Family Dermacoccaceae Research Articles

Metallococcus carri gen. nov., sp. nov., a novel member of the family Dermacoccaceae isolated from an automotive air conditioning system.

Strain designated DB0510T was isolated from an automobile evaporator core collected in Korea. Cells are gram-stain-positive, aerobic, and coccoid. The strain grew at 15-45℃, pH 5.0-8.5 and 0-8.0% (w/v) NaCl. Growth occurs on R2A, trypticase soy agar, Luria-Bertani agar, and nutrient agar. Phylogenetic analysis showed that the strain belongs to the family Dermacoccaceae and strain DB0510T was distinctly separated from validly named genera of this family. Signature nucleotides in 16S rRNA gene sequence revealed that the strain contained the Dermacoccaceae family-specific 16S rRNA signature nucleotides patterns. The major fatty acids were C17:0 and C17:1 cis-9. The only menaquinone was MK-8 (H4). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, and two unidentified lipids. The diagnostic cell-wall amino acid at position 3 of the peptide subunit was found to be lysine. The cell-wall peptidoglycan contained alanine, aspartic acid, glutamic acid, glycine, lysine, and serine and thus the peptidoglycan type was concluded to be of A4α type with Lys-Gly-Ser-Asp interpeptide bridge. The genome size was 3.49 Mbp and G + C content of the genome DNA was 69.4mol%. On the basis of the phenotypic, genomic, and chemotaxonomic characteristics, strain DB0510T is considered to represent a novel genus and species within the family Dermacoccaceae, for which the name Metallococcus carri gen. nov., sp. nov. is proposed. The type strain of Metallococcus carri is DB0510T (= KACC 19663T = NBRC 113349T).

Leekyejoonella antrihumi gen. nov., sp. nov., a new member of the family Dermacoccaceae isolated from a cave soil.

A novel Gram-stain-positive, actinobacterial strain, designated C5-26T, was isolated from soil from a natural cave in Jeju, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The organism was aerobic, and cells were non-spore-forming, non-motile cocci that occurred singly, in pairs, in triplets, in tetrads, in short chains or in irregular clusters. Colonies of the cells were circular, convex, entire and white. The peptidoglycan type was A4α with an l-Ser-d-Asp interpeptide bridge. The whole-cell sugars comprised glucose, rhamnose, mannose, arabinose, galactose and ribose. The major menaquinone was MK-8(H4). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The major fatty acids were iso-C16 : 0 and iso-C16 : 1 h. The size of the draft genome was 5.32 Mbp with depth of coverage of 161×. The G+C content of the genomic DNA was 67.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel isolate belonged to the family Dermacoccaceae and formed a distinct subcluster at the base of the radiation of the genus Luteipulveratus. Highest sequence similarities of the novel isolate were found to the type strains of Luteipulveratus halotolerans (96.2 %), Branchiibius hedensis (95.4 %), Luteipulveratus mongoliensis (95.4 %) and Branchiibius cervicis (95.3 %). The whole genome-based phylogeny supported the novelty of the isolate at the genus level in the family Dermacoccaceae. On the basis of data from this polyphasic study, strain C5-26T (=KCTC 39632T=DSM 108676T) represents a novel species of a new genus in the family Dermacoccaceae, for which the name Leekyejoonella antrihumi gen. nov., sp. nov. is proposed.

Allobranchiibius huperziae gen. nov., sp. nov., a member of Dermacoccaceae isolated from the root of a medicinal plant Huperzia serrata (Thunb.).

A Gram-stain-positive, non-spore-forming actinobacterial strain, designated CPCC 204077T, was isolated from the surface-sterilized root of a medicinal plant Huperzia serrata (Thunb.) collected from Sichuan Province, south-west China. The peptidoglycan type of strain CPCC 204077T was detected as A4α with an l-Lys-l-Ser-d-Asp interpeptide bridge. Galactose, glucose, rhamnose and ribose were the sugar compositions in the whole-cell hydrolysates. MK-8(H4) was the only menaquinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified phospholipid and one unidentified glycolipid. The major fatty acid was iso-C16 : 0. The genomic DNA G+C content was 71.0 mol%. The phylogenetic tree based on 16S rRNA gene sequences showed that strain CPCC 204077T stood for a distinct lineage within the family Dermacoccaceaealongside the genera Branchiibius, Demetria and Barrientosiimonas, with the highest 16S rRNA gene sequence similarities to Branchiibius hedensis Mer 29717T (95.0 %), Calidifontibacter indicus PC IW02T (95.0 %), Barrientosiimonas humi 39T (94.9 %) and Demetria terragena HKI 0089T (94.7 %), and less than 94.7 % sequence similarities to all other species. Signature nucleotides in the 16S rRNA sequence showed that the strain contained the Dermacoccaceaefamily-specific 16S rRNA signature nucleotides and a genus-specific diagnostic nucleotide signature pattern. Combining the genotypic and phenotypic analyses, we propose that strain CPCC 204077T represents a novel species of a new genus in the family Dermacoccaceae with the name Allobranchiibius huperziae gen. nov., sp. nov. Strain CPCC 204077T (=NBRC 110719T=DSM 29531T) is the type strain of the type species.

Calidifontibacter terrae sp. nov., an actinomycete isolated from soil, with potential applications in cosmetics.

An aerobic, Gram-stain-positive, oxidase- and catalase-positive, non-motile, non-spore-forming, coccoid, creamish-white-coloured bacterium, designated strain R161T, was isolated from soil in Hwaseong, South Korea. The cell-wall peptidoglycan contained glycine, glutamic acid, alanine, aspartic acid, serine and lysine, and whole-cell sugars were galactose, rhamnose, glucose and ribose. Strain R161T showed antibacterial and enzyme inhibitory activities. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain R161T formed a lineage within the family Dermacoccaceae, and showed highest sequence similarity with type strains of Calidifontibacter indicus PC IW02T (97.71 % sequence similarity) and Yimella lutea YIM 45900T (97.58 %). The sequence similarity of strain R161T with type strains of members of the genus Dermacoccus was less than 96.5 %. The major menaquinone was MK-8(H4). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, anteiso-C17 : 1ω9c, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. The DNA G+C content of strain R161T was 73.9 mol%. The DNA-DNA hybridization value between strain R161T and C. indicus JCM 16038T was 52.1 %. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, strain R161T represents a novel species of genus Calidifontibacter, for which the name Calidifontibacter terrae sp. nov. is proposed. The type strain of Calidifontibacter terrae sp. nov. is R161T (=KEMB 9005-404T=KACC 18906T=JCM 31558T).

Yimella radicis sp. nov., an endophytic actinobacterium isolated from the root of Paris polyphylla Smith var. yunnanensis.

An endophytic actinobacterial strain, designated py1292T, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan province, China, and subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate in the family Dermacoccaceae and clustered with Yimella lutea (showing the highest similarity of 99.1 %). DNA-DNA relatedness between strain py1292T and Y. lutea YIM 45900T was 45.6±3.2 % (reciprocal 47.8±3.6 %). The novel isolate was found to be a Gram-staining-positive rod, catalase- and oxidase-positive. It grew at pH 6.0-8.0, with 0-9 % NaCl and at 20-45 ºC, optimally at pH 7.0, with 0-3 % NaCl and at 28 ºC. The predominant menaquinone was MK-8(H4), while the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, two unknown phospholipids and two unknown polar lipids. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. The whole-cell hydrolysates contained mannose, ribose, rhamnose, glucose and galactose. The peptidoglycan contained alanine, glycine, serine, aspartic acid, glutamic acid and lysine. The genomic DNA G+C content was determined to be 65.6 mol%. Phylogenetic, phenotypic and chemotaxonomic data (especially the same peptidoglycan type) showed that strain py1292T should be classified as a representative of a novel species of the genus Yimella, for which the name Yimella radicis sp. nov. is proposed. The type strain is py1292T (=KCTC 39612T=LMG 29070T).

Barrientosiimonas endolithica sp. nov., isolated from pebbles, reclassification of the only species of the genus Tamlicoccus, Tamlicoccus marinus Lee 2013, as Barrientosiimonas marina comb. nov. and emended description of the genus Barrientosiimonas.

Strain JC268(T) was isolated from pebbles collected from a dam located in Lalitpur, Uttar Pradesh, India. Cells of strain JC268(T) were coccoid, appeared in pairs/triads/tetrads or short chains and were Gram-stain-positive, non-spore-forming, non-motile and obligately aerobic. Strain JC268(T) was catalase- and oxidase-positive and utilized citrate for growth. The genomic DNA G+C content of strain JC268(T) was 65.3 mol%. The cell-wall peptidoglycan contained L-lysine-L-serine-D-aspartic acid as interpeptide bridge with the type A4α. The major menaquinone was MK-8(H4). Major (>10%) fatty acids were iso-C16 : 0, iso-C16 : 1H and anteiso-C17 : 1ω9c. Diphosphatidylglycerol, phosphoglycolipid, phosphatidylinositol, glycolipid, four unidentified lipids, an amino lipid and phospholipid were the polar lipids of strain JC268(T). EzTaxon-e blast search of 16S rRNA gene sequences showed that strain JC268(T) has highest similarity to Barrientosiimonas humi 39(T) (98.65%) and Tamlicoccus marinus MSW-24(T) (97.8%) of the family Dermacoccaceae. Genome reassociation (based on DNA-DNA hybridization) of strain JC268(T) with Barrientosiimonas humi CGMCC 4.6864(T) ( = 39(T)) and T. marinus KCTC 19485(T) ( = MSW-24(T)) yielded values of 32.5 ± 2% and 27.3 ± 2%, respectively. Based on the data from phylogenetic and polyphasic taxonomic analyses, strain JC268(T) represents a novel species of the genus Barrientosiimonas for which the name Barrientosiimonas endolithica sp. nov., is proposed. The type strain of Barrientosiimonas endolithica is JC268(T) ( = KCTC 29672(T) = NBRC 110608(T)). Our data suggest that T. marinus should be reclassified within the genus Barrientosiimonas. Thus, a reclassification is proposed for T. marinus, the type and only species of the genus Tamlicoccus, as Barrientosiimonas marina comb. nov., which implies the emendation of the description of the genus Barrientosiimonas.

A bumpy road to the diagnosis of a Kytococcus schroeteri shunt infection

We report a ventriculoperitoneal shunt infection associated with Kytococcus schroeteri, a Gram-positive bacterium from the family Dermacoccaceae. While the biochemical identification systems do not reliably identify this potential pathogen, sequence-based identification is recommended to guide the antibiotic treatment of this intrinsically meticillin-resistant species, which is susceptible to vancomycin, gentamicin and/or rifampicin.

Hexavalent chromium reduction by an actinobacterium Flexivirga alba ST13T in the family Dermacoccaceae

An isolated strain Flexivirga alba ST13(T) was examined for the reducing activity of hexavalent chromium (Cr(VI)). Strain ST13(T) grew in the liquid medium containing 0.33 mM Cr(VI) under aerobic cultivation, even though growth was inhibited on agar minimal media containing 0.31 mM Cr(VI). The growth in the liquid medium containing Cr(VI) at 3 mM was severely inhibited, and the concentration of Cr(VI) decreased below the detection limit within 13 days. Most of the Cr(VI) was eliminated from the liquid medium in the log phase and the stationary phase. XANES analysis of the precipitate shows the presence of Cr(OH)(3), indicating the bacterial reduction of Cr(VI) to trivalent chromium (Cr(III)). The bacterial Cr(VI) reduction was more efficient in minimal medium supplemented with molasses than with glucose. These results strongly suggest that the isolate F. alba ST13(T) is a novel actinobacterium with Cr(VI) reducing activity that is stimulated by molasses.

Branchiibius cervicis sp. nov., a novel species isolated from patients with atopic dermatitis

Novel actinobacterial strains, PAGU 1247 T, PAGU 1251 and PAGU 1252, were isolated from the skin of atopic dermatitis patients and were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that these isolates were located within the family Dermacoccaceae. The most closely related species of PAGU 1247 T in phylogenetic terms was Branchiibius hedensis Mer 29717 T, with 16S rRNA gene sequence similarity of 99.6%, although the DNA–DNA relatedness value was less than 43.9%. Some biochemical traits, such as lipase (C14) and α-galactosidase activity, could distinguish these isolates from B. hedensis. Strain PAGU 1247 T contained iso-C 16:0 and brC 18:0 as the major fatty acids. The quinone system consisted of menaquinone MK-8(H 6 and H 4). The G + C content of the genomic DNA was 67.6 mol%. On the basis of its phenotypic properties and genetic distinctiveness, strains PAGU 1247 T, PAGU 1251 and PAGU 1252 represents a novel species of the genus Branchiibius, for which the name Branchiibius cervicis sp. nov. is proposed. The type strain is PAGU 1247 T (=NBRC 106593 T = DSM 24166 T).

Flexivirga alba gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae

A novel actinobacterial strain ST13(T) isolated from soil near wastewater treatment facilities of an electroplating plant was subjected to a polyphasic taxonomic study. Cells of this organism were non-sporulating, and were irregular coccoid to comma shaped. The peptidoglycan of strain ST13(T) contained glutamic acid, serine, alanine, glycine and lysine, and represented the peptidoglycan type A4α. The whole-cell sugars contained ribose, glucose, galactose, rhamnose and mannose. The predominant menaquinone was MK-8(H(4)). The major fatty acid was iso-C(16:0). The polar lipid contained phosphatidylglycerol. The DNA G+C content was 67.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ST13(T) fell within the radius of the family Dermacoccaceae, and its closest neighbor was Luteipulveratus mongoliensis MN07-A0370(T) (95.1%). However, strain ST13(T) did not make a coherent clade with members of the recognized organisms. On the basis of the phylogenetic and phenotypic characteristics of this actinobacterium, a novel genus and species, Flexivirga alba gen. nov., sp. nov., is proposed. The type strain of F. alba is ST13(T) (= NBRC 107580(T) = DSM 24460(T)).

Calidifontibacter indicus gen. nov., sp. nov., a member of the family Dermacoccaceae isolated from a hot spring, and emended description of the family Dermacoccaceae

During the course of a study on the bacterial diversity in Western Ghats, India, an actinobacterial strain, designated PC IW02(T), was isolated and characterized by a polyphasic taxonomic approach. Strain PC IW02(T) was a non-motile, Gram-positive, short rod that formed creamish white to yellow coloured colonies. 16S rRNA gene sequence analysis showed that the novel strain showed highest sequence similarity with type strains of members of the genus Dermacoccus: Dermacoccus barathri (96.6 %), Dermacoccus profundi (96.5 %), Dermacoccus abyssi (96.4 %) and Dermacoccus nishinomiyaensis (95.9 %). The phylogenetic tree suggested that strain PC IW02(T) could represent a member of a new genus of the family Dermacoccaceae with the genus Demetria as closest clade. Pairwise sequence alignment with Demetria terragena HKI 0089(T) and Kytococcus sedentarius DSM 20547(T) showed similarities of 94.2 and 93.7 %, respectively. Strain PC IW02(T) had MK-8(H(4)) as the major menaquinone. The major fatty acids were iso-C(16 : 0) (43.4 %), iso-C(16 : 1) H (17.2 %) and anteiso-C(17 : 0) (9.9 %). The diagnostic cell-wall amino acid at position 3 of the peptide subunit was lysine; the interpeptide bridge consisted of Gly-Ser-Asp. The polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and phosphatidylserine, along with two unknown phospholipids. The genomic DNA G+C content of the isolate was 77 mol%. On the basis of phenotypic characteristics, including chemotaxonomic data, and 16S rRNA gene sequence similarities, strain PC IW02(T) represents a novel species in a new genus of the family Dermacoccaceae for which the name Calidifontibacter indicus gen. nov., sp. nov. is proposed. The type strain of Calidifontibacter indicus is PC IW02(T) ( = MTCC 8338(T) = DSM 22967(T) = JCM 16038(T)). An emended description of the family Dermacoccaceae is provided.

Branchiibius hedensis gen. nov., sp. nov., an actinobacterium isolated from a Japanese codling (Physiculus japonicus)

A novel, Gram-stain-positive bacterial strain, Mer 29717(T), was isolated from the branchia (gills) of a Japanese codling, Physiculus japonicus, collected from bottom waters of Suruga Bay in Shizuoka, Japan. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain represents a distinct lineage within the family Dermacoccaceae and was related most closely to members of the genera Demetria and Yimella. It shared highest 16S rRNA gene sequence similarity (95.1 %) with Yimella lutea YIM 45900(T). Strain Mer 29717(T) contained MK-8(H(2)) and MK-8(H(4)) as menaquinones, and iso-C(16 : 0), C(16 : 0), C(17 : 1) cis-9, C(17 : 0), C(18 : 1) cis-9 and C(19 : 1) cis-10 were the major cellular fatty acids. The cell-wall peptidoglycan of strain Mer 29717(T) was composed of l-Lys, d-Ser, l-Ser, Gly, d-Glu and d-Ala. Polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and one unidentified phospholipid. Mycolic acids were not detected. The G+C content of the DNA of strain Mer 29717(T) was 68 mol%. On the basis of differential chemotaxonomic, physiological and biochemical data, strain Mer 29717(T) is considered to represent a novel species of a new genus, for which the name Branchiibius hedensis gen. nov., sp. nov. is proposed. The type strain of Branchiibius hedensis is Mer 29717(T) ( = NBRC 106121(T) = DSM 22951(T)).

Yimella lutea gen. nov., sp. nov., a novel actinobacterium of the family Dermacoccaceae

A Gram-stain-positive, coccoid, non-motile, halotolerant actinobacterium, designated YIM 45900(T), was found as a contaminant on an agar plate in the laboratory of Yunnan Institute of Microbiology, China. The peptidoglycan type was A4alpha with an (L)-Lys-(L)-Ser-(D)-Asp interpeptide bridge. The cell-wall sugars contained galactose and fucose. The predominant menaquinone was MK-8(H(4)). The major fatty acids were iso-C(15 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0). The polar lipids contained diphosphatidylglycerol, phosphatidylinositol, a glucosamine-containing phospholipid and an unknown phospholipid. The DNA G+C content was 65.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism falls within the radius of the suborder Micrococcineae and its closest phylogenetic neighbours are the genera of the family Dermacoccaceae. Strain YIM 45900(T) showed 16S rRNA gene sequences similarity values of 93.1-95.9 % with members of the genera Dermacoccus, Demetria and Kytococcus. On the basis of the phylogenetic and phenotypic characteristics of the actinobacterium, a novel genus and species, Yimella lutea gen. nov., sp. nov., are proposed. The type strain of Yimella lutea is YIM 45900(T) (=DSM 19828(T) =KCTC 19231(T) =CCTCC AB 207007(T)).

Luteipulveratus mongoliensis gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae

A novel actinobacterial strain, MN07-A0370(T), was isolated from Mongolian soil and its taxonomic status was determined using a polyphasic approach. Comparative 16S rRNA gene sequence studies revealed that strain MN07-A0370(T) represented a novel lineage within the actinobacteria. Strain MN07-A0370(T) formed a distinct clade in the family Dermacoccaceae and was most closely related to the members of the genera Dermacoccus (16S rRNA gene sequence similarity, 96.2 %-96.4 %), Demetria (94.1 %) and Kytococcus (93.7 %). The cell-wall peptidoglycan of the novel strain contained l-lysine, alanine, aspartic acid, glutamic acid and serine and represented peptidoglycan type A4alpha. The menaquinones were MK-8(H(4)) and MK-8(H(6)). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol and the whole-cell sugars were galactose, mannose, rhamnose, ribose and glucose. Mycolic acids were absent. The fatty acid profile was characterized by the presence of large amounts of saturated iso- and anteiso-branched-chain fatty acids as well as smaller amounts of saturated straight-chain and unsaturated acids. The major fatty acids were iso-C(16 : 0), anteiso-C(17 : 0), iso-C(16 : 1) H, C(17 : 1)omega9c and C(17 : 0) 10-methyl. The G+C content of the DNA was 68.2 mol%. On the basis of chemotaxonomic, physiological and biochemical differences from other genera of the family Dermacoccaceae, strain MN07-A0370(T) should be classified as representing a novel species in a new genus, for which we propose the name Luteipulveratus mongoliensis gen. nov., sp. nov. The type strain is MN07-A0370(T) (=NBRC 105296(T)=VTCC D9-09(T)).

Complete genome sequence of Kytococcus sedentarius type strain (541).

Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. Kytococcus sedentarius is known for the production of oligoketide antibiotics as well as for its role as an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted keratolysis. It is strictly aerobic and can only grow when several amino acids are provided in the medium. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long single replicon genome with its 2639 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.