Discovery of a new bacterium, Microbacterium betulae sp. nov., in birch wood associated with hypersensitivity pneumonitis in woodworkers

A Gram-positive, aerobic, rod-shaped mesophilic bacterium was isolated from birch wood, referred to as the AB strain. Allergological tests suggest that this strain may cause allergic alveolitis in sawmill workers. Employing a polyphasic taxonomic approach, the AB strain's 16S rRNA gene sequence showed high similarity to Microbacterium barkeri and M. oryzae, with 97.25% and 96.91%, respectively, a finding supported by rpoB and gyrB sequence analysis. Further genome sequence comparison with the closely related M. barkeri type strain indicated a digital DNA-DNA hybridization value of 25.5% and an average nucleotide identity of 82.52%. The AB strain's cell wall peptidoglycan contains ornithine, and its polar lipids comprise diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Its major fatty acids include anteiso C15:0, anteiso C17:0, and iso C16:0, while MK-10 is its predominant respiratory quinone. Comprehensive analysis through 16S rRNA, whole-genome sequencing, phenotyping, chemotaxonomy, and MALDI-TOF MS profiling indicates that the AB strain represents a new species within the Microbacterium genus. It has been proposed to name this species Microbacterium betulae sp. nov., with ABT (PCM 3040T = CEST 30706T) designated as the type strain.

Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium

The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the Microbacterium type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus Microbacterium was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a Microbacterium liquefaciens clade and distributed further into four subclusters in the core genome-based phylogenetic tree. In vitro phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA-DNA hybridization supported that the study strains constituted four new species of the genus Microbacterium. In addition, some Microbacterium type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family Microbacteriaceae based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, Microbacterium aurugineum sp. nov., Microbacterium croceum sp. nov., Microbacterium galbinum sp. nov., and Microbacterium sufflavum sp. nov., are described, along with the proposal of Paramicrobacterium gen. nov. containing five reclassified Microbacterium species from the "Microbacterium agarici clade", with Paramicrobacterium agarici gen. nov., comb. nov. as the type species.

Draft Whole-Genome Sequences of Microbacterium oxydans and Microbacterium maritypicum Strains

Microbacterium spp. are a group of microbes that have been recovered from a wide variety of environments in nature. Here, I report the complete genomic data for Microbacterium oxydans and Microbacterium maritypicum type strains that are already present in public culture repositories. The genome of the M. oxydans strain was 3,894,869 bp long, with a G+C content of 68.26%. The genome of the M. maritypicum strain was 3,668,377 bp long, with a G+C content of 68.44%.

Microbacterium algeriense sp. nov., a novel actinobacterium isolated from Algerian oil production waters

A non-motile, straight-rod-shaped, Gram-stain-positive and facultative anaerobic bacterium (i.e., strain G1^T) was isolated from production waters from an Algerian oilfield. Growth was observed in the presence of 0.3-3.5 % (w/v) NaCl, at 20-50 °C and at pH 6.0-9.0. Results of phylogenetic analyses based on 16S rRNA gene sequences showed that strain G1^T belonged to the genus Microbacterium. Strain G1 ^T was closely related to Microbacterium oxydans (DSM 20578^T) and Microbacterium maritypicum (DSM 12512^T) with 99.8 % sequence similarity and to Microbacterium saperdae (DSM 20169^T) with 99.6 % sequence similarity. Strain G1 ^T contained MK9, MK10, MK11, MK12 and MK13 as respiratory quinones, and phosphatidylglycerol, diphosphatidylglycerol and glycolipid as the major polar lipids. The major cellular fatty acids were anteiso-C_15:0, iso-C_16:0 and anteiso-C_17:0. The estimated DNA G+C content was 69.57 mol% based on its draft genome sequence. Genome annotation of strain G1^T predicted the presence of 3511 genes, of which 3483 were protein-coding and 47 were tRNA genes. The DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) values between strain G1^T and M. oxydans (DSM 20578^T) and M. maritypicum (DSM 12512^T) were in both cases far below the respective species boundary thresholds (27.5 and 28.0 % for DDH; and 84.40 and 84.82% for ANI, respectively). Based on the data presented above, strain G1^T was considered to represent a novel species for which the name Microbacterium algeriense is proposed with the type strain G1^T (=DSM 109018^T=LMG 31276^T).

Draft Genome Sequence of Microbacterium oryzae Strain MB-10, Isolated from a Rice Field in India

We report the draft genome sequence of Microbacterium oryzae strain MB-10 T , which was isolated from rice field soil. The genome is 3.04 Mb, with a G+C content of 71.10%, and encodes 2,727 proteins. The genome sequence provides further information about strain MB-10 T and the genus Microbacterium .

Microbacterium rhizosphaerae sp. nov., isolated from a Ginseng field, South Korea

A novel Gram-stain positive, aerobic, short rod-shaped, non-motile bacterium, designated strain CHO1^T, was isolated from rhizosphere soil from a ginseng agriculture field. Strain CHO1^T was observed to form yellow colonies on R2A agar medium. The cell wall peptidoglycan was found to contain alanine, glycine, glutamic acid, D-ornithine and serine. The cell wall sugars were identified as galactose, mannose, rhamnose and ribose. Strain CHO1^T was found to contain MK-11, MK-12, MK-13 as the predominant menaquinones and anteiso-C_15:0, iso-C_16:0, and anteiso-C_17:0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, an unidentified phospholipid and three unidentified glycolipids were found to be present in strain CHO1^T. Based on 16S rRNA gene sequence analysis, strain CHO1^T was found to be closely related to Microbacterium mangrovi DSM 28240^T (97.81 % similarity), Microbacterium immunditiarum JCM 14034^T (97.45 %), Microbacterium oryzae JCM 16837^T (97.33 %) and Microbacterium ulmi KCTC 19363^T (97.10 %) and to other species of the genus Microbacterium. The DNA G+C content of CHO1^T was determined to be 70.1 mol %. The DNA-DNA hybridization values of CHO1^T with M. mangrovi DSM 28240^T, M. immunditiarum JCM 14034^T, M. oryzae JCM 16837^T and M. ulmi KCTC 19363^T were 46.7 ± 2, 32.4 ± 2, 32.0 ± 2 and 29.2 ± 2 %, respectively. On the basis of genotypic, phenotypic and phylogenetic properties, it is concluded that strain CHO1^T represents a novel species within the genus Microbacterium, for which the name Microbacterium rhizosphaerae sp. nov. is proposed. The type strain of M. rhizosphaerae is CHO1^T (= KEMB 7306-513^T = JCM 31396^T).

Microbacterium nanhaiense sp. nov., an actinobacterium isolated from sea sediment

A Gram-staining-positive, heterotrophic, anaerobic, non-spore-forming, non-motile, rod-shaped strain, OAct400T, belonging to the genus Microbacterium was isolated from a sediment collected from a depth of 2093 m in the South China Sea, China. The strain was identified using a polyphasic taxonomic approach. The strain grew well on yeast extract/malt extract agar (ISP 2) and nutrient agar media, and formed no aerial mycelium and no diffusible pigments on any media tested. The strain grew in the presence of 0-8 % (w/v) NaCl (optimum, 2-4 %), at pH 5.0-10.0 (optimum, pH 7.0) and at 4-37 °C (optimum, 28 °C). Strain OAct400T contained ornithine as the diagnostic diamino acid. The whole-cell sugars were dominated by glucose and galactose. The predominant menaquinones were MK-11 (51 %) and MK-10 (24 %). The major phospholipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were anteiso-C15 : 0 (59.35 %), iso-C16 : 0 (17.89 %) and anteiso-C17 : 0 (16.09 %). DNA-DNA relatedness with Microbacterium amylolyticum DSM 24221T and Microbacterium gubbeenense CIP 107184T, the nearest phylogenetic relatives (97.73 and 97.44 % 16S rRNA gene sequence similarity, respectively) was 31.3 ± 2.1 and 28.7 ± 1.2 %, respectively. On the basis of phenotypic, phylogenetic and genotypic data, a novel species, Microbacterium nanhaiense sp. nov., is proposed. The type strain is OAct400T ( = CGMCC 4.7181T = DSM 26811T = KCTC 29185T).

Vibrio panuliri sp. nov., a marine bacterium isolated from spiny lobster, Panulirus penicillatus and transfer of Vibrio ponticus from Scophthalmi clade to the newly proposed Ponticus clade

A novel marine bacterium, strain LBS2(T) was isolated from eggs carried on pleopods of the spiny lobster collected from Andaman Sea. Heterotrophic growth occurred at 1-7% NaCl. 16S rRNA gene sequence similarity revealed the strain LBS2(T) belonged to the genus Vibrio and showed above 97% similarity with eight type strains of the genus Vibrio. Multilocus analysis based on ftsZ, gapA, gyrB, mreB, pyrH recA, rpoA, and topA revealed LBS2(T) formed a separate cluster with Vibrio ponticus DSM 16217(T) with 89.8% multilocus gene sequence similarity. However, strain LBS2(T) is distantly related with other members of the Scophthalmi clade in terms of 16S rRNA signatures, phenotypic variations and multilocus gene sequence similarity, for which we propose LBS2(T) belongs to a new clade i.e. Ponticus clade with V. ponticus DSM 16217(T) as the representative type strain of the clade. DNA-DNA homologies between strain LBS2(T) and closely related strains were well below 70%. DNA G + C content was 45.3 mol%. On the basis of our polyphasic study, strain LBS2(T) represents a novel species of the genus Vibrio, for which the name Vibrio panuliri sp. nov. is proposed. The type strain is LBS2(T) (= JCM 19500(T) = DSM 27724(T) = LMG 27902(T)).

Microbacterium hydrothermale sp. nov., an actinobacterium isolated from hydrothermal sediment

A Gram-stain-positive, aerobic, non-motile, rod-shaped bacterium, strain 0704C9-2(T), was isolated from hydrothermal sediment of the Indian Ocean. The organism grew with 0-5% (w/v) NaCl and at 10-37 °C, with optimal growth occurring with 1% NaCl and at 28-30 °C. Comparative 16S rRNA gene sequence analysis revealed that strain 0704C9-2(T) belonged to the genus Microbacterium. It exhibited highest 16S rRNA gene sequence similarity with Microbacterium testaceum DSM 20166(T) (98.4%). Levels of similarity with the type strains of all other recognized species of the genus Microbacterium were less than 98.0%. DNA-DNA hybridization experiments with strain 0704C9-2(T) and its closest relative, M. testaceum DSM 20166(T), revealed a low reassociation value of 42.9%. The DNA G+C content of strain 0704C9-2(T) was 73.3 mol%. The cell-wall peptidoglycan contained ornithine and the acyl type was glycolyl. The major whole-cell sugars were mannose, galactose, rhamnose and glucose. The major cellular fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C16:0 and iso-C15:0. The predominant menaquinones were MK-11, MK-10 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids and an unknown phospholipid. On the basis of phenotypic, phylogenetic and genotypic data, strain 0704C9-2(T) represents a novel species within the genus Microbacterium, for which the name Microbacterium hydrothermale sp. nov. is proposed. The type strain is 0704C9-2(T) ( = LMG 27542(T) = CGMCC 1.12512(T)).

Marinomonas fungiae sp. nov., isolated from the coral Fungia echinata from the Andaman Sea

A novel aerobic marine bacterium, strain AN44T, was isolated from the coral Fungia echinata sampled from the Andaman Sea, India. Cells were Gram-negative, motile and rod-shaped. Oxidase and catalase tests were positive. Heterotrophic growth was observed at pH 5.5–10 and at 16–42 °C, with optimum growth at pH 7–8 and 28 °C. Strain AN44T grew in the presence of 0.5–11 % (w/v) NaCl; the optimal NaCl concentration for growth was 3–5 %. The DNA G+C content was 47.8 mol%. Predominant cellular fatty acids of strain AN44T were C18 : 1ω7c, C16 : 1ω7c/C16 : 1ω6c, C16 : 0, C10 : 0 3-OH, C12 : 0, C10 : 0, C14 : 0 and C18 : 0. The sole isoprenoid ubiquinone was Q-8. The polar lipids were an unidentified phospholipid, an unidentified aminophospholipid and two unidentified glycolipids. 16S rRNA gene sequence comparisons revealed that strain AN44T clustered within the radiation of the genus Marinomonas and showed similarity of 97.9 % with Marinomonas ostreistagni UST010306-043T, 97.8 % with Marinomonas aquimarina 11SM4T, 97.1 % with Marinomonas brasilensis R-40503T and 97.0 % with Marinomonas communis 8T. However, DNA–DNA relatedness between strain AN44T and closely related type strains was well below 70 %. On the basis of the data from the present polyphasic taxonomic study, strain AN44T is considered to represent a novel species of the genus Marinomonas , for which the name Marinomonas fungiae sp. nov. is proposed. The type strain is AN44T ( = JCM 18476T = LMG 27065T).

Taxonomic study of the genus Tepidiphilus: transfer of Petrobacter succinatimandens to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov., emended description of the genus Tepidiphilus and description of Tepidiphilus thermophilus sp. nov., isolated from a terrestrial hot spring

Comparative phenotypic, chemotaxonomic and genetic analysis revealed significant similarities among strains of the genera Tepidiphilus and Petrobacter. Analysis of 16S rRNA gene sequences and DNA-DNA relatedness of the type strains Tepidiphilus margaritifer N2-214(T) and Petrobacter succinatimandens 4BON(T) showed sequence similarity of 98.9 % and less than 40 % relatedness, indicating that these strains represent different species of same genus. Both strains had phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol as major polar lipids. Their fatty acid profiles were almost identical, with the predominant fatty acids C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. In view of this, we propose to transfer the member of the genus Petrobacter to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov. and to emend the description of the genus Tepidiphilus. Further, a novel bacterium, strain JHK30(T), was isolated from a terrestrial hot spring located at Jharkhand, India, and was identified following a polyphasic approach. Cells were non-sporulating, aerobic, Gram-stain-negative rods and motile by a single polar flagellum. Optimum temperature for growth was 50-55 °C at pH 6.5-7.0. 16S rRNA gene sequence analysis revealed 99.71 % similarity with P. succinatimandens 4BON(T) ( = DSM 15512(T)) and 98.71 % with T. margaritifer N2-214(T) ( = DSM 15129(T)). However, DNA-DNA relatedness of strain JHK30(T) with these two type strains was well below 70 %. The DNA G+C base composition was 66.1 mol%. Strain JHK30(T) represents a novel species of the genus Tepidiphilus for which the name Tepidiphilus thermophilus sp. nov. is proposed. The type strain is JHK30(T) ( = JCM 19170(T) = LMG 27587(T)= DSM 27220(T)).