Strains of two novel Corynebacterium species were cultured from samples of human nostrils and skin collected in the USA and Botswana. These strains demonstrated growth on Columbia Colistin-Nalidixic Acid agar with 5% sheep blood and in liquid media (brain-heart infusion and tryptic soy broth) supplemented with Tween 80, a source of the fatty acid oleic acid. Cells were Gram-positive, non-spore-forming, non-motile bacilli that showed catalase but not oxidase activity. Major fatty acids in both of these species were C18 : 1 ω9c (oleic acid), C16 : 0 (palmitic acid) and C18 : 0 (stearic acid). Analysis of the 16S rRNA gene sequences identified these strains as belonging to the genus Corynebacterium (family Corynebacteriaceae). Whole-genome sequencing revealed that these strains formed distinct branches on a phylogenomic tree, with average nt identities of <95% relative to all previously described species. These results indicate that these strains represent novel species of Corynebacterium, for which we propose the names Corynebacterium hallucis sp. nov., with the type strain CTNIH22[T] (=ATCC TSD-435[T]=DSM 117774[T]), and Corynebacterium nasorum sp. nov., with the type strain KPL3804[T] (=ATCC TSD-439[T]=DSM 117767[T]). These data also indicate that 'Corynebacterium kefirresidentii' is designated C. nasorum sp. nov.

Two Gram-stain-negative, non-motile and rod-shaped bacterial strains, designated F1114[T] and F2636L[T], were isolated from a coastal sediment sample collected from Jingzi Port, Weihai, China. The 16S rRNA gene sequence similarity between the two strains was 96.8%. Both strains shared the highest 16S rRNA gene sequence similarities with Xanthomarina spongicola KCTC 22662[T] (94.9% and 96.2%, respectively). Phylogenomic analyses confirmed that strains F1114[T] and F2636L[T] belong to the genus Xanthomarina. Based on the results of phylogenetic, phenotypic and chemotaxonomic data and genomic comparison, strains F1114[T] and F2636L[T] could be distinguished from their closest taxa, representing two novel species of the genus Xanthomarina, for which the names Xanthomarina sediminis sp. nov. and Xanthomarina flava sp. nov. are proposed, respectively. The type strains are F1114[T] (=KCTC 92650[T]=MCCC 1H01355[T]) and F2636L[T] (=KCTC 92651[T]=MCCC 1H01398[T]).

Two Gram-negative, aerobic, motile and rod-shaped bacterial strains, designated D34-3ᵀ and BC02-3-A7ᵀ, were isolated from deep-sea sediments of the eastern Pacific Ocean. Both strains were able to grow in the presence of 1.0-10.0% (wt/v) NaCl, at pH 6-9 and at 10-37 °C. The 16S rRNA gene sequence comparisons confirmed that these two isolates belonged to the genus Christiangramia of the family Flavobacteriaceae, exhibiting the highest 16S rRNA gene sequence similarity of D34-3ᵀ to Christiangramia sediminicola SM2212[T] (98.8%) and BC02-3-A7ᵀ to Christiangramia oceanisediminis GC03-9ᵀ (97.2%), respectively. The complete genomes of D34-3ᵀ and BC02-3-A7ᵀ were 3.40 Mb (G+C content 37.5 mol%) and 4.43 Mb (G+C content 40.6 mol%) in size, with average nucleotide identity and digital DNA-DNA hybridization values with other reference Christiangramia species below 79.3/21.7% and 76.5/19.7%, respectively. Strain D34-3ᵀ contained menaquinone-6 as the sole respiratory quinone while menaquinone-7 was detected as the only respiratory quinone for BC02-3-A7ᵀ. These two strains possessed phosphatidylethanolamine as the dominant polar lipid. The predominant cellular fatty acids of both these strains were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 9 (iso-C17 : 1 ω9c and/or 10-methyl C16 : 0). Based on phenotypic, chemotaxonomic and genomic characteristics, strains D34-3ᵀ and BC02-3-A7ᵀ were identified as two novel species of the genus Christiangramia, for which the names Christiangramia pacifica sp. nov. and Christiangramia profundi sp. nov. are proposed; the type strains are D34-3ᵀ (=MCCC 1A13342[T]=DSM 121736[T]) and BC02-3-A7ᵀ (=MCCC M23243[T] =DSM 121737[T]), respectively.

Arcobacter cryaerophilus is genomically heterogeneous with a type strain that is aberrant from most other strains in this species. Consequently, several infraspecific subdivisions have been introduced, including DNA-DNA hybridization groups, subgroups and genomovars. Recent comparative whole-genome sequence studies have corroborated and extended this heterogeneity and revealed the presence of four species among historical strains and new isolates which are now classified as A. cryaerophilus. The present study aimed to establish a simple formal classification of A. cryaerophilus-like bacteria that facilitate transparent communication by integrating genome sequence data of taxonomically well-characterized strains with biochemical characteristics. To this end, we propose three novel species: Arcobacter crypticus sp. nov. [with strain LMG 9065[T] (=CCUG 12019[T]) as the type strain], Arcobacter occultus sp. nov. [with strain LMG 29976[T] (=CCUG 17808[T]) as the type strain] and Arcobacter thermotolerans sp. nov. [with LMG 10829[T] (=ATCC 49615[T]) as the type strain]. This revised classification provides a robust basis for future investigations into the ecological roles and pathogenic potential of these taxa.

Two actinobacterial strains with resistance to selenite and molybdate, designated as ZXT2-3[T] and ZXT2-6[T], were isolated from the river sediment sample of Jinshui River in Xingtai City, Hebei Province, China. Based on 16S rRNA gene sequence analysis, strain ZXT2-3[T] showed the highest sequence similarity to Agromyces binzhouensis CGMCC 4.7180[T] (98.5%), and strain ZXT2-6[T] was most closely related to Agromyces arachidis JCM 19251[T] (99.1%), Agromyces indicus CCTCC AB 2011122[T] (98.8%), Agromyces aurantiacus DSM 14598[T] (98.6%), Agromyces tropicus JCM 15672[T] (98.4%), Agromyces mediolanus JCM 3346[T] (98.2%) and Agromyces soli JCM 16247[T] (98.0%). The 16S rRNA gene sequence similarity between strains ZXT2-3[T] and ZXT2-6[T] was 98.4%. Phylogenetic analysis based on 16S rRNA gene sequences and whole-genome sequences indicated that strains ZXT2-3[T] and ZXT2-6[T] belong to the genus Agromyces. The genome sizes of strains ZXT2-3[T] and ZXT2-6[T] were 3.9 and 4.0 Mb, with DNA G+C contents of 72 and 71.5 %, respectively. The average nucleotide identity and digital DNA-DNA hybridization values with the closest relatives were below species delineation thresholds. The major fatty acids detected in strain ZXT2-3[T] included anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0, C16 : 0 and iso-C15 : 0. For strain ZXT2-6[T], the major cellular fatty acids were identified as anteiso-C15 : 0, anteiso-C15 : 1A, iso-C16 : 0 and anteiso-C17 : 0. The major respiratory quinones of strains ZXT2-3[T] and ZXT2-6[T] were MK-11 and MK-12. The polar lipid profiles of both strains contained diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids. Both isolates could reduce Se(IV) to produce selenium-containing particles. Strain ZXT2-3[T] was also capable of reducing Mo(VI) to molybdenum blue. According to the phenotypic, genotypic and phylogenetic data, strains ZXT2-3[T] and ZXT2-6[T] represent two novel species of the genus Agromyces, for which Agromyces molybdatiresistens sp. nov. and Agromyces selenitireducens sp. nov. are proposed, respectively. The type strains are ZXT2-3[T] (=GDMCC 1.4963[T]=JCM 37791[T]=MCCC 1K10748[T]) and ZXT2-6[T] (=GDMCC 1.4965[T]=JCM 37792[T]=MCCC 1K10749[T]), respectively.

A Gram-negative, aerobic, halophilic bacterium, designated as strain TD01[T], was isolated from an environmental sample collected from Aydingkol Lake, a saline lake in Xinjiang, China. Cells were rod-shaped and formed light yellow, circular, smooth and glossy colonies on Luria-Bertani agar supplemented with 60 g l[-1] NaCl. Strain TD01[T] grew at 20-41 °C (optimum 30 °C), pH 5.0-10.0 (optimum 7.0-8.0) and in the presence of 2-20% (w/v) NaCl [optimum 8-11% (w/v)]. The strain was catalase- and oxidase-positive, reduced nitrate and did not grow anaerobically in the absence or presence of nitrate, nitrite or fumarate as an exogenous electron acceptor. The strain was capable of accumulating intracellular polyhydroxybutyrate. The predominant respiratory quinone was ubiquinone-9. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TD01[T] belonged to the genus Vreelandella and was most closely related to Vreelandella zhaodongensis (99.65%), Vreelandella alkaliphila (98.94%) and Vreelandella venusta (98.73%). Analysis of the previously published complete genome sequence showed a genome size of 4.13 Mb with a DNA G+C content of 52.71 mol%. Average nucleotide identity and digital DNA-DNA hybridization values between strain TD01[T] and its closest relatives were below the accepted thresholds for species delineation. Based on the results of polyphasic taxonomic analyses, we propose that strain TD01[T] be classified as the type strain of a novel species named Vreelandella aydingkolensis sp. nov. Strain TD01[T] has been deposited in the China General Microbiological Culture Collection Center (CGMCC), Beijing, China, under the collection number CGMCC 4353[T], in the Spanish Type Culture Collection (CECT), Valencia, Spain, under the collection number CECT 31432[T], and in the American Type Culture Collection (ATCC), Manassas, VA, USA, under the collection number ATCC TSD-628ᵀ.

Six strains of a Gram-stain-negative, psychrotrophic, aerobic, rod-shaped, motile bacterium were recovered from water samples of the Port Washington, WI, USA, potable water system. Strain 201[T] was designated as the type strain. Phylogenetic analysis based upon the 16S rRNA gene sequence showed that strain 201[T] represents a novel species belonging to the genus Asticcacaulis. Strain 201[T] grows between 5 and 40 °C and has a salt tolerance range of 0-1.5%. The primary quinone was ubiquinone Q-10 (98.8%) with a minor amount of Q-9 (1.2%), while the polar lipids included three glycolipids, one unidentified lipid and phosphatidylglycerol. The predominant cellular fatty acids are C16 : 0 and sum in feature 8 (C18:1 ω9c/C18:1 ω7c/C18:1 ω6c). The genomic DNA G+C content of strain 201[T] was 58.8 mol%, with a genome size of 4.7 Mb. The average nt identity and digital DNA-DNA hybridization between strain 201[T] and its closest phylogenetic relative Asticcacaulis taihuensis CGMCC 1.3431[T] were 77 and 20.7%, respectively, well below the values used to delineate species. Based upon phenotypic, genomic and phylogenetic data, strain 201[T] represents a novel species of the genus Asticcacaulis, for which we propose the name Asticcacaulis aquihabitans. The type strain is 201[T] (=LMG 33251[T]=NRRL B-65659[T]).

While studying the spoilage microbiome of commercially manufactured marinated rainbow trout (Oncorhynchus mykiss), two strains, Mkasi1-1[T] and Mkahm2-6, that could not be identified as any known species of the family Lactobacillaceae by MALDI Biotyper MSP Identification Standard Method 1.1 analysis were isolated. In phylogenetic analyses, the two strains were positioned closest to Latilactobacillus (L.) fuchuensis. Genetically, Mkasi1-1[T] and Mkahm2-6 were highly similar to each other, having 100% average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) identities. The ANI and dDDH pair values of both Mkasi1-1[T] and Mkahm2-6 with the L. fuchuensis type strain DSM14340[T] were 94.9 and 59.8%, respectively, suggesting that they represent a novel species distinct from L. fuchuensis. Phenotypic properties of Mkasi1-1[T] and Mkahm2-6 were quite similar to those of L. fuchuensis type strain DSM14340[T], differing only in the utilization of fewer carbon sources. Due to the close relation of Mkasi1-1[T] and Mkahm2-6 to L. fuchuensis, we propose the name Latilactobacillus parafuchuensis sp. nov. for this novel species. The type strain is Mkasi1-1[T] (=LMG 34323[T]=DSM 121188[T]), and a second strain is Mkahm2-6 (=LMG 34324=DSM 121189).

A Gram-stain-negative, facultatively anaerobic, motile and rod-shaped bacterium, designated as strain SCSIO 43001[T], was isolated from the gastric cavity of the stony coral Galaxea fascicularis in the South China Sea. Previous studies identified this strain as a temperature-dependent coral pathogen, and further ecological analysis revealed that this species is also distributed among other marine invertebrates, including the Pacific oyster Magallana gigas. Strain SCSIO 43001[T] grew at 10-40 °C (optimum, 28 °C), pH 6.0-10.0 (optimum, 7.0) and in 0.5-10% (w/v) NaCl (optimum, 3-4%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCSIO 43001[T] belongs to the genus Vibrio, sharing the highest similarities with Vibrio japonicus LMG 29636[T] (98.2%) and Vibrio xuii LMG 21346[T] (97.9%). However, phylogenomic comparisons showed that the average nucleotide identity and digital DNA-DNA hybridization values between strain SCSIO 43001[T] and its closest relatives were below 86.6 and 31.1%, respectively, well below the species-delimitation thresholds. The major cellular fatty acids were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω6c or C18 : 1 ω7c) and C16 : 0. The DNA G+C content was 44.5 mol%. Based on combined phenotypic, chemotaxonomic, phylogenetic and phylogenomic polyphasic evidence, strain SCSIO 43001[T] represents a novel species within the genus Vibrio, for which the name Vibrio coralinecrosis sp. nov. is proposed with the type strain SCSIO 43001[T] (=MCCC 1K09368[T]=KCTC 18156[T]).

Two novel Gram-stain-negative, aerobic, heterotrophic, motile bacterial strains, designated AN558[T] and AN641[T], were isolated from riverbank soil in South Korea. To determine their taxonomic positions, the strains were characterized using a polyphasic taxonomic approach based on 16S rRNA gene phylogeny, phenotypic and chemotaxonomic characteristics and genome-based analyses. Phylogenetic and genome-based analyses revealed that the two novel isolates, AN558[T] and AN641[T], belong to the genus Sphingobium. AN558[T] showed the highest 16S rRNA gene similarity (97.3%) with Sphingobium yanoikuyae ATCC 51230[T]. In addition, AN641[T] showed 97.6% 16S rRNA gene similarity with Sphingobium arseniciresistens H39-3-25[T]. The genome of strains AN558[T] and AN641[T] consisted of 3,717,653 and 3,426,895 bp, with DNA G+C content of 62.8 and 63.6 mol%, respectively. The average nucleotide identity between the two strains and other related species was below 79.1%, and the digital DNA-DNA hybridization values with closely related species were below 22.4%, both lower than the species delineation threshold. Strains AN558[T] and AN641[T] contained ubiquinone Q-10 as the major respiratory quinone and exhibited a polyamine pattern, with spermidine as the predominant polyamine. The major fatty acids were characterized by C16 : 0, C16 : 1 ω7c/C16 : 1 ω6c (summed feature 3) and C18 : 1 ω7c/C18 : 1 ω6c (summed feature 8). The major polar lipids of AN558[T] and AN641[T] were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Therefore, AN558[T] and AN641[T] represent novel species of the genus Sphingobium, for which the names Sphingobium fluminis sp. nov. (type strain AN558[T]=KACC 23515[T]=LMG 33415[T]) and Sphingobium anseongense sp. nov. (type strain AN641[T]=KACC 23516[T]=LMG 33416[T]) are proposed.

The majority of legume species (plant family Fabaceae) can fix atmospheric nitrogen (N2) via symbiotic bacteria (general term 'rhizobia') in root nodules. Symbiovars are defined as strains of rhizobia that can establish an N2-fixing symbiosis with distinct legume species and have specific symbiosis gene phylogenies. Here, symbiovar occurrence across rhizobial species was related to rhizobia and legume host taxonomy and geographic location of the symbiosis, and then their specificity was assessed in relation to legume species they did or did not nodulate. Sixty-eight rhizobial symbiovars occurred across 183 of the 275 described rhizobial species in all main rhizobial genera in different countries on all continents except Antarctica. Generally, individual symbiovars occurred within one rhizobial genus, but there were exceptions. Symbiovars associated with widely grown crop legume species were of different rhizobial species on different continents. Most other symbiovars occurred within rhizobial species isolated from one legume species, genus or clade/tribe in a single country. Data on legume nodulation are limited for half of the symbiovars, such that judgements on their wider specificity are not possible. However, several of these symbiovars were shown to be specific to particular legume species within a genus. All other symbiovars showed legume specificity, but this was variable. Overall, further nodulation and symbiosis gene phylogenetic studies are required to more clearly define symbiovars.

Salinomycin is a polyether ionophore discovered from a streptomycete strain designated 80614 (=DSM 41398=NBRC 107858), and the producer has been published as Streptomyces albus. In this study, the taxonomic position was investigated using a polyphasic approach. The 16S rRNA gene sequence of S. albus 80614 showed similarities of 99.8 and 98.8% to those of 'Streptomyces physcomitrii' LD120[T] and Streptomyces levis NBRC 15423[T], respectively, as the closest, but the similarity to S. albus NBRC 13014[T] was only 96.1%. S. albus 80614 was not close to S. albus NBRC 13014[T] and rather formed a clade with 'S. physcomitrii' LD120[T] in the phylogenetic tree based on 16S rRNA gene sequences. The digital DNA-DNA hybridization (dDDH) values were 67.8, 23.3 and 21.6% to 'S. physcomitrii' LD120[T], S. levis JCM 6924[T] and S. albus NBRC 13014[T], respectively. The average nucleotide identity based on MUMmer (ANIm) was 96.5% between S. albus 80614 and 'S. physcomitrii' LD120[T]. These dDDH and ANIm values were below the thresholds, 70 and 96.7% for bacterial and streptomycetal species delineation, respectively. The strain was differentiated from these three referenced species in major phenotypic characteristics such as spore morphology, NaCl tolerance and carbon source utilization. Therefore, Streptomyces salinomycinicus sp. nov. was proposed for the strain. This new species included S. albus ZD11, S. albus BK3-25, Streptomyces sp. SCSIO ZS0520, 'S. physcomitrii' NPDC020937 and 'S. physcomitrii' NPDC020938. Additionally, Streptomyces rubiginosus is reclassified as a later heterotypic synonym of Streptomyces pseudogriseolus; Streptomyces niveoruber as a later heterotypic synonym of Streptomyces griseoviridis; Streptomyces griseomycini as a later heterotypic synonym of Streptomyces griseostramineus; Streptomyces roseoviolaceus as a later heterotypic synonym of Streptomyces violaceus; Streptomyces violaceochromogenes as a later heterotypic synonym of Streptomyces collinus; and Streptomyces virens as a later heterotypic synonym of Streptomyces calvus.

Two yeast strains, CICC 33533 and NYNU 26815, belonging to the basidiomycetous yeast genus Yunzhangomyces, were isolated from the leaf surfaces of Sedum aizoon and Sorbus alnifolia, respectively, collected in the Baotianman Nature Reserve, Henan Province, China. Phylogenetic analyses of the internal transcribed spacer (ITS) region and the D1/D2 domain of the large subunit rRNA gene, together with detailed phenotypic characterization, indicated that these two strains, along with an additional strain NRP040 isolated from a plant in Japan, represent a novel asexual species of the genus Yunzhangomyces in the order Exobasidiales. The name Yunzhangomyces sedi sp. nov. (MycoBank MB 863876) is, therefore, proposed with strain CICC 33533 designated as the holotype. The novel species differs from its closely related species, Yunzhangomyces orchidis, Yunzhangomyces clavatus, Yunzhangomyces cylindricus, Yunzhangomyces nandinae and Yunzhangomyces scirpi by 24-32 nucleotide substitutions (4.2-5.7%) in the D1/D2 domain. In the ITS region, the novel species also exhibited more than 23 nucleotide mismatches (6.4%) from Y. orchidis, Y. clavatus, Y. cylindricus and Y. nandinae. The ITS sequence of Y. scirpi was not available for comparison. Minor physiological differences were also observed: the novel species was able to assimilate galactitol, thereby differentiating it from the closely related yeast-like species Y. orchidis, Y. clavatus, Y. cylindricus and Y. nandinae.

A novel strain of the genus Ureaplasma, designated TOSA-KAIYU[T], was isolated from the faeces of a whale shark (Rhincodon typus). This study reports the first isolation of a member of the genus Ureaplasma from a poikilothermic vertebrate. TOSA-KAIYU[T] was characterized phenotypically and genotypically and compared with known species of the genus Ureaplasma. TOSA-KAIYU[T] hydrolysed urea, but arginine catabolism and acid production from glucose were not detected under the aerobic conditions tested. TOSA-KAIYU[T] grew in serum- and urea-supplemented pleuropneumonia-like organism (PPLO) broth under both aerobic and anaerobic conditions at 25 °C; however, colour-changing unit titres were 10-100-fold higher under anaerobic conditions and colony formation on PPLO agar occurred only under anaerobic conditions. Transmission electron microscopy revealed a typical mollicute cellular morphology. 16S rRNA gene sequence analysis indicated that the most closely related type strain of a species with a validly published name was Ureaplasma ceti JCM 39153[T] (92.8% similarity). The average nt identity and digital DNA-DNA hybridization values between TOSA-KAIYU[T] and closely related species were below the accepted thresholds for species delineation. Phylogenetic analysis further showed that TOSA-KAIYU[T] belongs to an uncultured-dominated clade of the genus Ureaplasma, together with U. ceti, which has previously been the only cultured representative of this lineage. Based on the genomic, phenotypic and phylogenetic properties, TOSA-KAIYU[T] represents a novel species of the genus Ureaplasma, for which the name Ureaplasma rhincodontis sp. nov. with type strain TOSA-KAIYU[T] (=JCM 39612[T] =KCTC 25996[T]) is proposed. The genomic G+C content and draft genome size of the type strain were 26.0 mol% and 625,683 bp, respectively.