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The genus Rothia are emerging as opportunistic pathogens associated with various infections in immunocompromised and immunocompetent individuals. This review describes the taxonomy, cell wall structure, pathogenesis, phenotypic and molecular characteristics, clinical diseases, treatment and, as well as, the related genera that may be misidentified by Rothia species., (Copyright © 2021. Published by Elsevier B.V.)

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants having health hazards. PAH-utilizing bacterial strains were isolated from petroleum-contaminated soil from siding area, Bijwasan supply location of BPCL, Delhi, India. Bacterial strains with different morphology were isolated and acclimatized to a mixture of low molecular weight PAH compounds in the concentration range of 50-10,000 mg/L. Two bacterial strains surviving at 10,000 mg/L PAH concentration were identified as Kocuria flava and Rhodococcus pyridinivorans, based on 16S rRNA gene sequencing and phylogenetic analysis over MEGA X, are reported for the first time for PAH degradation. The strain K. flava could degrade phenanthrene, anthracene, and fluorene with efficiency of 55.13%, 59.01%, and 63.46%, whereas R. pyridinivorans exhibited 62.03%, 64.99%, and 66.79% degradation for respective PAHs at initial PAH concentration of 10 mg/L. Slightly lower degradation of phenanthrene could be attributed to its more stable chemical structure. The consortium of both the strains degraded 61.32%, 64.72%, and 66.64%, of 10 mg/L of phenanthrene, anthracene, and fluorene, respectively, in 15 days of incubation period indicating no synergistic or antagonistic effect towards degradation. Catechol 2,3-dioxygenase (C23O), dehydrogenase and peroxidase enzyme activities during PAH degradation coincided with degradation of PAHs, thus highlighting the role of these enzymes in catabolising three-ring PAHs. This is the first investigation confirming the participation of C23O, dehydrogenase and peroxidases enzyme profiles throughout the period of degradation. The study concludes that these strains can play significant role in microbial remediation of PAH-contaminated environment., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

A Gram-staining positive, non-spore forming, non-pigmented and non-motile bacterium, designated strain NCCP-1664 T , was isolated from Cholistan desert, Pakistan. Cells of strain NCCP-1664 T were strictly aerobic, catalase positive and oxidase negative with a rod to coccus growth cycle and can grow at pH 6.0-9.0 (optimum pH 7-8) at 28-45 °C (optimum 37 °C) and could tolerate 0-16% NaCl (optimum 2%). Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain NCCP-1664 T belongs to the family Micrococcaceae and was related to members of the genus Arthrobacter having highest sequence similarities with Arthrobacter ginkgonis (98.9%), A. halodurans (97.7%) and A. oryzae (97.1%) and less than 97% with other related taxa. DNA-DNA relatedness values of strain NCCP-1664 T with above mentioned type strains were found to be less than 54%, whereas digital DDH and average nucleotide identity (ANI) values with A. oryzae were 20.9 and of 74.3%, respectively. DNA G + C content of strain NCCP-1664 T was 70.0 mol%. Chemotaxonomic data of strain NCCP-1664 T showed the peptidoglycan type as A3α L-Lys-L -Ala; menaquinones as MK-9(H 2 ) (67%), MK-8(H 2 ) (32%) and MK-7(H 2 ) (1%), major fatty acids as anteiso -C 15:0 (51.2%), anteiso-C 17:0 (9.6%) and C 18:1 ω9c (6.9%) and polar lipids profile comprising of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, digalactosyldiacylglycerol, small amounts of monogalactosyldiacylglycerol, trimannosyldiacylglycerol and three unidentified lipids. The phylogenomic analyses along with chemotaxonomic data, physiological, biochemical characteristics allowed to describe it as representative of a novel genus, for which the name Zafaria cholistanensis gen. nov. sp. nov. is proposed with the type strain NCCP-1664 T (= DSM 29936 T  = KCTC 39549 T ).

An alkaliphilic actinobacterial strain, designated Hz 6-5 T , was isolated from saline-alkaline soil from Songnen Plain in north-eastern China. The isolate formed light yellow-colored colonies and its cells were Gram-staining positive, non-motile, and non-spore-forming short rods. The strain was aerobic with optimal growth at 33 °C, pH 9.0, and in the presence of 0.5% (w/v) NaCl or 3% (w/v) KCl. It was catalase-positive and oxidase-negative. The isolate had highest 16S rRNA gene sequence similarities to the type strains of the species Nesternkonia natronophila M8 T (98.2%), N. salmonea GY074 T (98.1%), and N. sphaerica GY239 T (97.4%), and the isolate formed a subclade with the type strains of these species in the neighbor-joining tree based on the 16S rRNA gene sequences. The phylogenetic tree based on the phylogenomic analysis also showed the same results. The DNA‒DNA relatedness (DDH) values of isolate Hz 6-5 T with N. natronophila M8 T , N. halophila DSM 16378 T , and N. halobia CGMCC 1.2323 T were 21.2%, 36.5%, and 32.0%, respectively. The characteristic diamino acid of strain Hz 6-5 T was found to be lysine. The respiratory quinones were MK-9, MK-8, MK-7(H 4 ), MK-7(H 2 ) and MK-7 and the major cellular fatty acids (> 10%) were anteiso-C 15:0 , anteiso-C 17:0 and iso-C 16:0 . The polar lipids detected for strain Hz 6-5 T were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid, and two unidentified phospholipids. The DNA G + C content of isolate Hz 6-5 T was 60.8%. Based on the results of phylogenetic analysis supported by morphological, physiological, chemotaxonomic, and other differentiating phenotypic evidence, strain Hz 6-5 T is considered to represent a novel species of the genus Nesterenkonia, for which the name Nesterenkonia haasae sp. nov. is proposed. The type strain is Hz 6-5 T (=CPCC 205100 T =NBRC 113521 T ).

Promotion of mushroom growth by means of biological agents replacing chemicals is an emerging and highly demanded issue in the sector of mushroom cropping. The present study was aimed to search for a novel bacterium potentially able to enhance mushroom growth and yield. A total of 2165 bacterial isolates purified from different samples were scrutinized through various growth-promoting attributes. As a consequence of rigorous screening, 26 isolates found exhibiting positive traits of mushroom growth promotion. Thereafter, in response to the cocultivation (fungus and bacteria), a potent bacterial strain was isolated capable to improve significantly the mycelial growth. In cocultivation the highest radial and linear growth rate was 7.6 and 8.1 mm/day on 10th and 11th days, respectively. The fruitbody yields and biological efficiency (BE) of the inoculated sets were 28% and 58% higher than the uninoculated control sets. The bacterium was molecularly identified based on 16S ribosomal RNA sequencing and confirmed as Glutamicibacter arilaitensis MRC119. Therefore, the bioinoculant of the current bacterium can be potentially useful as an ecofriendly substitute stimulating the production of mushroom fruit bodies with improved BE., (© 2020 Wiley-VCH GmbH.)

A novel cold-tolerant bacterium, designated strain YJ56 T , was isolated from Antarctic soil collected from the Cape Burk area. Phylogenetic analysis through 16S rRNA gene sequence similarity revealed that strain YJ56 T was most closely related to the genus Pseudarthrobacter , including Pseudarthrobacter oxydans DSM 20119 T (99.06 % similarity), Pseudarthrobacter polychromogenes DSM 20136 T (98.98 %) and Pseudarthrobacter sulfonivorans ALL T (98.76 %). The genome size (5.2 Mbp) of strain YJ56 T was the largest among all the published genomes of Pseudarthrobacter type strains (4.2-5.0 Mbp). The genomic G+C content of strain YJ56 T (64.7 mol%) was found to be consistent with those of other Pseudarthrobacter strains (62.0-71.0 mol%). The average nucleotide identity and average amino acid identity values between strain YJ56 T and P. sulfonivorans ALL T were estimated at 84.1 and 84.2 %, respectively. The digital DNA-DNA hybridization value between the two strains was calculated to be 28.0 %. This rod-shaped and obligate aerobic strain exhibited no swimming or swarming motility. It had catalase activity but no oxidase activity. Cells grew at 4-28 °C (optimum, 13 °C) and pH 5.0-11.0 (optimum, pH 7.0) and with 0-6.0 % (w/v) NaCl (optimum, 0%) in Reasoner's 2A medium. MK-9 (H2) was the sole menaquinone. Two-dimensional TLC results revealed that the primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two glycolipids and phosphatidylinositol. Fatty acid methyl ester analysis showed that anteiso-C 15 : 0 , anteiso-C 17 : 0 , iso-C 15 : 0 , C 16 : 0 and iso-C 16 : 0 were the major cellular fatty acids in strain YJ56 T . Based on phenotypic and genotypic characteristics, strain YJ56 T represents a novel species of the genus Pseudarthrobacter , and thus the name Pseudarthrobacter psychrotolerans sp. nov is proposed. The type strain is YJ56 T (=JCM 33881 T =KACC 21510 T ).

Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as biodegradable versions of common plastics. PHA-producing microbes are therefore in great demand and a plethora of different environments, especially extreme habitats, have been probed for the presence of PHA-accumulators. However, the polar region has been neglected in this regard, probably due to the low accessibility of the sampling material and unusual cultivation regime. Here, we present the results of a screening procedure involving 200 bacterial strains isolated from 25 habitats of both polar regions. Agar-based tests, microscopy, and genetic methods were conducted to elucidate the biodiversity and potential of polar-region PHA-accumulators. Microscopic observation of Nile Red stained cells proved to be the most reliable screening method as it allowed to confirm the characteristic bright orange glow of the Nile Red-PHA complex as well as the typical morphology of the PHA inclusions. Psychrophilic PHA-producers belonged mostly to the Comamonadaceae family (Betaproteobacteria) although actinobacterial PHA synthesizers of the families, Microbacteriaceae and Micrococcaceae also featured prominently. Glacial and postglacial habitats as well as developed polar region soils, were evaluated as promising for PHA-producer bioprospection. This study highlights the importance of psychrophiles as biodiverse and potent polyhydroxyalkanoate sources for scientific and application-aimed research.

In the context of increasingly airtight homes, there is currently little known about the type and diversity of microorganisms in the home, or factors that could affect their abundance, diversity and nature. In this study, we examined the type and prevalence of cultivable microorganisms at eight different sites in 100 homes of older adults located in Glasgow, Scotland. The microbiological sampling was undertaken alongside a household survey that collated information on household demographics, occupant behaviour, building characteristics, antibiotic use and general health information. Each of the sampled sites revealed its own distinct microbiological character, in both species and number of cultivable microbes. While some potential human pathogens were identified, none were found to be multidrug resistant. We examined whether the variability in bacterial communities could be attributed to differences in building characteristics, occupant behaviour or household factors. Sampled sites furnished specific microbiological characteristics which reflected room function and touch frequency. We found that homes that reported opening windows more often were strongly associated with lower numbers of Gram-negative organisms at indoor sites (p < 0.0001). This work offers one of the first detailed analysis of cultivable microbes in homes of older adults and their relationship with building and occupancy related factors, in a UK context.

A novel aerobic marine actinobacterium (strain S5-52 T ) belonging to the genus Glutamicibacter was isolated from the coral Favia veroni sampled from the Andaman Sea, India. Cells are Gram stain positive and rod shaped. The DNA G+C content was 58.7 mol%. The major quinones were MK-8 and MK-9. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid, trimannosyldiacylglycerol, phospholipid and dimannosylglyceride. The peptidoglycan type was A4α. Strain S5-52 T showed a maximum 16S rRNA similarity of 99.36% with Glutamicibacter halophytocola DSM 101718 T . The genome of strain S5-52 T was 3.57 Mb that contains 3274 protein coding sequences (CDS). DNA-DNA similarity and ANI values between S5-52 T and the reference strains were below 70% and 95-96%, respectively. Analysis of genomic reduction events in the evolutionary path from the LUCA (last universal common ancestor) to G. mishrai LMG 29155 T and G. halophytocola DSM 101718 T exhibit a number of genes involved in amino acid metabolism, cell wall biogenesis and replication, recombination and repair mechanism that reduced in both the species. Based on phenotypic, chemotaxonomic properties and comparative genomic studies, the strain S5-52 T is considered a novel species of the genus Glutamicibacter, for which the name Glutamicibacter mishrai sp. nov. is proposed. The type strain is S5-52 T (= KCTC 39846 T  = LMG 29155 T ).

The environment affects the composition and function of soil microbiome, which indirectly influences the quality of plants. In this study, 16S amplicon sequencing was used to reveal the differences in soil microbial community composition of Cistanche deserticola in three ecotypes (saline-alkali land, grassland and sandy land). Through the correlation analysis of microbial community abundance, phenylethanoid glycoside contents and ecological factors, the regulatory relationship between microbial community and the quality variation of C. deserticola was expounded. The metabolic function profile of soil microbiome was predicted using Tax4Fun. Data showed that the soil microbial communities of the three ecotypes were significantly different (AMOVA, P < 0.001), and the alpha diversity of grassland soil microbial community was the highest. Core microbiome analysis demonstrated that the soil microbial communities of C. deserticola were mostly have drought, salt tolerance, alkali resistance and stress resistance, such as Micrococcales and Bacillales. The biomarkers, namely, Oceanospirillales (saline-alkali land), Sphingomonadales (grassland) and Propionibacteriales (sandy land), which can distinguish three ecotype microbial communities, were excavated through LEfSe and random forest. Correlation analysis results demonstrated that 2'-acetylacteoside is positively correlated with Oceanospirillales in saline-alkali land soil. The metabolic function profiles displayed highly enriched metabolism (carbohydrate and amino acid metabolisms) and environmental information processing (membrane transport and signal transduction) pathways. Overall, the composition and function of soil microbiomes were found to be important factors to the quality variation of C. deserticola in different ecotypes. This work provided new insight into the regulatory relationship amongst the environment, soil microbial community and plant quality variation.

Mucosal immunity develops in the human fetal intestine by 11-14 weeks of gestation, yet whether viable microbes exist in utero and interact with the intestinal immune system is unknown. Bacteria-like morphology was identified in pockets of human fetal meconium at mid-gestation by scanning electron microscopy (n = 4), and a sparse bacterial signal was detected by 16S rRNA sequencing (n = 40 of 50) compared to environmental controls (n = 87). Eighteen taxa were enriched in fetal meconium, with Micrococcaceae (n = 9) and Lactobacillus (n = 6) the most abundant. Fetal intestines dominated by Micrococcaceae exhibited distinct patterns of T cell composition and epithelial transcription. Fetal Micrococcus luteus, isolated only in the presence of monocytes, grew on placental hormones, remained viable within antigen presenting cells, limited inflammation ex vivo and possessed genomic features linked with survival in the fetus. Thus, viable bacteria are highly limited in the fetal intestine at mid-gestation, although strains with immunomodulatory capacity are detected in subsets of specimens.

A novel, Gram-stain-positive, aerobic, non-endospore-forming, non-motile and rod-shaped bacterium designated RB2 T was isolated from sap of Populus euphratica collected in Mulei county, Xinjiang province, PR China. RB2 T was able to grow at 10-45 °C (optimum 35 °C), pH 6.0-12.0 (optimum 8.0) and with 0-12 % (w/v) NaCl (optimum 1 %). The genomic DNA G+C content was 63.5 % (from the genome sequence). The results of the chemotaxonomic analysis indicated that the predominant isoprenoid quinones were MK-8 and MK-9. The major fatty acids were anteiso-C 15 : 0 and anteiso-C 17 : 0 . The major polar lipids of RB2 T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two glycolipids. The peptidoglycan type of RB2 T was A4 α , l-Lys-Gly-l-Glu. The results of the phylogenetic analysis, along with the phenotypic and chemotaxonomic characteristics, indicate that strain RB2 T represents a novel species of the genus Nesterenkonia , for which the name Nesterenkonia muleiensis sp. nov. is proposed. The type strain is RB2 T (=MCCC 1K03528 T =KCTC 49017 T ).

An actinobacterial strain, SCSIO 13007 T , was isolated from seawater collected from the Luhuitou fringing reef at a depth of 4.2 m. Phylogenetic and phenotypic properties of the organism supported the hypothesis that it represented a member of the genus Kocuria . Phylogenetic analysis indicated that the levels of 16S rRNA gene sequence similarity between SCSIO 13007 T and type strains of other recognized members of the genus Kocuria were lower than 96.99 %. Growth in the presence of up to 15 % (w/v) NaCl was a distinctive characteristic of SCSIO 13007 T . Other biochemical and physiological properties and the major fatty acids also differentiated the isolate from its phylogenetically closest relative Kocuria subflava YIM 13062 T . The menaquinone types were MK-7(H 2 ) and MK-8(H 2 ). Major cellular fatty acids were anteiso-C 15 : 0 , iso-C 15 : 0 and anteiso-C 17 : 0 . The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified lipid and an unidentified aminolipid. The DNA G+C content was 73.7 mol%. The combined genotypic and phenotypic data indicated that strain SCSIO 13007 T represents a novel species of the genus Kocuria , for which the name Kocuria coralli sp. nov. is proposed; the type strain is SCSIO 13007 T (=DSM 27811 T =NBRC 109942 T ).

Two Gram-positive, aerobic, non-motile and non-spore-forming actinobacteria, strains GY074 T and GY239 T , were isolated from deep-sea sediment of the Southern Atlantic Ocean. The results of phylogenetic analysis of 16S rRNA gene sequences placed both isolates within the genus Nesterenkonia , and showed a sequence similarity of 98.3 % between the two strains and similarites of 94.3-97.2 % with respect to Nesterenkonia species with validly published names. Based on whole-genome sequences, the values of in silico DNA-DNA hybridization and the average nucleotide identity between strains GY074 T and GY239 T were 21.2 and 78.1 %, respectively, less than the proposed cut-off level for species delineation, i.e. 70 and 95 %. For both strains, the major cellular fatty acids were anteiso-C 17 : 0 and anteiso-C 15 : 0 , and the major menaquinones were MK-7, MK-8 and MK-9. The major polar lipid contents of the two strains were similar with phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C contents of strains GY074 T and GY239 T were 61.1 and 64.2 mol%, respectively. On the basis of the phylogenetic analysis and physiological and chemotaxonomic data, the isolates represent two novel species of the genus Nesterenkonia , for which the names Nesterenkonia salmonea sp. nov. (type strain GY074 T =KCTC 39639 T =MCCC 1A11256 T ) and Nesterenkonia sphaerica sp. nov. (type strain GY239 T =KCTC 39640 T =MCCC 1A10688 T ) are proposed.

Auritidibacter ignavus is a Gram-stain-positive bacillus derived from otorrhea. Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from Auritidibacter ignavus IMMIB L-1656 T (accession number FN554542) by 16S rRNA gene sequencing (97.5 % similarity), were thought to represent a novel species of the genus Auritidibacter . Auritidibacter ignavus DSM 45359 T (=IMMIB L-1656 T ) was acquired to compare with Canadian and Swiss strains by whole-genome sequencing (WGS). Unexpectedly, those isolates were observed to be consistent with A. ignavus DSM 45359 T by WGS (ANIb scores >98 %), MALDI-TOF (Bruker), cellular fatty acid analysis and biochemically (some differences were observed). A nearly full 16S rRNA gene sequence could not be readily prepared from A. ignavus DSM 45359 T , even after multiple attempts. A 16S rRNA gene chimeric consensus sequence created from the genome assembly of A. ignavus DSM 45359 T had only 97.5 % similarity to that of A. ignavus IMMIB L-1656 T , implying that 16S rRNA sequence accession number FN554542 could not be replicated. We concluded that our isolates of members of the genus Auritidibacter were consistent with A. ignavus DSM 45359 T , did not represent a novel species, and that the sequence corresponding to FN554542 was not reproducible. By WGS, A. ignavus DSM 45359 T had genome of 2.53×10 6  bp with a DNA G+C content of 59.34%, while genomes of Canadian and Swiss isolates ranged from 2.47 to 2.59×10 6  bp with DNA G+C contents of 59.3-59.52 %. A. ignavus NML 100628 (=NCTC 14178=LMG 30897) did not demonstrate a rodcoccus cycle. Emendation of Auritidibacter ignavus was proposed based on these results.

Arthrobacterenclensis was reported to cluster with species of the genus Pseudarthrobacter but the peptidoglycan containing lysine, alanine and glutamic acid and the presence of minor amounts of menaquinone MK-8(H 4 ) were not in line with the description of the genus. Re-analysis of these traits revealed a peptidoglycan with l-Lys-l-Ser-l-Thr-l-Ala and no MK-8(H 4 ), but major amounts of MK-9(H 2 ) in the quinone system of A. enclensis DSM 25279 T . These data demonstrate that A. enclensis shares the characteristics of the genus Pseudarthrobacter. Since the reported quinone systems of Pseudarthrobacterphenanthrenivorans [MK-8 and MK-9(H 2 )] and Pseudarthrobacterscleromae [MK-8(H 2 ] were clearly different from those of other species of the genus, the quinone systems of the two species were re-analyzed. Since the polar lipid profile of P. phenanthrenivorans was reported to contain phosphatidylethanolamine, which is unusual for a member of the Micrococcaceae , and the polar lipid profile of P. scleromae was unknown, the polar lipids of these two species were also analysed. The quinone system of P. phenanthrenivorans DSM 18606 T was composed of the major menaquinones MK-9(H 2 ), MK-8(H 2 ) and MK-10(H 2 ) and that of P. scleromae DSM 17756 T was composed of the major menaquinones MK-9(H 2 ) and MK-8(H 2 ) and MK-9. In the polar lipid profile of P. phenanthrenivorans DSM 18606 T no phosphatidylethanolamine could be detected. Based on these results we here propose the reclassification of A. enclensis as Pseudarthrobacterenclensis comb. nov. and emend the descriptions of the genus Pseudarthrobacter and the two species P. phenanthrenivorans and P. scleromae .

Four Gram-stain positive, rod-shaped bacterial isolates, strains JZ R-183 T , JZ RK-117, DI-46 and JZ R-35 T , were recovered from bulk tank raw cow's milk from three different dairy farms in Germany. Analysis of their 16S rRNA gene sequences indicated that these isolates belonged to the family Micrococcaceae , closely related to the genera Arthrobacter , Neomicrococcus,Glutamicibacter and Citricoccus . The 16S rRNA gene sequence similarity between the isolates and the next related type strains was below 97.3 %. Phylogenetic analysis of 16S rRNA, recA and gyrB genes revealed that these isolates formed two different groups in an independent cluster within the family Micrococcaceae . Chemotaxonomic analyses determined anteiso-C 15 : 0 as predominant fatty acid, but also large amounts of iso-C 15 : 0 , iso-C 16 : 0 and iso-C 17 : 0 were detected. The menaquinones MK-9(H 2 ) and MK-7(H 2 ) were present in all of the isolates and the polar lipid pattern contained the phospholipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol and a glycolipid. The peptidoglycan type of the isolates was A4α, with alanine, lysine and glutamate as dominating cell wall amino acids. The fatty acid and menaquinone profile differentiated the strains from the genera Arthrobacter , Neomicrococcus,Citricoccus and Glutamicibacter . The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that the isolates belonged to two novel species of a novel genus, for which the names Galactobacter caseinivorans gen. nov., sp. nov. and Galactobacter valiniphilus sp. nov. are proposed. The type strains are JZ R-183 T (=DSM 107700 T =LMG 30902 T ) and JZ R-35 T (=DSM 107699 T =LMG 30901 T ).

A Gram-stain-positive, aerobic, coccoid-shaped, non-spore-forming actinobacterial strain, designated M5W7-7 T , was isolated from a hot spring soil sample collected from Anshan, Liaoning province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain M5W7-7 T clustered closely with species of the genus Kocuria, and showed the highest sequence similarity of 97.1 % to Kocuria subflava YIM 13062 T . Strain M5W7-7 T grew at 10-37 °C (optimum, 37 °C), pH6.0-11.0 (pH 6.0-7.0) and in the presence of 0-7 % (w/v) NaCl (0 %). Substrate mycelia and aerial mycelia were not formed, and diffusible pigments were not observed on any media tested. Strain M5W7-7 T contained MK-6(H2) and MK-7(H2) as the dominant menaquinones. The polar lipid profile of strain M5W7-7 T contained diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and an unidentified lipid. The predominant whole-cell sugars were galactose and glucose. The predominant fatty acid was anteiso-C15 : 0. The DNA G+C content of strain M5W7-7 T was 67.0 mol%. On the basis of phylogenetic relationships, phenotypic characterization and chemotaxonomic analyses, strain M5W7-7 T represents a novel species of the genus Kocuria, for which the name Kocuriasoli sp. nov. is proposed. The type strain is M5W7-7 T (=KCTC 49195 T =CGMCC 1.13744 T ).

A Gram-stain-positive, alkaliphilic, moderately halophilic, cocci-shaped actinobacterium (strain M8 T ) was isolated from a sample of soda lake sediment (Lake Magadi, Tanzania). The isolate was heterotrophic, strictly aerobic, catalase-positive, oxidase-negative and formed orange-pigmented colonies in solid media. It utilized various sugars and organic acids as sole carbon sources. The organism grew at 10-38 °C, at pH 7.5-12.0 and in the presence of 1-12 % (w/v) NaCl, with optimal growth occurring at 30 °C, at pH 10 and in the presence of 5 % (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain M8 T belonged to the genus Nesterenkonia, sharing the closest similarities to Nesterenkoniahalobia DSM 20541 T , Nesterenkoniahalophila YIM 70179 T and Nesterenkoniaaethiopica DSM 17733 T (97.5, 97.5 and 97.1 %, respectively). The characteristic diamino acid of strain M8 T was found to be lysine and the polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified glycolipids and two unidentified phospholipids. The DNA G+C content was 61.8 mol% (genome). The strain contained MK-7, MK-9 and MK-10 as the respiratory quinones, and the major fatty acids (>10 %) comprised anteiso-C17 : 0 and anteiso-C15 : 0. On the basis of phylogenetic analyses and phenotypic data, strain M8 T is considered to represent a novel species, for which the name Nesterenkonianatronophila sp. nov. is proposed. The type strain is M8 T (=JCM 32100 T =CGMCC 1.16706 T =MCC 3367 T ).

To complete the valid publication of the new species names resulting from reclassification of the genus Clavibacter, we here provide descriptions of Clavibacter insidiosus sp. nov. and Clavibacter tessellarius sp. nov.

A Gram-reaction-positive, non-spore-forming, rod-shaped bacterium, strain C1-50 T , was isolated from a natural cave in Jeju, Republic of Korea by using the serial dilution plating method. Results of phylogenetic analysis using 16S rRNA gene sequences showed that strain C1-50 T belonged to the family Micrococcaceae but had the highest sequence similarity to Arthrobacter halodurans JSM 078085 T (96.18 %) and Arthrobacter globiformis DSM 20124 T (96.04 %). The 16S rRNA gene sequence similarities between strain C1-50 T and other members of the family were lower than 96.0 %. The cell-wall peptidoglycan type was A3α with an l-Lys-l-Ala2. Whole-cell sugars consisted largely of glucose and galactose. The predominant menaquinone was MK-9(H2) with smaller components of MK-7(H2) and MK-8(H2). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The cellular fatty acids consisted of saturated, unsaturated, anteiso-branched and iso-branched components. The G+C content of genomic DNA was 68.8 mol% (draft genome sequence). On the basis of morphological and chemotaxonomic differences and distinct phylogenetic clustering, it was concluded that the organism represents a novel species of a new genus in the family Micrococcaceae, for which the name Specibacter cremeus gen. nov., sp. nov. is proposed. The type strain is C1-50 T (=KCTC 39557 T =DSM 100066 T ).

The species Arthrobacterendophyticus is phylogenetically placed within the Glutamicibacter clade and shares 97.3-98.4 % 16S rRNA gene sequence similarities with the species of this genus. The quinone system with the major menaquinone MK-9 and the peptidoglycan amino acids alanine, glutamic acid and lysine are consistent with the characteristics of the members of the genus Glutamicibacter but the polar lipid profile with phosphatidylinositol distinguishes A. endophyticus from species of the genus Glutamicibacter. Re-analysis of both peptidoglycan structure and polar lipid profile revealed peptidoglycan type l-Lys-l-Ala-l-Glu (A11.35) and a polar lipid profile lacking phosphatidylinositol. These traits are consistent with those of representatives of the genus Glutamicibacter and distinguish A. endophyticus from members of the genus Arthrobacter sensu stricto. Due to its phylogenetic position and congruence with the key characteristics of members of the genus Glutamicibacter we here propose the reclassification of Arthrobacter endophyticus as a species of the genus Glutamicibacter, Glutamicibacter endophyticus comb. nov. (EGI 6500322 T =DSM 28750 T =KCTC 29490 T =JCM 30091 T ).

Although birds are hosts to a large number of microorganisms, microbes have rarely been found in avian oil glands. Here, we report on two strains of a new bacterial species from the preen oil of American barn owls (Tyto furcata). Phenotypic as well as genotypic methods placed the isolates to the genus Kocuria. Strains are non-fastidious, non-lipophilic Gram-positive cocci and can be unambiguously discriminated from their closest relative Kocuria rhizophila DSM 11926 T . In phylogenetic trees, the owl bacteria formed a distinct cluster which was clearly separated from all other known Kocuria species. The same conclusion was drawn from MALDI-TOF MS analyses. Once again, the new bacterial strains were very similar to one another, but exhibited substantial differences when compared to the most closely related species. Besides, the results of the biochemical tests, optimum growth conditions and pigmentation differed from closely related Kocuria spp. Finally, ANIb values of less than 87% provided striking evidence that the isolates recovered from American barn owls represent a hitherto undescribed species, for which we propose the name Kocuria tytonicola sp. nov. The type strain is 489 T (DSM 104133 T =LMG 29945 T , taxonumber TA00340)., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

Avian uropygial glands have received increasing attention in recent years, but little is known about micro-organisms in uropygial glands. In this study, we isolated a strain of Gram-stain-positive, non-motile, non-spore-forming cocci, designated 442 T , from the uropygial gland of an American barn owl (Tyto furcata) and characterized it using a polyphasic approach. 16S rRNA gene sequence analysis placed the isolate in the genus Kocuria. The G+C content was 70.8 mol%, the major menaquinone was MK-7(H2) and the predominant cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. Phylogenetic analyses based on the 16S rRNA gene identified Kocuria rhizophila DSM 11926 T (99.6 % similarity), Kocuria salsicia DSM 24776 T (98.7 %), Kocuria varians DSM 20033 T (98.3 %) and Kocuria marina DSM 16420 T (98.3 %) as the most closely related species. However, average nucleotide identity values below 86 % indicated that the isolate differed from all species hitherto described. Chemotaxonomic analyses and whole-cell protein profiles corroborated these findings. Accordingly, the isolate is considered to be a member of a novel species, for which the name Kocuria tytonis sp. nov. is proposed. The type strain is 442 T (=DSM 104130 T =LMG 29944 T ).

Aims: Clavibacter michiganensis is an important bacterial plant pathogen that causes vast destruction to agriculturally important crops worldwide. Early detection is critical to evaluate disease progression and to implement efficient control measures to avoid serious epidemics. In this study, we developed a sensitive, specific and robust loop-mediated isothermal amplification (LAMP) assay for detection of all known subspecies of C. michiganensis., Methods and Results: Whole genome comparative genomics approach was taken to identify a unique and conserved region within all known subspecies of C. michiganensis. Primer specificity was evaluated in silico and with 64 bacterial strains included in inclusivity and exclusivity panels; no false positives or false negatives were detected. Both the sensitivity and spiked assay of the developed LAMP assay was 1 fg of the pathogen DNA per reaction. A 100% accuracy was observed when tested with infected plant samples., Conclusions: The developed LAMP assay is simple, sensitive, robust and easy to perform using different detection platforms and chemistries., Significance and Impact of the Study: The developed LAMP assay can detect all known subspecies of C. michiganensis. The LAMP process can be performed isothermally at 65°C and results can be visually assessed, which makes this technology a promising tool for monitoring the disease progression and for accurate pathogen detection at point-of-care., (© 2018 The Society for Applied Microbiology.)

A Gram-positive bacterium (DCY118 T ) was isolated from ginseng-cultivated soil in Gochang-gun, Republic of Korea. This isolate was assigned to the genus Ornithinimicrobium and is closely related to Ornithinimicrobium kibberense K22-20 T (98.8%), O. pekingense DSM 21552 T (98.5%), O. algicola JC311 T (98.2%), and O. humiphilum DSM 12362 T (97.9%) based on 16S rRNA gene sequence analysis. However, strain DCY118 T showed < 55% DNA-DNA homology with closely related reference strains. Cells were non-motile, non-sporulating, catalase- and oxidase-positive, aerobic, short rods, and cocci, and produced light-yellow, circular, and smooth colonies on TSA medium. MK-8(H 4 ) was the predominant menaquinone. The major cellular fatty acids were iso-C 15:0 , anteiso-C 15:0 , and C 16:0 . The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), an unknown phospholipid (PL1), an unknown amino lipid (AL1), and unidentified polar lipids (L1-5). The genomic DNA G+C content was 71.1 mol%. The peptidoglycan contained L-ornithine as the diagnostic diamino acid. Whole-cell sugars were composed of glucose, arabinose, and xylose. Overall, data collected from phenotypic and genotypic tests during this study indicated that strain DCY118 T could not be assigned to a recognized species. Strain DCY118 T showed antagonistic activity against the fungal pathogens causing root rot in ginseng, i.e., Fusarium solani (KACC 44891 T ) and Cylindrocarpon destructans (KACC 44660 T ). The results from this study confirm the DCY118 T strain as a new species within the genus Ornithinimicrobium, for which the name Ornithinimicrobium panacihumi is proposed. The type strain is DCY118 T (=KCTC 39962 T =JCM 32156 T ).

The potato phytopathogen Clavibacter michiganensis subsp. sepedonicus (Cms) is a causative agent of bacterial ring rot, which is a serious threat to crops. In EU member countries, Cms is subject to quarantine and has to be combated. The knowledge about the transmission of C. michiganensis strains is limited due to a lack of methods which could be used for epidemiological analysis. In this study, PCR melting profile (PCR MP) and variable number tandem repeat methods were used in Cms epidemiological analysis for the first time. PCR MP was based on the melting temperature analysis of BamHI restriction fragments of chromosomal DNA. Respectively, for the variable number tandem repeat (VNTR) method, six loci were identified and used in the differentiation of Cms isolates. PCR MP was used for 93 Cms isolated in Poland. Both PCR MP and VNTR methods were used for the differentiation of 47 Cms strains in this collection. Both these methods were found to be useful for the epidemiological analysis of Cms. SIGNIFICANCE AND IMPACT OF THE STUDY: The potato phytopathogen, Clavibacter michiganensis subsp. sepedonicus (Cms), is a serious threat to crops and lead to significant economic losses. The only way to control and eliminate the disease caused by this pathogen is the use of certified seed potato and strict quarantine of infected fields. Here, for the first time, two molecular typing methods (PCR melting profile (PCR MP) and variable number tandem repeat (VNTR)) were evaluated in respect of their potential in differentiation of Cms isolates. As a result, we obtained characteristic profiles of DNA fragments (PCR MP) and numeric patterns (VNTR), which enable the intraspecies genotyping of Cms strains confirming the effectiveness of PCR MP and VNTR methods in differentiation of Cms strains., (© 2018 The Society for Applied Microbiology.)

The interest in and demand for natural dyes has increased significantly in recent years; however, very few natural blue dyes are commercially available, because blue colored compounds in nature are relatively rare. In this study, a blue pigment-producing bacteria from Lake Chungará (Atacama Desert, Chile) was isolated, and its blue pigment was purified and chemically characterized. The pigment-producing strain was identified as Pseudarthrobacter sp. by 16S rRNA gene sequencing. The pigment was separated from the filtered culture medium by column chromatography/solid-phase extraction using different resins (ionic exchange, C-18, size exclusion). The strain produced up to 2.5 g L -1 of blue pigment, which was very soluble in water, partially soluble in methanol and insoluble in other organic solvents. The pigment was analyzed and characterized by analytical HPLC, UV-Vis, FT-IR, and H-NMR, and purified by semi-preparative HPLC. The pigment was non-toxic to brine shrimp (LD 50  > 2.3 g L -1 ) and was stable at pH 6-10 at temperatures below 60 °C. HPLC analysis shows that the pigment is composed of four major blue fractions. The physicochemical properties and structural analysis demonstrate that this pigment belongs to the indochrome isomers, whose properties have yet to have been characterized. The high solubility in water, good stability in neutral and basic pH, and negligible toxicity of the blue pigment make it a good candidate suitable for several industrial and possibly some food applications.

The novel strain IHBB 11108 T was a psychrotolerant and alkaliphilic bacterium isolated from the subsurface water of Chandra Tal Lake in the Lahaul-Spiti valley located in the Indian trans-Himalayas. Cells were Gram-stain-positive, aerobic, non-motile, catalase-positive and oxidase-negative. The strain grew at 5-37 °C (optimum 28 °C), pH 5.0-12.0 (optimum pH 7.0) and with up to 8 % NaCl (optimum 1 %). The 16S rRNA gene sequence analysis revealed the highest relatedness of strain IHBB 11108 T with Psychromicrobium silvestre DSM 102047 T (97.5 %), Arthrobacter russicus DSM 14555 T (97.4 %) and Renibacterium salmoninarum ATCC 33209 T (97.4 %). The strain contained a quinone system with 57.2 % MK-9(H2), 39.1 % MK-10(H2), 3.0 % MK-8(H2) and 0.7 % MK-7(H2). The polar lipids detected were diphosphatidylglycerol, dimannosylglyceride, phosphatidylinositol, phosphatidylglycerol, monogalactosyldiacylglycerol, one unidentified glycolipid and four unidentified lipids. The cell-wall peptidoglycan structure type was A3α l-Lys-l-Thr-l-Ala with substitution of the α-carboxyl group of d-Glu by alanine amide. Anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 were the predominant fatty acids. The genomic DNA G+C content was 59.0 mol%. The DNA-DNA relatedness of strain IHBB 11108 T was 46.7±2.2, 43.1±2.5 and 19.1±2.4 % with P. silvestre DSM 102047 T , A. russicus DSM 14555 T and R. salmoninarum ATCC 33209 T , respectively. On the basis of the results of the phenotypic, chemotaxonomic and phylogenetic analyses, IHBB 11108 T is considered to represent a novel species of the genus Psychromicrobium for which the name Psychromicrobium lacuslunae sp. nov. is proposed. The type strain is IHBB 11108 T (=MTCC 12460 T =MCC 2780 T =JCM 31143 T =KACC 19070 T ).

Renibacterium salmoninarum is the causative agent of bacterial kidney disease (BKD), which is a commercially important disease of farmed salmonids. Typing by conventional methods provides limited information on the evolution and spread of this pathogen, as there is a low level of standing variation within the R. salmoninarum population. Here, we apply whole-genome sequencing to 42 R. salmoninarum isolates from Chile, primarily from salmon farms, in order to understand the epidemiology of BKD in this country. The patterns of genomic variation are consistent with multiple introductions to Chile, followed by rapid dissemination over a 30 year period. The estimated dates of introduction broadly coincide with major events in the development of the Chilean aquaculture industry. We find evidence for significant barriers to transmission of BKD in the Chilean salmon production chain that may also be explained by previously undescribed signals of host tropism in R. salmoninarum. Understanding the genomic epidemiology of BKD can inform disease intervention and improve sustainability of the economically important salmon industry. This article contains data hosted by Microreact.

A Gram-positive and non-motile actinobacterium, designated strain EGI 60016 T , was isolated from healthy roots of Glycyrrhiza uralensis F. collected from Xinyuan County, Xinjiang Province, China. The 16S rRNA gene sequence of strain EGI 60016 T was found to show 97.5 and 97.3 % sequence similarities to Nesterenkonia rhizosphaerae EGI 80099 T and Nesternkonia massiliensis NP1 T , respectively. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain EGI 60016 T formed a distinct clade with N. rhizosphaerae EGI 80099 T and N. massiliensis NP1 T . The polar lipids detected for strain EGI 60016 T were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid, an unidentified lipid and an unidentified phospholipid. The DNA G+C content was determined to be 64.1 mol%. Other chemotaxonomic features of strain EGI 60016 T included MK-7, MK-8 and MK-9 as the respiratory quinones, and anteiso-C15 : 0 and anteiso-C17 : 0 as the major fatty acids. Based on the results of the phylogenetic analysis supported by morphological, physiological, chemotaxonomic and other differentiating phenotypic characteristics, strain EGI 60016 T is considered to represent a novel species of the genus Nesterenkonia, for which the name Nesterenkonia endophytica sp. nov. is proposed. The type strain is EGI 60016 T (=CCTCC AB 2017176 T =NBRC 112398 T ).

Most of the species from the genus Kocuria are environmental or commensals of mammalian skin and oral bacteria, and had rarely been associated with human infection. However, recent reports showed an increase of the clinical role of these bacteria in human infectious diseases. Most of the cases occurred in hospitals and were device related. They included bacteremia, peritonitis, abscess, endocarditis and ocular infection. We here describe the main characteristics and the draft genome of Kocuria massiliensis sp. nov., strain P3598 T (CSURP3598), a new Kocuria species that caused foot osteomyelitis in a 78-year-old woman. The improvement of diagnostic tools for the identification of bacteria in microbiological laboratories, including MALDI-TOF MS and 16S rRNA sequencing, largely contributed to the emergence and to the expansion of the clinical spectrum of infections caused by Kocuria spp. To the best of our knowledge, we report here the first case of osteomyelitis with a bacterial species from the genus Kocuria.

Although the genus Clavibacter was originally proposed to accommodate all phytopathogenic coryneform bacteria containing B2γ diaminobutyrate in the peptidoglycan, reclassification of all but one species into other genera has resulted in the current monospecific status of the genus. The single species in the genus, Clavibacter michiganensis, has multiple subspecies, which are all highly host-specific plant pathogens. Whole genome analysis based on average nucleotide identity and digital DNA-DNA hybridization as well as multi-locus sequence analysis (MLSA) of seven housekeeping genes support raising each of the C. michiganensis subspecies to species status. On the basis of whole genome and MLSA data, we propose the establishment of two new species and three new combinations: Clavibacter capsici sp. nov., comb. nov. and Clavibacter tessellarius sp. nov., comb. nov., and Clavibacter insidiosus comb. nov., Clavibacter nebraskensis comb. nov. and Clavibacter sepedonicus comb. nov.

Two new species of Gram-positive cocci were isolated from the uropygial glands of wild woodpeckers (Dendrocopos major) originating from different locations in Germany. A polyphasic approach confirmed the affiliation of the isolates to the genus Kocuria. Phylogenetic analysis based on the 16S rRNA gene showed high degree of similarity to Kocuria koreensis DSM 23367 T (99.0% for both isolates). However, low ANIb values of <80% unequivocally separated the new species from K. koreensis. This finding was further corroborated by DNA fingerprinting and analysis of polar lipid profiles. Furthermore, growth characteristics, biochemical tests, MALDI-TOF MS analysis, and G+C contents clearly differentiated the isolates from their known relatives. Besides, the woodpecker isolates significantly differed from each other in their whole-cell protein profiles, DNA fingerprints, and ANIb values. In conclusion, the isolated microorganisms constitute members of two new species, for which the names Kocuria uropygioeca sp. nov. and Kocuria uropygialis sp. nov. are proposed. The type strains are 36 T (DSM 101740 T =LMG 29265 T ) and 257 T (=DSM 101741 T =LMG 29266 T ) for K. uropygialis sp. nov. and K. uropygioeca sp. nov., respectively., (Copyright © 2017 Elsevier GmbH. All rights reserved.)

In the last decade several new genera have been isolated in alkaline and halophile growth conditions. The studies conducted in the Texcoco Lake soils have shown a generalized microbial adaptation to the specific conditions. In this research work, morphological and phylogenetic characterization of the HN31(22) strain that was isolated from the cited soil is presented. The strain was identified as a Gram-positive halophile and alkaline tolerant bacteria from the Nesterenkonia genus, which uses different substrates in metabolic processes., (© 2018 Marisela Yadira Soto-Padilla et al.)

Aims: Screening of seaweed-associated bacteria capable of producing antimicrobials., Methods and Results: Fifteen microbial strains, associated to the brown seaweed Pelvetia canaliculata (Linnaeus) attached to the rocks of Sonmiani Beach (Karachi, Pakistan), were screened. Crude extract filtrates of CMG S2 strain grew on Zobell marine agar (ZMA) had the most remarkable antimicrobial activity. Based on its phenotypic aspects (e.g. Gram-positive, microccoid form), biochemical characteristics (e.g. halotolerance) and genetic analyses, CMG S2 is identified as a putatively new Kocuria marina type strain belonging to the actinobacteria's class and micrococcaceae family. Thereby, the nucleotide sequence analysis of its full-length 16S ribosomal ribonucleic acid (rRNA) gene (GenBank accession number EU073966.1) displayed highest identity (i.e. 99%) and score (2630) with K. marina KMM 3905. Phylogenic trees analysis using the neighbor-joining method showed closest evolutionary distance of CMG S2 with KMM 3905 strain and K. carniphila (DC2201) specie. Interestingly, a unique ultraviolet (UV)-bioactive compound was purified from CMG S2 crude extracts by flash silica gel column and thin-layer chromatography (TLC) techniques. Its chemical structure was unraveled as 4-[(Z)-2 phenyl ethenyl] benzoic acid (PEBA, later named kocumarin) by nuclear magnetic resonance (NMR) spectroscopy techniques. Importantly, kocumarin demonstrated prominent and rapid growth inhibition against all tested fungi and pathogenic bacteria including methicillin-resistant Staphylococcus aureus (MRSA), with a minimal fungal inhibitory concentration (MFC) of 15-25μg/mL and a minimal (bacterial) inhibitory concentration (MIC) of 10-15μg/mL., Significance and Impact of the Study: Kocumarin represents a new promising natural antibiotic for in vivo and environmental applications., (Copyright © 2017 Elsevier GmbH. All rights reserved.)

A novel, non-motile coccoid, Gram-positive and non-endospore forming bacterium, designated Hv14b T , was isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum. It was observed to be catalase positive and oxidase negative and able to hydrolyse starch. MK-8(H2) was identified as the dominant menaquinone and the major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The 16S rRNA genes showed the highest 16S rRNA sequence identity with K. polaris DSM 14382 T , K. rosea DSM 20447 T and K. turfanensis DSM 22143 T . Based on the phenotypic and molecular features and DNA-DNA hybridization data, it is concluded that strain Hv14b T is proposed to represent a novel species in the genus Kocuria, Kocuria salina sp. nov., with the type strain Hv14b T =DSM 28714 T =CECT 9229 T .

Infectious diseases affecting wildlife are drivers of global biodiversity loss. Here we report a bacterial threat to endangered wild reptiles. Since April 2011, a severe skin disease has affected free-ranging, endangered Lesser Antillean iguanas (Iguana delicatissima) on the French Caribbean island of Saint Barthélemy and we identified Devriesea agamarum as the causative agent. The presence of this bacterium was also demonstrated in healthy lizards (anoles) co-inhabiting the island. All isolates from the iguanas corresponded to a single AFLP genotype that until now has exclusively been associated with infections in lizard species in captivity. The clonal relatedness of the isolates and recent emergence of the disease suggest recent arrival of a virulent D. agamarum clone on the island. The presence of healthy but infected lizards suggests the presence of asymptomatic reservoir hosts. This is the first description of a bacterial disease that poses a conservation threat towards free-ranging squamates.

Background: Kocuria species are Gram-positive, aerobic cocci, and members of the Micrcoccaceae family that are known to be opportunistic pathogens. Although there have been sporadic reports of infections caused by Kocuria species, little is known regarding their human pathogenicity and clinical characteristics., Case Report: We herein report a case of a peripherally inserted central catheter (PICC)-related bloodstream infection caused by Kocuria marina in a 90-year-old Japanese with multiple cancer. The patient, who was admitted due to adhesive intestinal obstruction, suddenly developed sepsis on day 29 following admission. Three sets of blood cultures and a culture of the PICC tip revealed the growth of Gram-positive cocci arranged in clusters. The patient improved quickly after treatment with an antimicrobial agent and catheter removal. The organism was identified as Kocuria varians using the MicroScan Walkaway system and K. varians/Kocuria rosea with a 99.7% probability using an API Staph system. However, 16S rRNA gene sequencing analysis identified the pathogen as K. marina., Conclusion: Although K. marina is a rare pathogen, physicians should consider it in case of catheter-related infections in patients with serious underlying conditions. As commercial identification systems can misidentify species within the Kocuria genus, the use of genomic methods such as 16S rRNA sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry may be useful for the precise identification of Kocuria to the species level.

An alkaliphilic and moderately halophilic bacterial strain characterized by optimal growth at pH 9.0-10.0 and with 5-7 % (w/v) NaCl, designated BV-35 T , was isolated from water of a soda pan located in Kiskunság National Park, Hungary. Cells of the orange-pigmented colony were Gram-stain-positive, non-motile and non-endospore-forming coccoid rods. The isolate was strictly aerobic, catalase-positive and oxidase-negative. Strain BV-35 T displayed a peptidoglycan similar to type A4α, l-Lys-l-Glu (A11.54 according to www.peptidoglycan-types.info) but containing additionally 4-aminobutyric acid. Menaquinone-7 (MK-7) was the predominant isoprenoid quinone, and anteiso-C15 : 0 and anteiso-C17 : 0 were its major cellular fatty acids. The DNA G+C content of strain BV-35 T was 65.4 mol%. Based on 16S rRNA gene sequence similarities, the novel isolate showed the closest relationship to Nesterenkonia populi GP 10-3 T (97.9 %). The DNA-DNA relatedness between BV-35 T and N. populi was 46.7 %. The distinguishing phenotypic and genetic results of this polyphasic study revealed that strain BV-35 T represents a novel member of the genus Nesterenkonia, for which the name Nesterenkonia pannonica sp. nov. is proposed. The type strain is BV-35 T (=DSM 29786 T =NCAIM B 02606 T ).

A Gram-stain-positive bacterium, designated TSL3T, was isolated from faeces of a porcupine, Hystrix indica, from the Budapest Zoo and Botanical Garden, Hungary. On the basis of 16S rRNA gene sequence analysis, the strain is phylogenetically related to the family Micrococcaceae. The highest 16S rRNA gene sequence similarity was found with Micrococcus terreus V3M1T (96.50 %) followed by Arthrobacter humicola KV-653T (96.43 %). Cells of strain TSL3T were aerobic, non-motile and coccoid-shaped. The main fatty acids were anteiso-C15 : 0 (54.4 %), iso-C16 : 0 (18.2 %) and iso C15 : 0 (9.7 %). The major menaquinone was MK-7, and the polar lipid profile included phosphatidylglycerol, diphosphatidylglycerol, dimannosylglyceride, trimannosyldiacylglycerol, phosphatidylinositol, three unknown phospholipids and two unknown glycolipids. Strain TSL3T showed the peptidoglycan structure A4alpha l-Lys - Gly - l-Glu. The DNA G+C content of strain TSL3T was 58.4 mol%. Phenotypic and genotypic characterisation clearly showed that strain TSL3T could be differerentiated from the members of other genera in the family Micrococcaceae. According to these results, strain TSL3T represents a novel genus and species, for which the name Micrococcoides hystricis gen. nov., sp. nov. is proposed. The type strain is TSL3T (=DSM 29785T=NCAIM B. 02604T).

A Gram-stain-positive, aerobic, non-motile, rod-shaped, non-endospore-forming bacterial strain, 10CT, was isolated from Lonar soda lake in India. Based on the 16S rRNA gene sequence analysis, this strain was identified as belonging to the genus Nesterenkonia and was most closely related to the type strains of Nesterenkonia lacusekhoensis (99.1 %, sequence similarity), Nesterenkonia aethiopica (96.9 %), Nesterenkonia flava (96.9 %) and related of the genus Nesterenkonia (<96.6 %, sequence similarity). However, the DNA-DNA relatedness of strain 10CT with N. lacusekhoensis KCTC 19283T was only 34.6±0.9. The DNA G+C content of strain 10CT was 68.6 mol%. Strain 10CT was an aerobic microbe with optimal growth at 37 °C, pH 7.5-8.0 and 5-6 % (w/v) NaCl. The cell-wall peptidoglycan of strain 10CT was of the type A4α (l-Lys-l-Glu). The major polar lipids present were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. The major isoprenoid quinones were MK-7, MK-8 and MK-9. Major fatty acids of strain 10CT were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain 10CT, which represents a novel member of the genus Nesterenkonia for which the name Nesterenkonia cremea sp. nov. is proposed. The type strain is 10CT (=LMG 29100T=KCTC 39636T=CGMCC 1.15388T).

A novel actinobacterium, designated KLBMP 5180T, was isolated from the surface-sterilized root of a coastal halophyte, Limonium sinense, collected from the city of Lianyungang, Jiangsu Province, eastern China. The isolate was Gram-stain-positive, aerobic and non-motile. The components of the cell-wall peptidoglycan were lysine, glutamic acid and alanine. The predominant menaquinone was MK-9. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phospholipid, one unidentified glycolipid and two unidentified lipids. anteiso-C15 : 0 and iso-C16 : 0 were the major cellular fatty acids. The DNA G+C content of strain KLBMP 5180T was 60.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KLBMP 5180T belongs to the genus Glutamicibacter and was related most closely to Glutamicibacter nicotianae DSM 20123T (99.3 % similarity), Glutamicibacterarilaitensis Re117T (99.3 %) and Glutamicibacter mysorens LMG 16219T (99.1 %); similarity to other type strains of the genus Glutamicibacter was lower than 98.5 %. However, DNA-DNA relatedness values between strain KLBMP 5180T, G . nicotianae DSM 20123T, G. arilaitensis Re117T and G. mysorens LMG 16219T were 47.5±2.6, 51.3±3.1 and 41.2±4.3 %, respectively. The combination of DNA-DNA hybridization, phylogenetic, phenotypic and chemotaxonomic data supported the suggestion that strain KLBMP 5180T represents a novel species of the genus Glutamicibacter, for which the name Glutamicibacterhalophytocola sp. nov. is proposed. The type strain is KLBMP 5180T (=DSM 101718T=KCTC 39692T).

Two Gram-stain-variable, non-motile, catalase-positive and cytochrome c oxidase-negative bacteria, designated AK20-18 T and AM20-54, were isolated from forest soil samples collected in the Italian Alps. Growth occurred at a temperature range of 5-30 °C, at pH 6-9 and in the presence of 0-5 % (w/v) NaCl. The 16S rRNA gene sequence similarity between strains AK20-18 T and AM20-54 was 100 %. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain AK20-18 T had highest 16S rRNA gene sequence similarity with the type strain of Arthrobacter psychrochitiniphilus (96.9 %). The cell-wall peptidoglycan structure of strain AK20-18 T was of the type A3alpha l-Lys-l-Thr-l-Ala2 (A11.27). The whole-cell sugars were galactose, ribose and lesser amounts of mannose. The major respiratory quinone of the two strains was menaquinone 9(H2) [MK-9(H2)], whereas MK-10(H2) was a minor component. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown glycolipids. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 59.9 mol%. Combined data of phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strains AK20-18 T and AM20-54 represent a novel genus and species, for which the name Psychromicrobium silvestre gen. nov., sp. nov. is proposed. The type strain of Psychromicrobium silvestregen. nov., sp. nov. is AK20-18 T (=DSM 102047 T =LMG 29369 T ).

Three strains, FXJ8.095T, FXJ8.057 and H201, were isolated from deep-sea hydrothermal plume water collected at the Southwest Indian Ridge at a depth of 2800 m. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates formed a closely related subcluster within the genus Kocuria. The 16S rRNA gene sequence of strain FXJ8.095T shared 99.90 and 99.60 % similarity with those of strains FXJ8.057 and H201, respectively, and 98.81, 98.75, 98.68 and 98.10 % with those of 'Kocuria sediminis' JCM 17929, Kocuria flava HO-9041T, Kocuria turfanensis HO-9042T and Kocuria rosea JCM 11614T, respectively. DNA-DNA hybridization values among the three new isolates were higher than 70 %, while the values between each of the isolates and the closely related type strains were well below 70 %. Random amplified polymorphic DNA fingerprint patterns and a combination of physiological and biochemical properties also distinguished the isolates from the related species. The major cellular fatty acids of the isolates were anteiso-C15 : 0 and iso-C15 : 0, the predominant menaquinones were MK-7(H2) and MK-8(H2), and the main polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C contents of strains FXJ8.095T, FXJ8.057 and H201 were 75.6, 72.8 and 70.4 mol%, respectively. Based on the phylogenetic, phenotypic and chemotaxonomic data, we propose to classify the three strains in a novel species named Kocuria oceani sp. nov., with FXJ8.095T (=CGMCC 4.6946T=DSM 24949T) as the type strain.

Background: Knowledge regarding microaerophilic and anaerobic specific spoilage organisms (SSOs) is crucial for an appropriate evaluation of vacuum-packed ham. The objective of this study was to characterize the SSO community in vacuum-packed ham by a culture-dependent technique and MiSeq next-generation sequencing (NGS) platform. The relation between changes among the SSO group in the ham and changes in sensory characteristics of the product was also assessed., Results: In the study, conventional microbiological analyses were employed in order to establish the participation of several groups of microorganisms in the deterioration of vacuum-packed ham. The diversity of the SSO group in the product was further assessed with the use of MiSeq NGS technology. The bacteria identified in sliced cooked ham belonged mostly to four phyla, namely Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes. A temperature of 4 °C favoured the development of mesophilic and psychrophilic/psychrotrophic flora, mainly Lactobacillaceae, Enterobacteriaceae and Micrococcaceae families. A high ratio of Brochothrix thermosphacta species and new, cold-tolerant Clostridium spp. was also observed. The growth of these microorganisms facilitated changes in the pH value and organoleptic characteristics of the product., Conclusion: This study confirms that the combination of culturing and MiSeq NGS technology improves the microbial evaluation of food. © 2016 Society of Chemical Industry., (© 2016 Society of Chemical Industry.)

A Gram-stain-positive, aerobic, non-motile, coccoid bacterial strain, 36AT, was isolated from Munnar, in India. Based on the results of 16S rRNA gene sequence analysis, this strain was identified as representing a member of the genus Tersicoccus and was most closely related to the type strain of Tersicoccus phoenicis (98.9 %, sequence similarity), the only other member of the genus, and to members of the related genus Arthrobacter (<96.1 %, sequence similarity). However, the DNA-DNA relatedness of strain 36AT with T. phoenicis DSM 30849T was only 31.9±0.8. The DNA G+C content of strain 36AT was 70.9 mol%. Strain 36AT was an aerobic microbe with optimal growth at 37 °C, pH 6.0-8.0 and NaCl 0.5-3 % (w/v). Cell-wall peptidoglycan of strain 36AT was of type A11.20 (Lys-Ser-Ala2). Polar lipids present were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, two phospholipids, a glycolipid and four unknown lipids. The major isoprenoid quinones were MK-9 (H2) and MK-8 (H2). Major fatty acids of strain 36AT were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain 36AT, which represents a novel member of the genus Tersicoccus, for which the name Tersicoccus solisilvae sp. nov., is proposed. The type strain is 36AT (=KCTC 33776T=CGMCC 1.15480T).

A novel actinobacterium, designated strain JXJ CY 21 T , was isolated from the culture mass of Microcystis sp. FACHB-905 collected from Lake Dianchi, South-west China. Polyphasic taxonomic study revealed that the isolate should be a member of the genus Citricoccus. Comparison of the 16S rRNA gene sequence of strain JXJ CY 21 T with the available sequences in the GenBank database showed that the strain is closely related to Citricoccus zhacaiensis FS24 T (97.8 % similarity), Citricoccus parietis 02-Je-010 T (97.7 %), Citricoccus terreus V3M1 T (97.6 %), Citricoccus nitrophenolicus PNP1 T (97.2 %), Citricoccus alkalitolerans YIM 70010 T (97.2 %) and Citricoccus muralis 4-0 T (97.0 %). The DNA-DNA hybridization values between strain JXJ CY 21 T and the related type strains C. zhacaiensis FS24 T and C. parietis 02-Je-010 T were 16.0 ± 2.6 and 5.4 ± 1.7 %, respectively. The peptidoglycan in the cell wall was A4α type containing lysine-glutamic acid-glycine. The major respiratory menaquinone was found to be MK-8 (H 2 ) (98.5 %), while the major cellular fatty acids (>10 %) were anteiso-C 15:0 , iso-C 16:0 , iso-C 15:0 and iso-C 14:0 . The polar lipids detected were diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. The DNA G + C content was determined to be 62.7 mol%. Strain JXJ CY 21 T can solubilize both insoluble inorganic and organic phosphates up to 24.7 and 1.7 mg/l respectively. This property of the novel actinobacterium acts as a modulator for enhancement of growth of Microcystis sp. FACHB-905 in the lake ecosystem where the amount of soluble phosphate is limited. On the basis of the above taxonomic data, strain JXJ CY 21 T represents a novel species of the genus Citricoccus, for which the name Citricoccus lacusdiani sp. nov. is proposed. The type strain is JXJ CY 21 T (=KCTC 29653 T  = DSM 29160 T ).

Clavibacter michiganensis is a Gram-stain-positive bacterium with eight subspecies. One of these subspecies is C. michiganensis subsp. michiganensis, which causes bacterial canker disease in tomato. Bacterial strains showing very similar canker disease symptoms to those of a strain originally classified as C. michiganensis have been isolated from pepper. In this paper, we reclassified strains isolated from pepper. On the basis of phylogenetic analysis with 16S rRNA gene sequences, the strains isolated from pepper were grouped in a separate clade from other subspecies of C. michiganensis. Biochemical, physiological and genetic characteristics of strain PF008T, which is the representative strain of the isolates from pepper, were examined in this study. Based on multi-locus sequence typing and other biochemical and physiological features including colony color, utilization of carbon sources and enzyme activities, strain PF008T was categorically differentiated from eight subspecies of C. michiganensis. Moreover, genome analysis showed that the DNA G+C content of strain PF008T is 73.2 %. These results indicate that PF008T is distinct from other known subspecies of C. michiganensis. Therefore, we propose a novel subspecies, C. michiganensis subsp. capsici, causing bacterial canker disease in pepper, with a type strain of PF008T (=KACC 18448T=LMG 29047T).