Comparative genomic analysis and proposal of Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov., three novel Clostridium sensu stricto endophytes with diverse capabilities of acetic acid and ethanol production.

OBJECTIVES: Genus Clostridium sensu stricto is generally regarded as the true Clostridium genus, which includes important human and animal pathogens and industrially relevant microorganisms. Besides, it is also a prominent member of plant-associated endophytes. However, our knowledge of endophytic Clostridium is limited. METHODS: In this study, the endophytes were isolated under anaerobic condition from the roots of Paris polyphylla Smith var. yunnanensis. Subsequently, a polyphasic taxonomic approach was used to clarify their taxonomic positions. The fermentation products were measured in the isolates with HPLC analysis. Comparative genomics was performed on these new strains and other relatives. RESULTS: In total, nine endophytic strains belonging to the genus Clostridium sensu stricto were isolated, and three of them were identified as new species. Seven of nine strains could produce acetate, propionate, and butyrate. Only two strains could produce ethanol, although genomics analysis suggested that only two of them were without genes for solventogenesis. Different from the endophytic strains, the phylogenetically closely related non-endophytic strains showed significant enrichment effects on some metabolic pathways involving environmental information processing, carbohydrate, and amino acid metabolisms, etc. It suggests that the genomes of these endophytic strains had undergone subtle changes associated with environmental adaptations. CONCLUSION: Consequently, strains YIM B02505T, YIM B02515T, and YIM B02565T are proposed to represent a new species of the genus Clostridium sensu stricto, for which the names Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov. are suggested.

Genome-based analyses reveal heterotypic synonyms of Streptomyces species and associated subspecies.

In the genus Streptomyces, several validly described species have been reduced to synonyms of earlier described species though additional synonyms remain to be detected given the previous dependence on traditional phenotypic methods. In this study, genome-based procedures, including DNA-DNA hybridization analyses, overall genome-related indices, such as ANI, dDDH and AAI, revealed that certain strains recorded genomic indices above the threshold values used to define species boundaries. The results of phylogenetic and phylogenomic trees based on concatenated and phylogenomic analyses showed that 33 out of 364 tested species could be assigned to 15 species groups and that 18 Streptomyces species names be reclassified as later heterotypic synonyms of earlier validly published species. Consequently, it is proposed that S. albaduncus is a later heterotypic synonym of S. griseoloalbus; S. bellus is a synonym of S. coeruleorubidus; S. gancidicus and S. rubiginosus are synonyms of S. pseudogriseolus; S. niveoruber is a synonym of S. griseoviridis; S. griseomycini is a synonym of S. griseostramineus; S. jietaisiensis is a synonym of S. griseoaurantiacus; S. pluricolorescens is a synonym of S. rubiginosohelvolus; S. nashvillensis is a synonym of S. tanashiensis; S. yerevanensis is a synonym of S. flaveus; S. durhamensis is a synonym of S. filipinensis; S. recifensis is a synonym of S. griseoluteus; S. canaries and S. olivaceoviridis are synonyms of S. corchorusii; S. melanosporofaciens is a synonym of S. antimycoticus; S. albulus is a synonym of S. noursei; and S. janthinus and S. violarus are synonyms of S. violaceus. Additionally, seven of these 18 Streptomyces species have been designated subspecies.

Neobacillus paridis sp. nov., an endophyte of Paris polyphylla Smith var. yunnanensis.

A novel endophytic strain, designated YIM B02564T, was isolated from the root of Paris polyphylla Smith var. yunnanensis obtained from Yunnan Province, southwest China. By using a polyphasic approach, cells of the strain were characterized as facultative anaerobic, Gram-positive and rod-shaped. The growth conditions of the strain were found to occur at 20-55 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, pH 7.0). Strain YIM B02564T can tolerate 2% NaCl concentration. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM B02564T belonged to the genus Neobacillus and the 16S rRNA gene sequence similarity values of strain YIM B02564T to the type strains of members of this genus ranged from 95.6 to 97.8%. The DNA G+C content of strain YIM B02564T calculated from the whole genome sequence was 41.6 mol%. Values of the ANI and the dDDH between strain YIM B02564T and its closely related Neobacillus species were below 77.9% and 21.5%. Strain YIM B02564T contained MK-7 as the major menaquinone, iso-C15:0 and anteiso-C15:0 as the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and four unidentified lipids. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. On the basis of polyphasic analysis, strain YIM B02564T could be differentiated genotypically and phenotypically from recognized species of the genus Neobacillus. The isolate therefore represents a novel species, for which the name Neobacillus paridis is proposed. The type strain is YIM B02564T (= JCM 34668T = CGMCC 1.18655T).

Janibacter endophyticus sp. nov., an Endophytic Actinobacterium Isolated from the Root of Paris polyphylla Smith var. Yunnanensis.

A novel endophytic actinobacterium, designated as strain YIM B02568T, was isolated from the root of Paris polyphylla Smith var. Yunnanensis obtained from Yunnan Province, southwest China. Strain YIM B02568T was characterized using a polyphasic approach. Phylogenetic analysis indicated that this isolate belonged to the genus Janibacter. The 16S rRNA gene sequence similarity values of strain YIM B02568T to the type strains of members of this genus ranged from 95.8 to 98.6%. However, overall genome relatedness indices were significantly lower than the widely accepted species-defined threshold. The cell wall of strain YIM B02568T contained meso-diaminopimelic acid. The major menaquinone was MK-8(H4). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. The major cellular fatty acids were comprised of iso-C16:0 and C18:1 ω9c. The DNA G + C content was 71.6 mol%. Based on the data from the polyphasic studies, we propose that strain YIM B02568T represents a novel species within the genus Janibacter, Janibacter endophyticus sp. nov. The type strain is YIM B02568T (= JCM 34639T = CGMCC 1.18658T).

Azospirillum Endophyticum sp. nov., an Endophyte of Paris Polyphylla Smith var. Yunnanensis.

A Gram-negative, facultative anaerobic bacterial strain, designated YIM B02556T, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan Province, southwest China. By using a polyphasic approach, its taxonomic position was investigated. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM B02556T belonged to the genus Azospirillum and the 16S rRNA gene sequence similarity values of strain YIM B02556T to the type strains of members of this genus ranged from 94.9 to 98.3%. Overall genome relatedness index (OGRI) analysis estimated based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between YIM B02556T and other Azospirillum species type strains were <90.8% and <37.8%, lower than the limit of species circumscription. Cells of the strain were characterized as oxidase- and catalase-positive, with motility provided by flagella. The growth conditions of the strain were found to occur at 20-40 °C (optimum, 35 °C), and pH 6.0-9.5 (optimum, pH 7.5). Strain YIM B02556T can tolerate 2% NaCl concentration. Strain YIM B02556T contained Q-10 as the major ubiquinone. The major fatty acids were C18:1 ω7c and summed feature three (C16:1 ω7c and/or C16:1 ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Based on polyphasic analysis, strain YIM B02556T could be differentiated genotypically and phenotypically from recognized species of the genus Azospirillum. Therefore, the isolate represents a novel species, for which the name Azospirillum endophyticum is proposed. The type strain is YIM B02556T (=JCM 34631T=CGMCC 1.18654T).

A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation.

Nitrate is one of the major inorganic nitrogen sources for microbes. Many bacterial and archaeal lineages have the capacity to express assimilatory nitrate reductase (NAS), which catalyzes the rate-limiting reduction of nitrate to nitrite. Although a nitrate assimilatory pathway in mycobacteria has been proposed and validated physiologically and genetically, the putative NAS enzyme has yet to be identified. Here, we report the characterization of a novel NAS encoded by Mycolicibacterium smegmatis Msmeg_4206, designated NasN, which differs from the canonical NASs in its structure, electron transfer mechanism, enzymatic properties, and phylogenetic distribution. Using sequence analysis and biochemical characterization, we found that NasN is an NADPH-dependent, diflavin-containing monomeric enzyme composed of a canonical molybdopterin cofactor-binding catalytic domain and an FMN-FAD/NAD-binding, electron-receiving/transferring domain, making it unique among all previously reported hetero-oligomeric NASs. Genetic studies revealed that NasN is essential for aerobic M. smegmatis growth on nitrate as the sole nitrogen source and that the global transcriptional regulator GlnR regulates nasN expression. Moreover, unlike the NADH-dependent heterodimeric NAS enzyme, NasN efficiently supports bacterial growth under nitrate-limiting conditions, likely due to its significantly greater catalytic activity and oxygen tolerance. Results from a phylogenetic analysis suggested that the nasN gene is more recently evolved than those encoding other NASs and that its distribution is limited mainly to Actinobacteria and Proteobacteria. We observed that among mycobacterial species, most fast-growing environmental mycobacteria carry nasN, but that it is largely lacking in slow-growing pathogenic mycobacteria because of multiple independent genomic deletion events along their evolution.

Chryseobacterium paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis.

A Gram-negative, yellow-pigmented, rod-shaped bacterial strain YIM B02567T was isolated from the root of Paris polyphylla Smith var. yunnanensis in China. Strain YIM B02567T grew optimally at 25-30 °C and at pH 7.0 in the absence of NaCl on nutrient agar. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain YIM B02567T belong to the genus Chryseobacterium, and was closely related to Chryseobacterium piperi CTMT and Chryseobacterium soli DSM 19298T. Whole genome sequencing indicated that the genome size was 4,774,612 bp and with a G + C content of 34.5 mol%. Values of the ANI and the dDDH between strain YIM B02567T and its closely related Chryseobacterium species were below 81.72% and 24.7%. Strain YIM B02567T contained menaquinone-6 as the sole isoprenoid quinone, anteiso-C15:0, iso-C17:1 ω9c and iso-C17:0 3-OH as major fatty acids and phosphatidylethanolamine as major polar lipid. Based on the polyphasic analyses, strain YIM B02567T could be differentiated genotypically and phenotypically from recognized species of the genus Chryseobacterium. The isolate, therefore, represents a novel species, for which the name Chryseobacterium paridis sp. nov. is proposed. The type strain is YIM B02567T (= CGMCC 1.18657T).

Reclassification of Friedmanniella endophytica, Lysinimicrobium sediminis and Lechevalieria rhizosphaerae as Microlunatus kandeliicorticis nom. nov., Demequina sediminis comb. nov. and Lentzea rhizosphaerae comb. nov., respectively.

According to Rule 37a of the International Code of Nomenclature of Prokaryotes, the name of a taxon must be changed if the nomenclatural type of the taxon is excluded. Recently, in a transfer of actinobacterial species, three species - Friedmanniella endophytica Tuo et al. 2016, Lysinimicrobium sediminis Hamada et al. 2017 and Lechevalieria rhizosphaerae Zhao et al. 2017 - were not transferred with their type species. Therefore, to resolve these nomenclatural issues, Microlunatus kandeliicorticis nom. nov., Demequina sediminis comb. nov. and Lentzea rhizosphaerae comb. nov. are proposed, respectively.

Paenibacillus paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis.

A Gram-reaction-positive, endospore-forming and rod-shaped bacterial strain, designated py1325T, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan Province, PR China, and subjected to a polyphasic taxonomic characterization. It grew optimally with 0-1 % NaCl (w/v), at pH 7 and at 30 °C. The major respiratory quinone was MK-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major cellular fatty acid was anteiso-C15 : 0. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and two unidentified lipids. The results of 16S rRNA gene sequence analysis revealed the highest levels of sequence similarity with respect to Paenibacillus luteus R-3T (99.0 %), Paenibacillus sinopodophylli CCTCC AB 2016047T (97.9 %), Paenibacillus castaneae DSM 19417T (97.5 %) and Paenibacillus endophyticus LMG 27297T (97.2 %). The digital DNA-DNA hybridization and average nucleotide identity values between py1325T and these species ranged 20.6-53.3 % and 79.9-93.6 %. The G+C content of the genomic DNA was 47.7 mol%. According to the phylogenetic, phenotypic and chemotaxonomic evidence, strain py1325T clearly represents a novel species of the genus Paenibacillus, for which the name Paenibacillus paridis sp. nov. is proposed. The type strain is py1325T (=CCTCC AB 2015220T=LMG 29068T).

Elioraea thermophila sp. nov., a thermophilic bacterium from hot spring of the class Alphaproteobacteria, emended description of the genus Elioraea and proposal of Elioraeaceae fam. nov.

A Gram-staining-negative, aerobic, curved rod-shaped and thermophilic bacterial strain, designated YIM 72297T, was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China. Growth was observed at pH 5.0-9.0 with an optimum of pH 7.0-7.5, and at 45-60 °C with an optimum of 55 °C. Positive for catalase and oxidase. The 16S rRNA gene sequence comparison indicated that strain YIM 72297T was most closely related to Elioraea tepidiphila DSM 17972T (96.9 %) and showed <91 % sequence similarities to members of the order Rhodospirillales. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 72297T formed a distinct lineage within the genus Elioraea, and revealed that the genus Elioraea formed a novel family-level clade in the order Rhodospirillales. The ANI and the dDNA-DNA hybridization estimate values between strains YIM 72297T and Elioraea tepidiphila DSM 17972T were 70.8 and 20.1 %, respectively. Strain YIM 72297T contained Q-10 as the predominant ubiquinone. The major fatty acids (>5 %) were summed C18 : 0 (35.8 %), summed feature 8 (30.1 %), C16 : 0 (12.6 %), C18 : 1 2OH (5.6 %) and C16 : 0 2OH (5.4 %). The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, diphosphosphatidylglycerol and phosphatidylglycerol in addition to two unidentified aminolipids. The DNA G+C content of YIM 72297T was 70.8 mol% (draft genome). On the basis of the polyphasic taxonomic evidence presented in this study, strain YIM 72297T should be classified as representing a novel species of the genus Elioraea, for which the name Elioraea thermophila sp. nov. is proposed, with the type strain YIM 72297T (=CCTCC AB 2017169T=KCTC 62323T). In addition, a novel family, Elioraeaceae fam. nov., is proposed to accommodate the genus Elioraea.

Vallicoccus soli gen. nov., sp. nov., a novel actinobacterium isolated from soil, and description of Vallicoccaceae fam. nov., Motilibacterales ord. nov.

A novel Gram-stain-positive, aerobic, cocci-shaped actinobacterium, designated YIM 75000T, was isolated from a soil sample collected from a dry-hot river valley in Yunnan Province, P.R. China. Growth was observed at 10-45 °C (optimal 37 °C), 0-8% (w/v) NaCl (optimal at 0-3% NaCl) and pH 6.0-8.0 (optimal at pH 7.3). The peptidoglycan contained LL-diaminopimelic acid, glycine, glutamic acid as well as alanine and its type was A3γ with an LL-Dpm-Gly interpeptide bridge. The major cellular fatty acids (> 10%) were C16:0, Summed In Feature 3 (C16:1 ω6c/C16:1 ω7c) and C17:1 ω8c. The predominant menaquinone was MK-9(H4). The major whole-cell sugars contained rhamnose, ribose, arabinose and mannose. The DNA G+C content was 77.0 mol%. The 16S rRNA gene sequence similarities of strain YIM 75000T with other species were less than 94%. Phylogenetic analyses based on 16S rRNA gene sequences and genome data, revealed that strain YIM 75000T together with the genus Motilibacter formed a distinct phylogenetic lineage within the phylum Actinobacteria, separating them from members of all orders. Strain YIM 75000T showed 73.4-73.7% average nucleotide identity and 19.5-19.7% digital DNA-DNA hybridization identity with the closely related genus Motilibacter. Based on the phenotypic, phylogenetic and chemotaxonomic data, it is proposed that the new isolate represents the nomenclature type of the novel species Vallicoccus soli gen. nov., sp. nov. (YIM 75000T = DSM 45377T = KCTC 49228T = CGMCC 1.13844T) which is the nomenclature type of the novel genus Vallicoccus gen. nov. within Vallicoccaceae fam. nov and Motilibacterales ord. nov in the phylum Actinobacteria. The family Vallicoccaceae fam. nov. and the order Motilibacterales (contains Vallicoccaceae fam. nov. and Motilibacteraceae Lee 2013) ord. nov. are formally proposed.

Genome-based taxonomic classification within the family Thermoactinomycetaceae.

The family Thermoactinomycetaceaecomprises 43 validly published species, which were identified by a polyphasic taxonomic study based on molecular phylogenetics, physiological and biochemical characteristics. However, phylogenetic analysis merely based on 16S rRNA gene sequences cannot infer a robust and reliable phylogeny. For disentangling the phylogenetic relationships among members of this family, we used a large collection of genome data and the approach of phylogenomics, to re-examine their taxonomy. The topologies of phylogenomic trees are different from those of the 16S rRNA gene sequences. In addition, based on the average nucleotide identity, digital DNA-DNA hybridization, phenotypic and biochemical characteristics, we found that Laceyella sediminis should be reclassified as a later heterotypic synonym of Laceyella tengchongensis; and reclassified Thermoactinomyces guangxiensis as Paenactinomyces guangxiensis gen. nov., comb. nov.; and establish Novibacillaceae fam. nov. to accommodate the genus Novibacillus as the type genus. In addition, compared to values calculated directly from genome sequences, the genomic DNA G+C contents mentioned in some species descriptions are too imprecise; and the corrected G+C content values have a significantly better fit to the phylogeny. Thus, the corresponding emendations of species descriptions are also proposed. In this paper, phylogenomics has been used to resolve the classification of the family Thermoactinomycetaceae.

Aquabacterium tepidiphilum sp. nov., a moderately thermophilic bacterium isolated from a hot spring.

A Gram-stain-negative, aerobic, non-spore-forming and rod-shaped bacterium, designated YIM 730274T, was isolated from a sediment sample collected from a hot spring located in Tibet, PR China, and was characterized by using a polyphasic taxonomy approach. Cells were motile by means of a polar flagellum. The strain was oxidase- and catalase-positive, and contained polyalkanoates and polyphosphate as storage polymers. Growth occurred at 25-50 °C, at pH 6.0-8.5 and with 0.5-1.0 % NaCl. The major fatty acids (>10 %) were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The known polar lipids comprised of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine. The isoprenoid quinone was Q-8. The G+C content of genomic DNA was 70.7 mol%. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the strain forms a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Aquabacterium in the class Betaproteobacteria. The most closely related phylogenetic neighbours were Aquabacterium limnoticumABP-4T (97.8 % 16S rRNA gene sequence identity) and Aquabacterium communeB8T (97.2 % 16SrRNA gene sequence identity). DNA-DNA relatedness values between YIM 730274T and A. limnoticum KCTC 23306T (46.4±0.4 %) and A. commune DSM 11901T (42.2±1.2 %) were well below the 70 % limit for species identification. YIM 730274T was distinguishable from other members of the genus Aquabacterium by the differences in phenotypic, chemotaxonomic and genotypic characteristics. YIM 730274T merits recognition as a representative of a novel species of the genus Aquabacterium. It is proposed that the isolate should be classified in the genus Aquabacterium as representing a novel species, Aquabacteriumtepidiphilum sp. nov. The type strain is YIM 730274T (=KCTC 52716T=CCTCC AB 2016295T).

Bailinhaonella thermotolerans gen. nov., sp. nov., a new member of the order Streptosporangiales.

A Gram-positive, aerobic, non-motile actinobacterium, designated YIM 75507T, that was isolated from a soil sample collected from a dry-hot valley, was subjected to a polyphasic taxonomic study. The isolate formed branched hyphae and no fragmentation was found. Clustered spore chains were borne from aerial mycelium. The cell-wall peptidoglycan contained glutamic acid, alanine and meso-diaminopimelic acid. Whole-cell sugars were galactose, mannose, glucosamine, glucose and ribose. The major menaquinones were MK-9(H6), MK-9(H8) and MK-10(H6). The polar phospholipids contained phosphatidylmethylethanolamine, phosphatidylethanolamine and ninhydrin-positive phosphoglycolipid. Major fatty acids were iso-C16 : 0 and 10-methyl-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 75507T formed a stable and distinct lineage clustered with the genus Sinosporangium in the family Streptosporangiaceae. The draft genome sequence of strain YIM 75507T exhibited low average nucleotide identity to the closest related strain, Sinosporangium album CPCC 201354T (83.97 %), well below the 95-96 % species circumscription threshold. The G+C content of the genomic DNA was 73.8 mol%. On the basis of morphological, chemotaxonomic and phylogenetic evidence, strain YIM 75507T is assigned to a novel species of a new genus, for which the name Bailinhaonella thermotolerans gen. nov., sp. nov. is proposed. The type strain of Bailinhaonella thermotolerans is YIM 75507T (=KCTC 49229T=CGMCC 4.7547T).

Rhodobacter thermarum sp. nov., a novel phototrophic bacterium isolated from sediment of a hot spring.

An ovoid to rod-shaped, phototrophic, purple non-sulfur bacterium was isolated from a sediment sample of a hot spring in Tibet, China. Cells of strain YIM 73036T were Gram-stain negative, non-motile and multiplied by binary fission. Strain YIM 73036T grew optimally at pH 7.0-7.5 at 37-45 °C. Growth occurred in 0.5-3.5% (w/v) NaCl. Vitamins were not required for growth. The presence of photosynthesis genes pufL and pufM were shown and photosynthesis pigments were formed. Bacteriochlorophyll α, the bacteriopheophytin and carotenoids were present as photosynthetic pigments. Internal cytoplasmic membranes were of the lamellar type. The organism YIM 73036T was able to grow chemo-organoheterophically, chemo-lithoautotrophically and photo-organoheterotrophically but photo-lithoautotrophic and fermentative growth were not demonstrated. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain YIM 73036T is closely related to Rhodobacter blasticus ATCC 33485T (96.65% sequence similarity) and clustered with species of the genus Rhodobacter of the family Rhodobacteraceae. Whole-genome sequence analyses based on the average nucleotide BLAST identity (ANI < 82%) indicated that this isolate belongs to a novel species. The genomic DNA G+C content of organism YIM 73036T was determined to be 66.0 mol%. Strain YIM 73036T contained Q-10 as the predominant ubiquinone and C18:1ω7c, C18:1ω7c 11-methyl and C18:0 as the major fatty acids. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified phospholipid. Differential phenotypic and chemotaxonomic properties, together with the phylogenetic distinctiveness, demonstrated that strain YIM 73036T is distinguishable from other species of the genus Rhodobacter. On the basis of the data presented, strain YIM 73036T is considered to represent a novel species of the genus Rhodobacter, for which the name Rhodobacter thermarum sp. nov. [type strain YIM 73036T (= KCTC 52712T = CCTCC AB 2016298T)] is proposed.

Actinoplanes deserti sp. nov., isolated from a desert soil sample.

A novel actinomycete, designated strain YIM CF22T, was isolated from a desert soil sample collected from Turpan in Xinjiang Uyghur Autonomous Region, north-western China. The taxonomic position of the strain YIM CF22T is described based on a polyphasic approach. Strain YIM CF22T was found to form irregular sporangia on agar media. It contains meso-diaminopimelic acid in the cell wall peptidoglycan. The major menaquinone was identified as MK-9(H4); the polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified phospholipids and two unidentified glycolipids. The whole cell sugars were found to be ribose, mannose, galactose, glucose and xylose. The major cellular fatty acids were found to be (> 5%) iso-C16:0 (43.5%), anteiso-C17:0 (10.2%), iso-C15:0 (7.1%), C17:1 ω8c (6.3%) and iso H-C16:1 (5.9%). The G+C content was determined to be 70.8%. 16S rRNA gene sequence analysis of strain YIM CF22T showed high similarity (97.0%) to Actinoplanes rishiriensis NBRC 108556T. The strain also showed high 16S rRNA gene sequence similarities to Verrucosispora sediminis CGMCC 4.3550T (96.9%) and Micromonospora tulbaghiae DSM 45142T (96.8%). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM CF22T clusters with A. rishiriensis NBRC 108556T, Actinoplanes globisporus JCM 3186T and Actinoplanes rhizophilus NEAU-A-2T. Based on the differential phenotypic characteristics and the results of DNA-DNA relatedness and phylogenetic analysis, it is proposed that strain YIM CF22T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes deserti sp. nov. is proposed. The type strain is YIM CF22T (= KCTC 39543T = CCTCC AB2018113T).

Tepidimonas sediminis sp. nov. and Tepidimonas alkaliphilus sp. nov., two novel moderately thermophilic species isolated from a hot spring.

The taxonomic positions of two moderately thermophilic bacteria, strains YIM 72259T and YIM 72238T, isolated from a hot spring sediment sample were determined using polyphasic taxonomic approaches. Pairwise comparison of the 16S rRNA gene sequences showed that strains YIM 72259T and YIM 72238T are closely related to Tepidimonas ignava SPS-1037T (97.0 and 97.5%, respectively), Tepidimonas taiwanensis I1-1T (96.5 and 97.3%), while sharing 98.0% sequence similarity with each other. The DNA-DNA relatedness values of strains YIM 72238T with T. ignava SPS-1037T and T. taiwanensis I1-1T were determined to be 25.2 ± 1.2 and 24.6 ± 3.1%, respectively, while the two strains (YIM 72259T and YIM 72238T) had a relatedness value of 38.3 ± 4.4% between themselves. The two strains were aerobic, Gram-stain negative, motile by means of a polar flagellum and formed non-pigmented colonies. The DNA G+C contents of strains YIM 72259T and YIM 72238T were determined to be 71.6 and 68.9 mol%, respectively. The major fatty acids in both strains were identified as (> 10%) C16:0, C17:0 and summed feature 8, while the strain YIM 72238T contained a moderately high amount of summed feature 3 as well. The polar lipid profiles for strains YIM 72259T and YIM 72238T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and several unidentified phospholipids. Besides the morphological and chemotaxonomic characteristics, phylogenetic analyses of the 16S rRNA gene sequences and the biochemical characteristics indicated that the two strains represented two novel members of the genus Tepidimonas, for which the name Tepidimonas sediminis sp. nov. [type strain YIM 72259T (= NBRC 112410T = CGMCC 1.15971T) and Tepidimonas alkaliphilus sp. nov. [type strain YIM 72238T (= KCTC 52717T = CCTCC AB 2017168T)] are proposed.

Phenylobacterium terrae sp. nov., isolated from a soil sample of Khyber-Pakhtun-Khwa, Pakistan.

A Gram-stain negative, aerobic, motile, non-spore-forming and rod-shaped bacterial strain, designated YIM 730227T, was isolated from a soil sample, collected from Karak district, Khyber-Pakhtun-Khwa, Pakistan. The bacterium was characterized using a polyphasic taxonomic approach. Pairwise comparison of the 16S rRNA gene sequences showed that strain YIM 730227T is closely related to Phenylobacterium lituiforme FaiI3T (97.5% sequence similarity), Phenylobacterium muchangponense A8T (97.4%), Phenylobacterium panacis DCY109T (97.1%), Phenylobacterium immobile ET (97.1%) and Phenylobacterium composti 4T-6T (97.0%), while also sharing 98.0% sequence similarity with Phenylobacterium hankyongense HKS-05T after NCBI blast, showing it represents a member of the family Caulobacteraceae. The major respiratory quinone was Q-10 and the major fatty acids were C16:0, summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c), C18:1ω7c 11-methyl and C17:0. The polar lipids were phosphatidylglycerol, unidentified glycolipids, phospholipid and unidentified lipid. The G + C content of the genomic DNA was 68.2 mol%. The DNA-DNA relatedness values of strain YIM 730227T with P. hankyongense HKS-05T, P. lituiforme FaiI3T, P. muchangponense A8T, P. panacis DCY109T, P. immobile ET and P. composti 4T-6T were 31.3 ± 0.6, 26.1 ± 0.2, 24.3 ± 0.1, 21.8 ± 0.9, 19.8 ± 0.6 and 18.2 ± 1.1%, respectively, values lower than 70%. Besides the morphological and chemotaxonomic characteristics, phylogenetic analyses of 16S rRNA gene sequences and the biochemical characteristics indicated that the strain YIM 730227T represents a novel member of the genus Phenylobacterium, for which the name Phenylobacterium terrae sp. nov. (type strain YIM 730227T = KCTC62324T = CGMCC 1.16326T) is proposed.

Anoxybacillus sediminis sp. nov., a novel moderately thermophilic bacterium isolated from a hot spring.

A Gram-stain positive, moderately thermophilic, aerobic, spore-forming and rod-shaped bacterium, designated YIM 73012T, was isolated from a sediment sample collected from a hot spring located in Tibet, China, and was characterized by using a polyphasic taxonomy approach. The strain is oxidase positive and catalase negative. Growth occurred at 37-65 °C (optimum, 45-50 °C), at pH 6.0-8.5 (optimum, pH 7.0-7.5) and with 0.5-3.5% NaCl (optimum, 0.5-1.0%, w/v). The major fatty acids were iso-C15:0, iso-C16:0 and C16:0. The major polar lipids comprised of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylglycerol. The cell wall peptidoglycan contained meso-diaminopimelic acid. The respiratory quinone was MK-7. The G+C content of genomic DNA was 43.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain YIM 73012T forms a distinct lineage with respect to the genus Anoxybacillus in the family Bacillaceae. Based on 16S rRNA gene sequence identities the closely related phylogenetic neighbours are Anoxybacillus caldiproteolyticus DSM 15730T (96.7%) and Saccharococcus thermophilus DSM 4749T (96.6%). Strain YIM 73012T was distinguishable from the closely related reference strains by the differences in phenotypic, chemotaxonomic and genotypic characteristics, and represents a novel species of the genus Anoxybacillus, for which the name Anoxybacillus sp. nov. is proposed. The type species is Anoxybacillus sediminis sp. nov., with the type strain YIM 73012T (= KCTC 33884T = DSM 103835T).

Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus.

BACKGROUND: Staphylococcus argenteus and S. schweitzeri, were recently proposed as novel species within S. aureus complex (SAC). S. argenteus has been reported in many countries and can threaten human health. S. schweitzeri has not been associated with human infections, but has been isolated from non-human primates. Questions regarding the evolution of pathogenicity of these two species will remain elusive until an exploratory evolutionary framework is established. RESULTS: We present genomic comparison analysis among members of SAC based on a pan-genome definition, which included 15 S. argenteus genomes (five newly sequenced), six S. schweitzeri genomes and 30 divergent S. aureus genomes. The three species had divergent core genomes and rare interspecific recombination was observed among the core genes. However, some subtypes of staphylococcal cassette chromosome mec (SCCmec) elements and prophages were present in different species. Of 111 tested virulence genes of S. aureus, 85 and 86 homologous genes were found in S. argenteus and S. schweitzeri, respectively. There was no difference in virulence gene content among the three species, but the sequence of most core virulence genes was divergent. Analysis of the agr locus and the genes in the capsular polysaccharides biosynthetic operon revealed that they both diverged before the speciation of SAC members. Furthermore, the widespread geographic distribution of S. argenteus, sequence type 2250, showed ambiguous biogeographical structure among geographically isolated populations, demonstrating an international spread of this pathogen. CONCLUSIONS: S. argenteus has spread among several countries, and invasive infections and persistent carriage may be not limited to currently reported regions. S. argenteus probably had undergone a recent host adaption and can cause human infections with a similar pathogenic potential.