Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples.

Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.

Comamonas fluminis sp. nov., isolated from the Han River, Republic of Korea.

A Gram-stain-negative, aerobic and motile bacterial strain, designated CJ34T, was isolated from Han River water in the Republic of Korea. Strain CJ34T grew optimally on tryptic soy agar at 30 °C and pH 7.0 in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequence showed that strain CJ34T belonged to the genus Comamonas within the family Comamonadaceae and was most closely related to Comamonas testosteroni ATCC 11996T and Comamonas thiooxydans DSM 17888T (both 98.63 % similarity). The average nucleotide identity values between strain CJ34T and two closely related type strains C. testosteroni ATCC 11996T and C. thiooxydans DSM 17888T were 82.77 and 82.73 %, respectively. The major isoprenoid quinone of strain CJ34T was ubiquinone Q-8. The major cellular fatty acids of strain CJ34T were C16 : 0, C16 : 1 ω6c and/or C16 : 1 ω7c and C18 : 1 ω6c and/or C18 : 1 ω7c. The predominant polar lipids of strain CJ34T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Whole genome sequencing revealed that strain CJ34T had a genome of 4.9 Mbp and the G+C content of the genomic DNA was 59.73 mol%. On the basis of the results of this polyphasic taxonomy study, strain CJ34T represents a novel species in the genus Comamonas, for which the name Comamonas fluminis sp. nov. is proposed. The type strain is CJ34T (=KACC 22237T=JCM 34454T).

Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water.

A novel bacterial strain designated CJ43T was isolated from fresh water located in Gangwon-do, South Korea, displaying multi-drug resistance. The isolate was Gram-stain-negative, aerobic, orange-pigmented, and rod-shaped. Strain CJ43T grew optimally at 30 °C and pH 7 on R2A agar in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain CJ43T belonged to the genus Pedobacter in the family Sphingobacteriaceae and was most closely related to Pedobacter puniceum HX-22-1 T and P. glucosidilyticus 1-2 T (98.3 and 98.1% sequence similarity). The genome size of strain CJ43T was 3.9 Mb in a single contig with DNA G + C content of 34.9%. The genome included 3144 predicted protein-coding genes, as well as 55 tRNA, 9 rRNA and 3 ncRNA genes. The genome also contained 128 putative antibiotic resistance genes, reflecting its phenotypes. The average nucleotide identity values between strain CJ43T and two closely related strains P. puniceum HX-22-1 T and P. glucosidilyticus 1-2 T were 91.0 and 88.7%, respectively. In silico digital DNA-DNA hybridization results between strain CJ43T and the related strains were 42.8 and 38.6%, respectively. The major fatty acids of strain CJ43T were iso-C15:0, iso-C17:0 3-OH, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). Strain CJ43T contained phosphatidylethanolamine as the major polar lipid and menaquinone-7 as the sole respiratory quinone. Based on the polyphasic taxonomy data, strain CJ43T represents a novel species of the genus Pedobacter, for which the name Pedobacter aquae sp. nov. is proposed with the type strain CJ43T (= KACC 21350 T = JCM 33709 T).

Myroides fluvii sp. nov., isolated from the Han River, Republic of Korea.

A Gram-stain-negative, aerobic, short rod-shaped, pale yellow-pigmented, non-motile and gentamycin-resistant bacterial strain designated CJ210T was isolated from the Han River, Republic of Korea. Strain CJ210T grew optimally at 30 °C and pH 7.0 in the absence of NaCl on tryptic soy agar. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain CJ210T belonged to the genus Myroides within the family Flavobacteriaceae and was most closely related to Myroides odoratus KACC 14347T (98.1 % similarity), followed by M. injenensis KCTC 23367T (95.3 % similarity). The average nucleotide identity values between strain CJ210T and two closely related type strains M. odoratus KACC 14347T and M. injenensis KCTC 23367T were 83.7 and 73.8 %, respectively. The digital DNA-DNA hybridization results between strain CJ210T and the related type strains were 27.5 and 20.2 %, respectively. Strain CJ210T contained menaquinone 6 (MK-6) as the predominant menaquinone. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The major fatty acids of strain CJ210T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 9 (comprising iso-C17 : 1 ω9c and/or C16 : 0 10-methyl). Whole genome sequencing revealed that strain CJ210T had a genome of 3.8 Mbp with 36.5 % DNA G+C content. The genome contained several antimicrobial resistance genes including an aminoglycoside-resistant gene. On the basis of the polyphasic taxonomic study, strain CJ210T represents a novel species in the genus Myroides, for which name Myrodies fluvii sp. nov. is proposed. The type strain is CJ210T (=KACC 19954T=JCM 33306T).

Chryseobacterium aureum sp. nov., isolated from the Han River, Republic of Korea.

A Gram-stain-negative, yellow-pigmented, non-motile, non-spore-forming, aerobic and rod-shaped bacterial strain, designated 17S1E7T, was isolated from the Han River, Republic of Korea, and characterized by polyphasic taxonomy analyses. Strain 17S1E7T grew optimally on tryptic soy agar at 37 °C and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain 17S1E7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium culicis DSM 23031T (98.54 %). The average nucleotide identity value of strain 17S1E7T was 91.1 % to Chryseobacterium culicis DSM 23031T, which was lower than the cut-off of 95-96 %. The DNA G+C content of strain 17S1E7T was 37.4 mol%. Flexirubin-type pigments were produced. The predominant respiratory quinone was menaquinone 6. The major fatty acids of strain 17S1E7T were iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). The predominant polar lipid was phosphatidylethanolamine. Based on polyphasic taxonomy data, strain 17S1E7T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium aureum sp. nov. is proposed. The type strain is 17S1E7T (=KACC 19920T=JCM 33165T).

Paenibacillus limicola sp. nov., isolated from tidal flat sediment.

An aerobic, Gram-staining-variable, rod-shaped, endospore-forming and motile bacterial strain, designated CJ6T, was isolated from a tidal flat on Ganghwa Island, South Korea. The isolate was characterized based on a polyphasic taxonomy approach. Strain CJ6T grew optimally on R2A agar media at 30 °C and pH 7. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CJ6T belonged to the genus Paenibacillus, displaying the highest sequence similarity to Paenibacillus vulneris CCUG 53270T (97.0 %) and clearly defined strain CJ6T as a novel species within the genus. The G+C content of the genomic DNA was 49.9 mol%. The major polar lipid contents of strain CJ6T were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified glycolipids. MK-7 was detected as the major respiratory quinone. The dominant fatty acid was anteiso-C15 : 0. Analyses of phylogenetic, phenotypic, biochemical and chemotaxonomic characteristics indicated that strain CJ6T was distinguishable from its closely related type strains. Therefore, strain CJ6T represents a novel species in the genus Paenibacillus, for which name Paenibacilluslimicola sp. nov. is proposed; the type strain is CJ6T (=KACC 19303T=JCM 32079T).

Paenibacillus translucens sp. nov., isolated from tidal flat sediment.

A Gram-stain-variable, aerobic, rod-shaped, motile and spore-forming bacterial strain, designated CJ11T, was isolated from a tidal flat sediment sample from Ganghwa-do, Republic of Korea. Strain CJ11T grew optimally on R2A at 30 °C and pH 7.0. Sequencing results of the 16S rRNA gene revealed that strain CJ11T possesses two copies of the 16S rRNA gene varying at five nucleotide positions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CJ11T belonged to the genus Paenibacillus within the family Paenibacillaceae and was most closely related to Paenibacillus lacus KCTC 33691T (99.36-99.15 % similarity). DNA-DNA relatedness levels of strain CJ11T was 41.7 % (reciprocal, 57.8 %) to P. lacus KCTC 33691T. The G+C content of the genomic DNA was 51.0 mol%. Strain CJ11Tcontained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major isoprenoid quinone was menaquinone-7. The major cellular fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, an unidentified glycolipid and several unidentified lipids. On the basis of the polyphasic taxonomic study, strain CJ11T represents a novel species in the genus Paenibacillus, for which the name Paenibacillustranslucens sp. nov. is proposed. The type strain is CJ11T (=KACC 19304T=JCM 32080T).

Flavobacterium foetidum sp. nov., isolated from ginseng soil.

A Gram-staining-negative bacterial strain, designated CJ42T, was isolated from ginseng soil in Anseong, Republic of Korea. Cells were rod-shaped, yellow-pigmented, aerobic and devoid of flagella but showed gliding motility. Strain CJ42T grew optimally at 30 °C and pH 7.0 in the absence of NaCl on tryptic soy agar. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain CJ42T belonged to the genus Flavobacterium within the family Flavobacteriaceae and was most closely related to Flavobacterium tistrianum KCTC 42679T (97.3 % similarity). Flexirubin-type pigments were produced. The only respiratory quinone was menaquinone 6. The predominant polar lipids were phosphatidylethanolamine, an unknown aminolipid and two unknown lipids. The major fatty acids of strain CJ42T were iso-C15 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The G+C content of the genomic DNA was 30.7 mol%. Based on the polyphasic analyses, strain CJ42T represents a novel species in the genus Flavobacterium, for which the name Flavobacteriumfoetidum sp. nov. is proposed. The type strain is CJ42T (=KACC 19302=JCM 32085).

Functional characterization of a thermostable endoglucanase belonging to glycoside hydrolase family 45 from Fomitopsis palustris.

A gene encoding an endoglucanase belonging to subfamily C of glycoside hydrolase family 45 (GH45) was identified in the brown rot fungus Fomitopsis palustris and functionally expressed in Pichia pastoris. The recombinant protein displayed hydrolytic activities toward various substrates such as carboxymethyl cellulose, phosphoric acid swollen cellulose, glucomannan, lichenan, and ß-glucan. In particular, the enzyme had a unique catalytic efficiency on ß-1,4-glucans rather than mixed ß-1,3/1,4-glucans as compared to other GH45 endoglucanases. The fungal enzyme was relatively thermostable, retaining more than 91.4% activity at 80 °C for 1 h. Site-directed mutagenesis studies revealed that the mutants N95D and D117N had significantly reduced enzymatic activities, indicating that both residues are essential for the catalytic reaction. Our study expands knowledge and understanding of the catalytic mechanism of GH45 subfamily C enzymes and also suggests that this thermostable endoglucanase from F. palustris has great potential in industrial applications.

Ramlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng.

A novel bacterial strain, designated CJ661T, was isolated from soil of ginseng in Anseong, South Korea. Cells of strain CJ661T were white-coloured, Gram-staining-negative, non-motile, aerobic and rod-shaped. Strain CJ661T grew optimally at 30 °C and pH 7.0. The analysis of 16S rRNA gene sequence of strain CJ661T showed that it belongs to the genus Ramlibacter within the family Comamonadaceae and was most closely related to Ramlibacter ginsenosidimutans KCTC 22276T (98.1 %), followed by Ramlibacter henchirensis DSM 14656T (97.1 %). DNA-DNA relatedness levels of strain CJ661T were 40.6 % to R. ginsenosidimutans KCTC 22276T and 25.0 % to R. henchirensis DSM 14656T. The major isoprenoid quinone was ubiquinone (Q-8). The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids of strain CJ661T were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The G+C content of the genomic DNA was 65.4 mol%. On the basis polyphasic taxonomic data, strain CJ661T represents a novel species in the genus Ramlibacter, for which name Ramlibacter alkalitolerans sp. nov. is proposed; the type strain is CJ661T (=KACC 19305T=JCM 32081T).

Flavihumibacter sediminis sp. nov., isolated from tidal flat sediment.

A yellow, Gram-staining-positive, aerobic, rod-shaped and non-motile bacterial strain, designated CJ663T, was isolated from the tidal flat sediment in Ganghwa-do, South Korea. Strain CJ663T grew optimally on R2A at 30 °C and pH 7.0 and did not require NaCl for growth. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain CJ663T belonged to the genus Flavihumibacter within the family Chitinophagaceae and was most closely related to Flavihumibacter cheonanensis KACC 17467T (98.3 % similarity), followed by Flavihumibacter solisilvae KACC 17917T (97.4 %). DNA-DNA relatedness levels of strain CJ663T were 42.9 % to F. cheonanensis KACC 17467T and 48.6 % to F. solisilvae KACC 17917T. The major isoprenoid quinone was menaquinone 7 (MK-7). The predominant polar lipids were phosphatidylethanolamine, aminophospholipid and two unidentified lipids. The major cellular fatty acids of strain CJ663T were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The G+C content of the genomic DNA was 47.7 mol%. On the basis of data from this polyphasic taxonomic study, strain CJ663T represents a novel species in the genus Flavihumibacter, for which name Flavihumibacter sediminis sp. nov. is proposed; the type strain is CJ663T (=KACC 18874T=JCM 31431T).

Cohnella saccharovorans sp. nov., isolated from ginseng soil.

A novel bacterial strain, CJ22T, was isolated from soil of a ginseng field located in Anseong, Korea. Cells of strain CJ22T were aerobic, Gram-stain-positive, endospore-forming, motile, oxidase- and catalase-positive and rod-shaped. The isolate grew optimally at pH 7 and 30 °C. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CJ22T belonged to the genus Cohnella, displaying highest sequence similarity of 97.3% with Cohnella panacarvi Gsoil 349T. DNA-DNA relatedness between strain CJ22T and its closest relative was 35.5 % (reciprocal value, 23.8%). The phenotypic features of strain CJ22T also distinguished it from related species of the genus Cohnella. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major isoprenoid quinone was menaquinone MK-7 and the major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, lysyl-phosphatidylglycerol, two unidentified phospholipids and two unidentified aminophospholipids. The predominant cellular fatty acids of strain CJ22T were anteiso-C15 : 0, iso-C16:0 and C16:0. The DNA G+C content was 63.1 mol%. Based on data from this polyphasic taxonomic study, strain CJ22T is considered to represent a novel species of the genus Cohnella, for which the name Cohnella saccharovorans sp. nov. is proposed. The type strain is CJ22T (=KACC 17501T=JCM 19227T).

Changes in human gut microbiota influenced by probiotic fermented milk ingestion.

We investigated the effect of consuming probiotic fermented milk (PFM) on the microbial community structure in the human intestinal tract by using high-throughput barcoded pyrosequencing. Six healthy adults ingested 2 servings of PFM daily for 3 wk, and their fecal microbiota were analyzed before and after 3 wk of PFM ingestion period and for another 3 wk following the termination of PFM ingestion (the noningestion period). Fecal microbial communities were characterized by sequencing of the V1-V3 hypervariable regions of the 16S rRNA gene. All subjects showed a similar pattern of microbiota at the phylum level, where the relative abundance of Bacteriodetes species increased during the PFM ingestion period and decreased during the noningestion period. The increase in Bacteroidetes was found to be due to an increase in members of the families Bacteroidaceae or Prevotellaceae. In contrast to PFM-induced adaptation at the phylum level, the taxonomic composition at the genus level showed a considerable alteration in fecal microbiota induced by PFM ingestion. As revealed by analysis of operational taxonomic units (OTU), the numbers of shared OTU were low among the 3 different treatments (before, during, and after PFM ingestion), but the abundance of the shared OTU was relatively high, indicating that the majority (>77.8%) of total microbiota was maintained by shared OTU during PFM ingestion and after its termination. Our results suggest that PFM consumption could alter microbial community structure in the gastrointestinal tract of adult humans while maintaining the stability of microbiota.

Bacillus panacisoli sp. nov., isolated from ginseng soil.

A Gram-staining-positive, motile, facultatively anaerobic, endospore-forming and rod-shaped bacterium, designated strain CJ32(T), was isolated from ginseng soil at Geumsan in Korea. The isolate grew optimally at 30 °C, 2% (w/v) NaCl and pH 7.0. Colonies of strain CJ32(T) were beige and circular with an entire margin on LB agar plates. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CJ32(T) was associated with the genus Bacillus and was most closely related to Bacillus graminis YC6957(T) (97.3% similarity) and Bacillus lentus IAM 12466(T) (97.1%). DNA-DNA hybridization with closely related strains was below 31.3%. The major respiratory isoprenoid quinone was MK-7. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The polar lipid profile of strain CJ32(T) consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified lipids, including phospholipids, aminolipids and aminophospholipids. The predominant fatty acids of strain CJ32(T) were iso-C15:0 and anteiso-C15:0. The G+C content of the genomic DNA was 35.1 mol%. Based on phenotypic, genotypic and phylogenetic data, strain CJ32(T) should be classified within a novel species of the genus Bacillus, for which the name Bacillus panacisoli sp. nov. is proposed. The type strain is strain CJ32(T) ( = KACC 17503(T) = JCM 19226(T)).

Lysobacter panacisoli sp. nov., isolated from ginseng soil.

A novel bacterial strain, designated CJ29(T), was isolated from ginseng soil of Anseong in South Korea. Cells of strain CJ29(T) were Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile. Strain CJ29(T) grew optimally at 28-30 °C and pH 7.0. Based on 16S rRNA gene sequence analysis, strain CJ29(T) was shown to belong to the genus Lysobacter within the class Gammaproteobacteria and was related most closely to Lysobacter soli DCY21(T) (98.5% similarity) and Lysobacter niastensis GH41-7(T) (98.2%). DNA-DNA relatedness between strain CJ29(T) and its closest relatives was below 55.6%. The predominant cellular fatty acids of strain CJ29(T) were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major isoprenoid quinone was ubiquinone 8 (Q-8). The G+C content of the genomic DNA was 65.6 mol%. Phenotypic, genotypic and phylogenetic characteristics strongly supported the differentiation of strain CJ29(T) from related species of the genus Lysobacter. On the basis of data from this polyphasic taxonomic study, strain CJ29(T) is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter panacisoli sp. nov. is proposed. The type strain is CJ29(T) ( = KACC 17502(T) = JCM 19212(T)).

Bifidobacterium faecale sp. nov., isolated from human faeces.

A novel strain, designated strain CU3-7(T), was isolated from faeces of a two-week-old baby. The isolate was Gram-staining-positive, anaerobic and rod-shaped. Results from 16S rRNA gene sequence analysis revealed that strain CU3-7(T) was phylogenetically affiliated with members of the genus Bifidobacterium. Strain CU3-7(T) showed the highest level of sequence similarity with Bifidobacterium adolescentis KCTC 3216(T) (98.4 %), followed by Bifidobacterium ruminantium KCTC 3425(T) (97.9 %). Analysis of hsp60 sequences showed that strain CU3-7(T) was closely related to B. adolescentis KCTC 3216(T) (94.0 %) and B. ruminantium KCTC 3425(T) (92.5 %). The DNA-DNA hybridization values with the closely related strains were all below the cut-off value for species delineation, 17.0 % with B. ruminantium KCTC 3425(T) and 14.9 % with B. adolescentis KCTC 3216(T). Fructose-6-phosphate phosphoketolase activity was detected. The predominant cellular fatty acids were C16 : 0 (27.7 %), C18 : 1ω9c (27.4 %) and C18 : 1ω9c dimethylacetate (15.5 %). The DNA G+C content was 58.6 mol%. On the basis of polyphasic taxonomy, strain CU3-7(T) should be classified as the type strain of a novel species within the genus Bifidobacterium, for which the name Bifidobacterium faecale sp. nov. is proposed ( = KACC 17904(T) = JCM 19861(T)).

Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis.

Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. ß-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis. IMPORTANCE: A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.

2-nitrobenzoate 2-nitroreductase (NbaA) switches its substrate specificity from 2-nitrobenzoic acid to 2,4-dinitrobenzoic acid under oxidizing conditions.

2-Nitrobenzoate 2-nitroreductase (NbaA) of Pseudomonas fluorescens strain KU-7 is a unique enzyme, transforming 2-nitrobenzoic acid (2-NBA) and 2,4-dinitrobenzoic acid (2,4-DNBA) to the 2-hydroxylamine compounds. Sequence comparison reveals that NbaA contains a conserved cysteine residue at position 141 and two variable regions at amino acids 65 to 74 and 193 to 216. The truncated mutant Δ65-74 exhibited markedly reduced activity toward 2,4-DNBA, but its 2-NBA reduction activity was unaffected; however, both activities were abolished in the Δ193-216 mutant, suggesting that these regions are necessary for the catalysis and specificity of NbaA. NbaA showed different lag times for the reduction of 2-NBA and 2,4-DNBA with NADPH, and the reduction of 2,4-DNBA, but not 2-NBA, failed in the presence of 1 mM dithiothreitol or under anaerobic conditions, indicating oxidative modification of the enzyme for 2,4-DNBA. The enzyme was irreversibly inhibited by 5,5'-dithio-bis-(2-nitrobenzoic acid) and ZnCl(2), which bind to reactive thiol/thiolate groups, and was eventually inactivated during the formation of higher-order oligomers at high pH, high temperature, or in the presence of H(2)O(2). SDS-PAGE and mass spectrometry revealed the formation of intermolecular disulfide bonds by involvement of the two cysteines at positions 141 and 194. Site-directed mutagenesis indicated that the cysteines at positions 39, 103, 141, and 194 played a role in changing the enzyme activity and specificity toward 2-NBA and 2,4-DNBA. This study suggests that oxidative modifications of NbaA are responsible for the differential specificity for the two substrates and further enzyme inactivation through the formation of disulfide bonds under oxidizing conditions.

Gordonia alkaliphila sp. nov., an actinomycete isolated from tidal flat sediment.

A Gram-stain-positive, non-motile, aerobic actinobacterium, designated strain CJ10(T), was isolated from tidal flat sediment from the Yellow Sea in South Korea. Strain CJ10(T) grew on tryptic soy agar in the presence of 0-4 % (w/v) NaCl (optimum growth in the absence of NaCl) and at pH 6-11 (optimum pH 9). On the basis of 16S rRNA gene sequence analysis, strain CJ10(T) belonged to the genus Gordonia and showed the highest sequence similarity to Gordonia hirsuta DSM 44140(T) (97.9 %) and Gordonia hydrophobica DSM 44015(T) (97.6 %). DNA-DNA relatedness levels of strain CJ10(T) were 47.4 % (CJ10(T) as probe) and 42.2 % (G. hirsuta DSM 44140(T) as probe) to G. hirsuta DSM 44140(T) and 8.6 % (CJ10(T) as probe) and 9.3 % (G. hydrophobica DSM 44015(T) as probe) to G. hydrophobica DSM 44015(T). The major isoprenoid quinone was MK-9(H(2)). The polar lipid profile of strain CJ10(T) consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant cellular fatty acids were C(18 : 1)ω9c (38.0 %), C(16 : 0) (30.1 %) and summed feature 3 (C(16 : 1)ω6c and/or C(16 : 1)ω7c; 17.4 %). The DNA G+C content was 67.7 mol%. Therefore, the results from our polyphasic taxonomic study suggest that strain CJ10(T) represents a novel species in the genus Gordonia, for which the name Gordonia alkaliphila sp. nov. is proposed; the type strain is CJ10(T) (= KACC 16561(T) = JCM 18077(T)).

Ferrimonas gelatinilytica sp. nov., isolated from tidal flat sediment.

A novel beige-pigmented, Gram-staining-negative, coccoid, motile and facultatively anaerobic bacteria, designated strain CJ24(T), was isolated from the tidal flat sediment of the Yellow Sea in South Korea. Characterization of this strain was performed on the basis of polyphasic taxonomic methods. Phylogenetic analysis of the 16S rRNA and gyrB genes revealed that strain CJ24(T) belongs to the genus Ferrimonas, sharing the highest 16S rRNA gene sequence similarity of 96.9 % with Ferrimonas marina DSM 16917(T). Strain CJ24(T) was able to grow optimally at 30 °C, at pH 6.0 and in the presence of 2 % NaCl (w/v). As an isoprenoid quinone, menaquinone (MK-7) was predominantly identified from this strain, while ubiquinone (Q-7) was also present as a minor component. The DNA G+C content of strain CJ24(T) was 60.2 mol%. The most abundant cellular fatty acids were C15 : 0 iso, C18 : 1ω9c, C16 : 0 and C17 : 0 iso. Therefore, strain CJ24(T) represents a novel species in the genus Ferrimonas for which the name Ferrimonas gelatinilytica sp. nov. is proposed; the type strain is CJ24(T) ( = KACC 17065(T) = JCM 18720(T)).