECPSW1[T], was isolated from the Eastern Indian Ocean at a depth of 5318 m. The strain grows optimally at 32 °C and has a DNA G + C content of 70.0 mol%. Its major fatty acids are C16:0, C18:1 ω9c, and 10-methyl-C18:0. Genome analysis revealed a versatile metabolic repertoire, including complete central carbon metabolic pathways, dissimilatory nitrate reduction to ammonium (DNRA), anaplerotic CO2 fixation, and multiple genes associated with environmental stress responses. Furthermore, CAZyme profiling and 12 putative biosynthetic regions suggested potential for complex carbohydrate processing and secondary-metabolite biosynthesis. Comparative 16S rRNA gene sequence analysis showed that strain SKLECPSW1[T] shared the highest sequence similarity with Williamsia aurantiaca B375[T] (98.3%). Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) values with related Williamsia species ranged from 71.15% to 83.35% and 18.8% to 26.6%, respectively, supporting its novel status. Metagenomic analysis of 25 deep-ocean datasets showed broad high-identity genome-wide recruitment in 2 samples, with breadths of 45.60% and 34.64% at ≥95% nucleotide identity, remaining 42.76% and 34.09% at ≥97.5%. Complementary marker-gene analyses further supported the occurrence of low-abundance environmental populations related to W. profundi in these two samples. Collectively, strain SKLECPSW1[T] represents a novel species, for which the name Williamsia profundi sp. nov. is proposed. The type strain is SKLECPSW1[T] (= MCCC 1K09832[T] = JCM 37991[T]).

The families Clostridiaceae, Lachnospiraceae, and Oscillospiraceae are key but poorly cultured constituents of the human gut microbiota. From healthy Chinese adults, four anaerobic strains (SJQ-1[T], SJQ-5[T], SJQ-6[T], and SJQ-8[T]) were isolated. 16S rRNA gene phylogeny placed SJQ-1[T] and SJQ-5[T] in Clostridiaceae, SJQ-6[T] in Lachnospiraceae, and SJQ-8[T] in Oscillospiraceae. Genomic comparisons (16S rRNA gene similarity, ANI, AAI, and dDDH) indicated they represent novel species or genera. Their closest relatives are the "Anaeromassilibacillus senegalensis" mt9ᵀ (a non-validly published genus name), the Jutongia huaianensis NSJ-37ᵀ, and the Flintibacter porci P01025ᵀ, respectively. Strain SJQ-5ᵀ exhibited ANI/AAI/dDDH values far below genus boundaries, supporting a novel genus. All strains produced short-chain fatty acids and displayed distinct carbon utilization and enzymatic profiles. Based on those results, we propose new taxa Alvibacillus kangbaii gen. Nov., sp. nov. for type strain SJQ-1[T] and Dizhoua hominis gen. Nov., sp. nov. for type strain SJQ-5ᵀ, and 2 other new species Jutongia huiwenae sp. nov. (type strain SJQ-6ᵀ) and Flintibacter aciditolerans sp. nov. (type strain SJQ-8ᵀ). This study expands the cultured diversity of the order Eubacteriales and provides new bioresources and taxonomic foundation for future mechanistic and functional investigations.

Four aerobic, Gram-stain-negative, straight rod-shaped bacterial strains designated GZRe12ᵀ, GZRe14, GZRR33ᵀ and GZRR35ᵀ were isolated from tomato rhizosphere soil and characterised by polyphasic taxonomy. 16S rRNA gene analysis affiliated these isolates with the family Rhodanobacteraceae and the polyphyletic genus Frateuria. Phylogenomic reconstruction and genome-wide relatedness indices including ANI, dDDH and AAI supported the establishment of two novel genera Parafrateuria gen. nov. and Pseudofrateuria gen. nov., with Frateuria defendens transferred to Parafrateuria defendens comb. nov. Chemotaxonomic traits, including ubiquinone Q-8, polar lipid compositions and fatty acid profiles, together with genomic features (3.52-3.78 Mbp genome size, 67.7-68.5% G+C content) distinguished these strains as three novel species within Pseudofrateuria. The names Pseudofrateuria alba sp. nov. (GZRe12ᵀ = GDMCC 1.4121ᵀ = JCM 36337ᵀ), Pseudofrateuria humi sp. nov. (GZRR33ᵀ = GDMCC 1.4118ᵀ = JCM 36339ᵀ) and Pseudofrateuria lycopersici sp. nov. (GZRR35ᵀ = GDMCC 1.4119ᵀ = JCM 36340ᵀ) are proposed. Functional assays confirmed their capacities for indole-3-acetic acid and siderophore production, and strains GZRe12ᵀ and GZRe14 exhibited significant phosphate-solubilizing potential. Six previously published species originally classified within Frateuria and Fulvimonas were formally transferred to the genus Pseudofrateuria. This study resolves the polyphyletic taxonomic confusion of the traditional genus Frateuria and provides novel insights into the diversified ecological functions and plant-growth-promoting potential of rhizosphere colonising bacteria in the family Rhodanobacteraceae.

Rhizobiaceae is one of the most representative families, encompassing rhizobial species, valuable allies in the sustainable production of legumes such as cowpea (Vigna unguiculata). Interestingly, beyond rhizobia, studies have increasingly reported the presence of a wide diversity of non-symbiotic bacteria that compose the microbiome of cowpea nodules. In this study, we performed a systematic analysis, with an emphasis on phylogenomic aspects, of 12 strains trapped from cowpea in soils of indigenous lands in Mato Grosso do Sul, Central-Western Brazil (Cerrado biome), which had been preliminarily characterized. The results highlighted the rich and little-explored Rhizobiaceae biodiversity, revealing a novel genus, Brasilibacterium gen. nov., and three novel species: Brasilibacterium cachoeirinhense sp. nov. (CNPSo 3794[T] = BR 15710[T] = LMG 34800[T]), Brasilibacterium lagoinhense sp. nov. (CNPSo 3920[T] = BR 15708[T] = 34801[T]), and Martinezella lalimensis sp. nov. (CNPSo 3959[T] = BR 15709[T] = LMG 34802[T]). However, none of the strains belonging to these novel species was able to re-nodulate cowpea or the promiscuous legumes Phaseolus vulgaris and Macroptilium atropurpureum, suggesting either the loss of symbiotic genes or their endophytic nature. In addition to the novel species accessed, "Rhizobium atlanticum", "Martinezella aureum", "Martinezella centroccidentale", "Martinezella hainanensis", and "Martinezella dioscoreae" were also identified based on genomic sequences, with the latter two reported for the first time in Brazil.

A Gram-stain-negative, oxidase-positive, catalase-negative, motile, rod-shaped bacterium, designated strain M5-1[T], was isolated from a freshwater green alga. Strain M5-1[T] was obligately aerobic and contained ubiquinone-8 (Q-8) as the sole respiratory quinone. The major fatty acids (>10%) were C16:0, C12:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c), and summed feature 8 (C18:1ω7c and/or C18:1ω6c), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The genomic DNA G+C content was 67.3 mol%. Based on 16S rRNA gene sequence analysis, strain M5-1[T] was most closely related to Roseateles cavernae (proposed herein as Kinneretia cavernae) YIM B04394[T] (99.3%) and Kinneretia oligotropha CHU3[T] (98.3%). Genome-based phylogenomic analyses consistently placed strain M5-1[T] together with R. cavernae within the genus Kinneretia. Pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain M5-1[T] and R. cavernae were 96.1% and 66.9%, respectively, whereas comparisons with all other type strains yielded ANI and dDDH values of ≤81.1% and ≤23.6%, respectively, supporting its recognition as a novel species. Based on its phylogenomic, genomic, phenotypic, and chemotaxonomic characteristics, strain M5-1[T] (=KACC 22491[T]=JCM 34976[T]=FBCC-B22965[T]) represents a novel species of the genus Kinneretia, for which the name Kinneretia algicola sp. nov. is proposed. In addition, comprehensive phylogenomic and genome-relatedness analyses support the transfer of six Roseateles and Paucibacter species to Kinneretia, two Roseateles species to Pelomonas, and Aquabacterium humicola to Pseudaquabacterium, providing a revised genome-based taxonomic framework for the family Sphaerotilaceae.

Many species of family Sphaerotilaceae have been isolated from aquatic environments. In this study, we conducted the taxonomic characterization of five novel strains Y2R2-4[T], B2R-40[T], DJ2R-2[T], DJ1R-11 and DJ4R-1, isolated from crater lakes in Da Hinggan Mountain region of northern China. A polyphasic taxonomic approach was employed to determine the taxonomic affiliation of these strains. Based on the 16S rRNA gene sequence analysis, these novel strains showed the highest similarities (98.9-99.9%) to Kinneretia aquatilis CR182[T] and Kinneretia alba hw1[T]. While the digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between the five novel strains and their closely related species Kinneretia were significantly below the established taxonomic thresholds for species delineation, further supporting that these strains represent three novel species within the genus Kinneretia. Based on genomic annotation results, their metabolic potentials to produce terpene and RiPP-like compounds were further explored. In summary, the morphological, physiological, and biochemical characteristics of these novel strains indicated that the five isolates represent three novel species within the genus Kinneretia. The names, Kinneretia craterilacus sp. nov., Kinneretia daxingganlingensis sp. nov. and Kinneretia lacustris sp. nov., were proposed for them, with type strain Y2R2-4[T] (= CGMCC 1.19001[T] = KCTC 92188[T]), B2R-40[T] (= CGMCC 1.19003[T] = KCTC 92190[T]) and DJ2R-2[T] (= CGMCC 1.19002[T] = KCTC 92189[T]), respectively.

Genome-resolved phylogenomics reveals widespread misclassification of metal-reducing bacteria historically assigned to Geobacter based on 16S rRNA gene phylogeny, and highlights species that persist only as 16S rRNA entries without genomes for robust taxonomic resolution. Here, we resolve two such lineages by integrating whole-genome phylogeny with average amino acid identity (AAI) and percentage of conserved proteins (POCP) across 418 dereplicated genomes of Desulfuromonadia. We report a draft genome of the psychrophilic iron-reducing bacterium Geobacter psychrophilus (100% completeness). Phylogenomic analyses place both Geobacter psychrophilus and the GTDB placeholder genus g__JACRCG01 within the family 'Pseudopelobacteraceae', outside Geobacteraceae sensu stricto. Within this framework, G. psychrophilus forms a distinct, well-supported lineage separated from neighbouring genera by discontinuities in AAI and POCP, supporting its reclassification as Irobacter psychrophilus comb. nov. Additionally, we show that Geosyntrophus acetoxidans, a non-axenic syntrophic bacterium, forms a coherent genus with 51 other environmental genomes (placeholder genus g__JACRCG01), for which we propose the replacement name Geosyntrophus gen. nov. Comparative genome analysis revealed conserved family-level metabolic traits together with genus-specific differences in respiratory metabolism, while ANI-based clustering identified substantial species-level diversity within both proposed genera. Metagenome and 16S rRNA-gene survey data further show that Geosyntrophus and Irobacter occur in broadly similar aquatic and subsurface habitats spanning from the Arctic to the Antarctic. Together, these results resolve the taxonomy of two previously ambiguous Desulfuromonadales lineages and shed light on their environmental distribution.

Novel facultatively anaerobic moderately thermophilic bacteria, strains OK-6-Me[T] and OK-1-Me, were isolated from the hot springs of Karmadon (North Ossetia, Russian Federation). Gram-stain-negative, motile rods were present singly, in rosettes, and formed biofilms. Both strains grew optimally at 55 °C, pH 7.0 and did not require sodium chloride. They were chemoorganoheterotrophs, growing on mono-, di- and polysaccharides (cellulose, xylan, lichenan, xyloglucan, mannan, locust bean gum, pectin) as well as proteinaceous substrates (gelatin, casein). Growth under anaerobic conditions was observed both in the presence and absence of external electron acceptors (sulfur, thiosulfate, nitrite, arsenate, Fe-citrate, ferrihydrite). Major cellular fatty acids of both strains were iso-C15:0, anteiso-C15:0, and anteiso-C17:0. The size of the genomes were 3.3 and 3.2 Mb for strain OK-6-Me[T] and OK-1-Me, respectively. Genomic DNA G + C content was 37% for both strains. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, the strains represented a new species of the genus Melioribacter of family Melioribacteraceae within the class Ignavibacteria, for which the name Melioribacter sulfuriphilus sp. nov. is proposed, with type strain OK-6-Me[T] (= B-3972[T] = CGMCC 1.18264 [T] = BIM B-2154[T] = UQM 41932[T]). Analysis of OK-1 and OK-6 metagenomes revealed presence of various genes involved in carbon (CO2 fixation, carbohydrate hydrolysis, hydrocarbons degradation, fermentation), nitrogen (nitrate, nitrite, NO and N2O reduction) and sulfur cycles (sulfate reduction, sulfur or thiosulfate reduction, oxidation of sulfur compounds). MAGs OK-1-035 and OK-6-024 almost identical to genomes of strain OK-1-Me and OK-6-Me[T] presumably are integral part of these complex trophic chains.

Coastal tidal flats represent dynamic saline environments that harbor largely unexplored haloarchaeal communities. In this study, amplicon sequencing, metagenomic analyses, and cultivation-based approaches revealed substantial haloarchaeal diversity in tidal flats from four provinces of eastern China despite their relatively low salinity. Five haloarchaeal strains, designated YSMS36[T], DYSN1, QDMS2, CMSO5[T], and ZSTT2, were isolated from diverse tidal flats. Theses strains shared 16S rRNA gene sequence similarities of 92.1-92.2% with their closest validly named relative, Salinilacihabitans rarus AD-4[T]. Phylogenetic analyses based on 16S rRNA and rpoB' gene sequences showed that the five strains formed a distinct and well-supported monophyletic lineage, separated from currently recognized members of the class Halobacteria. Average amino acid identity (AAI), average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) values between these five strains and the related Halobacteria representatives were 49.3-62.7%, 66.9-74.9%, and 16.2-29.5%, respectively, and well below the accepted thresholds for species and genus delineation. Phylogenomic analyses further supported their placement within a novel family of the order Halobacteriales. Based on phylogenetic, genomic, chemotaxonomic, and phenotypic analyses, these five strains represent two novel species of a novel genus within a novel family. The names, Halolitoreaceae fam. nov., Halolitoreus marinus gen. nov., sp. nov., and Halolitoreus rarus sp. nov. are herein proposed.

Bacterial strains were isolated from different locations and screened for plant growth promoting (PGP) features. Comparative analyses of the 16S gene sequences of 5 of the strains indicated taxonomic relatedness within the genus Paenibacillus. A polyphasic taxonomic approach was employed to study the strains in detail to clarify their phylogenetic position. Genome-based analyses, including digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI), revealed values consistently below the accepted species delineation thresholds when compared with closest relatives of each strain. Additionally, the strains showed clear differences in their physiological and biochemical profiles to the type strains of the closest related species. A notably diverse set of genes potentially involved in plant growth promotion was detected in all strains. With respect to the analyses reported here, the following new names are proposed: Paenibacillus corni sp. nov., with AK-167[T] as the type strain (= LMG 34403[T] = DSM 121689[T]); Paenibacillus vaccinii sp. nov., with AK-264[T] as the type strain (= LMG 34404[T] = DSM 121714[T]); Paenibacillus ericacearum sp. nov., with AK-265[T] as the type strain (= CCM 6913[T] = LMG 34405[T] = DSM 121715[T]); Paenibacillus polytrichii sp. nov., with AK-286[T] as the type strain (= CCM 9614[T] = LMG 34406[T] = DSM 121716[T]); and Paenibacillus artemisiae sp. nov., with DT-106[T] as the type strain (= LMG 34409[T] = CCM 9610[T] = DSM 121690[T]).