Alishewanella maricola sp. nov., isolated from seawater of the Yellow Sea.

A Gram-stain-negative and facultative aerobic bacterium, strain 16-MAT, was isolated from seawater of Yellow Sea in South Korea. Cells were catalase- and oxidase-positive and non-motile rods. Growth occurred at 4-37 °C (optimum, 30 °C) and pH 6.0-11.0 (optimum, 8.0), and in the presence of 0-7.0% NaCl (optimum, 3 %). Strain 16-MAT contained ubiquinone-8 as the sole isoprenoid quinone, C16 : 0 and summed feature three as the major fatty acids (>10 %), and phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid, and an unidentified polar lipid as the major polar lipids. The genome size and DNA G+C content of strain 16-MAT were 3.69 Mb and 46.0 mol%, respectively. Strain 16-MAT was most closely related to Alishewanella alkalitolerans LNK-7.1T with a 97.9 % 16S rRNA gene sequence similarity. A phylogenomic tree based on whole genome sequences showed that strain 16-MAT formed a phylogenetic lineage within the genus Alishewanella. Based on the phenotypic, chemotaxonomic, and molecular analyses, strain 16-MAT represents a novel species of the genus Alishewanella, for which the name Alishewanella maricola is proposed. The type strain is 16-MAT (=KACC 22238T =JCM 34596T).

Complete Genome Sequence of a Sulfur-Oxidizing Bacterium, Alcaligenes faecalis Strain NLF5-7, Isolated from Livestock Wastewater.

The complete genome sequence of Alcaligenes faecalis strain NLF5-7, which was isolated from livestock wastewater, is reported. The genome of strain NLF5-7 contains genes for assimilatory sulfate reduction, dissimilatory sulfate reduction and oxidation, and an SOX system, based on its functional genetic characteristics.

Draft Genome Sequence of a Sulfur-Oxidizing Bacterium, Aquamicrobium lusatiense NLF2-7, Isolated from Livestock Wastewater.

Here, we report the draft genome sequence of Aquamicrobium lusatiense NLF2-7, a Gram-negative, aerobic, non-flagellum-forming, rod-shaped bacterium that was isolated from livestock wastewater in South Korea. The assembled genome sequence is 5,201,486 bp, with 4,972 protein-coding sequences in 12 contigs, and possess the genes for the sulfur oxidation pathway.

Draft Genome Sequence of Stenotrophomonas daejeonensis Strain NLF4-10 Isolated from Livestock Wastewater.

Here, we report the draft genome sequence of Stenotrophomonas daejeonensis strain NLF4-10, isolated from a livestock wastewater treatment plant in Nonsan, Republic of Korea. The whole-genome sequence of S. daejeonensis strain NLF4-10 was analyzed using the Pacific Biosciences Sequel and Illumina NovaSeq sequencing platforms. The genome comprises a 3,655,148 bp chromosome with a GC content of 68%, 3,274 coding DNA sequences (CDSs), 59 transfer RNAs (tRNAs), and 4 noncoding RNAs (ncRNAs).

Rhodococcus oxybenzonivorans sp. nov., a benzophenone-3-degrading bacterium, isolated from stream sediment.

A Gram-stain-positive, facultative aerobic, oxidase-negative, catalase-positive, non-sporulating, and non-motile bacterium, which degraded benzophenone-3, was isolated from stream sediment collected in the Republic of Korea and designated as strain S2-17T. Cells of this strain were rod-shaped during the early growth phase but became coccoid after the late exponential growth phase. Bacterial growth was observed at 15-37 °C (optimum, 25-30 °C) and pH 6.0-9.5 (optimum, pH 7.5-8.5) and in the presence of 0-9.0 % (w/v) NaCl (optimum, 0-1.0 %). Menaquinone-8 (H2) was the sole isoprenoid quinone, and C16 : 0, C17 : 1 ω8c, summed feature 3 (comprising C16 : 1 ω7c/C16 : 1 ω6c) and C18 : 1 ω9c were the major fatty acids. The cell wall of strain S2-17T contained meso-diaminopimelic acid, and arabinose, galactose and mycolic acid were found in whole-cell hydrolysates, suggesting a chemotype IV cell wall. The G+C content of the genome was 65.6 mol%. Phylogenetic analyses revealed that strain S2-17T formed a phyletic lineage within the genus Rhodococcus and was most closely related to Rhodococcus jostii DSM 44719T (99.2 % 16S rRNA gene sequence similarity). Average nucleotide identity and digital DNA-DNA hybridization values between strain S2-17T and R. jostii DSM 44719T were 82.6 and 26.5 %, respectively, indicating differences between the species. Based on its phenotypic, chemotaxonomic and molecular features, strain S2-17T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus oxybenzonivorans sp. nov. is proposed. The type strain is S2-17T (=KACC 19281T=JCM 32046T).

Elucidating the biodegradation pathway and catabolic genes of benzophenone-3 in Rhodococcus sp. S2-17.

A new bacterium, Rhodococcus sp. S2-17, which could completely degrade an emerging organic pollutant, benzophenone-3 (BP-3), was isolated from contaminated sediment through an enrichment procedure, and its BP-3 catabolic pathway and genes were identified through metabolic intermediate and transcriptomic analyses and biochemical and genetic studies. Metabolic intermediate analysis suggested that strain S2-17 may degrade BP-3 using a catabolic pathway progressing via the intermediates BP-1, 2,4,5-trihydroxy-benzophenone, 3-hydroxy-4-benzoyl-2,4-hexadienedioic acid, 4-benzoyl-3-oxoadipic acid, 3-oxoadipic acid, and benzoic acid. A putative BP-3 catabolic gene cluster including cytochrome P450, flavin-dependent oxidoreductase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, and α/ß hydrolase genes was identified through genomic and transcriptomic analyses. Genes encoding the cytochrome P450 complex that demethylates BP-3 to BP-1 were functionally verified through protein expression, and the functions of the other genes were also verified through knockout mutant construction and intermediate analysis. This study suggested that strain S2-17 might have acquired the ability to catabolize BP-3 by recruiting the cytochrome P450 complex and α/ß hydrolase, which hydrolyzes 4-benzoyl-3-oxoadipic acid to benzoic acid and 3-oxoadipic acid, genes, providing insights into the recruitment of genes of for the catabolism of emerging organic pollutants.

Complete Genome Sequence of Lacticaseibacillus paracasei Strain NSMJ15.

We report here the complete genome sequence of Lacticaseibacillus paracasei NSMJ15, isolated from makgeolli (a traditional Korean fermented liquor) and shown to have potentially probiotic characteristics. The genome consisted of a 2.79-Mbp chromosome contig and four plasmids having a total of 2,947 genes, including 2,690 coding sequences.

In-Vitro Characterization of Growth Inhibition against the Gut Pathogen of Potentially Probiotic Lactic Acid Bacteria Strains Isolated from Fermented Products.

Lactic acid bacteria (LAB) are probiotic candidates that may restore the balance of microbiota populations in intestinal microbial ecosystems by controlling pathogens and thereby promoting host health. The goal of this study was to isolate potential probiotic LAB strains and characterize their antimicrobial abilities against pathogens in intestinal microbiota. Among 54 LAB strains isolated from fermented products, five LAB strains (NSMJ15, NSMJ16, NSMJ23, NSMJ42, and NFFJ04) were selected as potential probiotic candidates based on in vitro assays of acid and bile salt tolerance, cell surface hydrophobicity, adhesion to the intestinal epithelium, and antagonistic activity. Phylogenetic analysis based on 16S rRNA genes showed that they have high similarities of 99.58-100% to Lacticaseibacillus paracasei strains NSMJ15 and NFFJ04, Lentilactobacillus parabuchneri NSMJ16, Levilactobacillus brevis NSMJ23, and Schleiferilactobacillus harbinensis NSMJ42. To characterize their antimicrobial abilities against pathogens in intestinal microbiota, the impact of cell-free supernatant (CFS) treatment in 10% (v/v) fecal suspensions prepared using pooled cattle feces was investigated using in vitro batch cultures. Bacterial community analysis using rRNA amplicon sequencing for control and CFS-treated fecal samples at 8 and 16 h incubation showed the compositional change after CFS treatment for all five LAB strains. The changed compositions were similar among them, but there were few variable increases or decreases in some bacterial groups. Interestingly, as major genera that could exhibit pathogenicity and antibiotic resistance, the members of Bacillus, Escherichia, Leclercia, Morganella, and Vagococcus were decreased at 16 h in all CFS-treated samples. Species-level classification suggested that the five LAB strains are antagonistic to gut pathogens. This study showed the probiotic potential of the five selected LAB strains; in particular, their antimicrobial properties against pathogens present in the intestinal microbiota. These strains would therefore seem to play an important role in modulating the intestinal microbiome of the host.

Paenibacillus agri sp. nov., isolated from soil.

A strict aerobic bacterium, strain JW14T was isolated from soil in the Republic of Korea. Cells were Gram-stain-positive, non-endospore-forming and motile rods showing catalase-positive and oxidase-negative activities. Growth of strain JW14T was observed at 20-37 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.0) and in the presence of 0-2.0% NaCl (optimum, 0%). Strain JW14T contained menaquinone-7 as the sole isoprenoid quinone, anteiso-C15:0, C16:0 and iso-C16 : 0 as the major fatty acids (>10.0%), and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and an unidentified lipid as the major polar lipids. The cell-wall peptidoglycan of strain JW14T contained meso-diaminopimelic acid. The DNA G+C content of strain JW14T calculated from the whole genome sequence was 48.1 mol%. Strain JW14T was most closely related to Paenibacillus graminis DSM 15220T with 97.4% 16S rRNA gene sequence similarity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JW14T formed a distinct phyletic lineage from closely related type strains within the genus Paenibacillus. Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain JW14T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus agri sp. nov. is proposed. The type strain is JW14T (=KACC 21840T=JCM 34279T).

Complete Genome Sequence of Bisphenol A-Degrading Bacterium Sphingobium sp. Strain A3, Isolated from Contaminated Soil.

This study reports the complete genome sequence of bisphenol A-degrading bacterium Sphingobium sp. strain A3, which was isolated from a contaminated soil sample from the site of a factory fire in South Korea. The genome consists of a 6.53-Mbp chromosome and eight plasmid contigs (532,947 bp), with 6,406 protein-coding sequences and a GC content of 63.82%.

Complete Genome Sequence of Gordonia rubripertincta SD5, a Soil Bacterium Isolated from a Di-(2-Ethylhexyl) Phthalate-Degrading Enrichment Culture.

We report the complete genome sequence of Gordonia rubripertincta SD5, isolated from a soil-derived di-(2-ethylhexyl) phthalate-degrading enrichment culture. The final genome assembly consists of a 5.10-Mbp chromosome and a plasmid (159 kbp). A total of 4,814 coding sequences were predicted, including 4,741 protein-coding sequences.

Flavobacterium microcysteis sp. nov., isolated from a culture of Microcystis aeruginosa.

A Gram-stain-negative, yellow-pigmented, strictly aerobic bacterium, designated strain MaA-Y11T, was isolated from a culture of Microcystis aeruginosa in the Republic of Korea. Cells were non-motile rods showing catalase- and oxidase-positive reactions. Growth of strain MaA-Y11T was observed at 25-37 °C (optimum, 30 °C) and pH 6.0-9.0 (optimum, 7.0) and in the presence of 0-1.0 % (w/v) NaCl (optimum, 0 %). Strain MaA-Y11T did not produce flexirubin-type pigments. Strain MaA-Y11T contained iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as major cellular fatty acids and menaquinone-6 as the sole isoprenoid quinone. Phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids were detected as the major polar lipids. The G+C content of the genomic DNA was 37.0 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain MaA-Y11T formed a phyletic lineage with Flavobacterium lindanitolerans IP-10T within the genus Flavobacterium. Strain MaA-Y11T was most closely related to Flavobacterium lindanitolerans IP-10T, with a 98.85 % 16S rRNA gene sequence similarity, and shared less than 93.87 % sequence similarities with other type strains. Average nucleotide identity and in silico DNA-DNA hybridization values between strain MaA-Y11T and the type strain of F. lindanitolerans were 87.0 and 32.3 %, respectively. Here, we conclude that strain MaA-Y11T represents a new species of the genus Flavobacterium, for which the name Flavobacterium microcysteis sp. nov. is proposed. The type strain is MaA-Y11T (=KACC 21225T=JCM 33501T).

Complete Genome Sequence of Lactobacillus harbinensis Strain NSMJ42, Isolated from Makgeolli, a Traditional Korean Alcoholic Beverage.

In the present work, we report the complete genome sequence of Lactobacillus harbinensis NSMJ42, isolated from makgeolli (a Korean traditional alcoholic beverage) in South Korea. The final genome assembly consists of a 3.29-Mbp chromosome with 3,082 protein-coding sequences and a G+C content of 53.36%.

Complete Genome Sequence of Leuconostoc kimchii Strain NKJ218, Isolated from Homemade Kimchi.

Leuconostoc kimchii strain NKJ218 was isolated from homemade kimchi in South Korea. The whole genome was sequenced using the PacBio RS II and Illumina NovoSeq 6000 platforms. Here, we report a genome sequence of strain NKJ218, which consists of a 1.9-Mbp chromosome and three plasmid contigs. A total of 2,005 coding sequences (CDS) were predicted, including 1,881 protein-coding sequences.

Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed.

A Gram-positive, facultative anaerobic, catalase-negative, non-motile, non-spore-forming and rod-shaped lactic acid bacterium strain, denoted as NFFJ11T and isolated from total mixed fermentation feed in the Republic of Korea, was characterized through polyphasic approaches, including sequence analyses of the 16S rRNA gene and housekeeping genes (rpoA and pheS), determination of average nucleotide identity and in silico DNA-DNA hybridization, fatty acid methyl ester analysis, and phenotypic characterization. Phylogenetic analyses based on 16S rRNA, rpoA and pheS gene sequences revealed that strain NFFJ11T belonged to the genus Companilactobacillus. The 16S rRNA gene sequence of strain NFFJ11T exhibited high similarity to Companilactobacillus formosensis S215T (99.66 %), Companilactobacillus farciminis Rv4 naT (99.53 %), Companilactobacillus crustorum LMG 23699T (99.19 %), Companilactobacillus futsaii YM 0097T (99.06 %), Companilactobacillus zhachilii HBUAS52074T (98.86 %) and Companilactobacillus heilongiiangensis S4-3T (98.66 %). However, average nucleotide identity and in silico DNA-DNA hybridization values for these type strains were in the range of 79.90-92.93 % and 23.80-49.30 %, respectively, which offer evidence that strain NFFJ11T belongs to a novel species of the genus Companilactobacillus. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp) and the G+C content of the genomic DNA was 35.7 mol%. The main fatty acids of strain NFFJ11T were C18 : 1 ω9c (43.3 %), C16 : 0 (20.1 %) and summed feature 7 (18.3 %; comprising any combination of C19 : 1 ω7c, C19 : 1 ω6c and C19 : 0 cyclo ω10c). Through polyphasic taxonomic analysis, it was observed that strain NFFJ11T represents a novel species belonging to the genus Companilactobacillus, for which the name Companilactobacillus pabuli sp. nov. is proposed. The type strain is NFFJ11T (= KACC 21771T= JCM 34088T).

Sphingobacterium humi sp. nov., isolated from soil.

A Gram-stain-negative, facultatively aerobic bacterium, designated strain D1T, was isolated from soil in South Korea. Cells of strain D1T were non-motile rods with oxidase- and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30-37 °C), at pH 5.5-9.0 (optimum, pH 7.0-8.0) and in the presence of 0.0-5.0 % (w/v) NaCl (optimum, 0.0-1.0 %). The only respiratory quinone detected was menaquinone 7 (MK-7), and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) were identified as the major fatty acids. Phosphatidylethanolamine was the major polar lipid, and two unidentified glycophospholipids and four unidentified lipids were also detected as minor polar lipids. Sphingolipids, a typical chemotaxonomic feature of the genus Sphingobacterium, were detected. The G+C content of the genomic DNA was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D1T formed a phyletic lineage with Sphingobacterium hotanense XH4T within the genus Sphingobacterium. Strain D1T was most closely related to S. hotanense XH4T (98.1 % 16S rRNA gene sequence similarity) and Sphingobacterium cellulitidis R-53603T (97.2 %), and the DNA-DNA relatedness level between strain D1T and the type strain of S. cellulitidis was 43.1±0.7 %. Based on the phenotypic, chemotaxonomic and molecular features, strain D1T clearly represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium humi sp. nov. is proposed. The type strain is D1T (=KACC 18595T=JCM 31225T).

Cloacibacterium caeni sp. nov., isolated from activated sludge.

A Gram-stain-negative, facultatively anaerobic bacterium, designated B6T, was isolated from activated sludge of a wastewater treatment plant in South Korea. Cells were oxidase- and catalase-positive and non-motile rods producing yellow carotenoid-type pigments. Growth of B6T was observed at 20-40 °C (optimum, 37 °C) and pH 6.6-8.2 (optimum, pH 7.0) and in R2A broth supplemented with 0-1 % (w/v) NaCl (optimum, 0 %). B6T contained iso-C15 : 0 as the major fatty acid. Menaquinone-6 was detected as the sole respiratory quinone. The G+C content of the genomic DNA of B6T was 31.5 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that B6T formed a tight phylogenetic lineage with members of the genus Cloacibacterium. B6T was most closely related to Cloacibacterium rupense R2A-16T (99.0 %), Cloacibacterium normanense NRS1T (98.7 %) and Cloacibacterium haliotis WB5T (97.4 %), but their DNA-DNA relatedness levels were less than 42.0 %. On the basis of phenotypic, chemotaxonomic and molecular properties, it is clear that B6T represents a novel species of the genus Cloacibacterium, for which the name Cloacibacterium caeni sp. nov. is proposed. The type strain is B6T (=KACC 18988T=JCM 31714T).

Draft Genome Sequence of Zhouia amylolytica AD3, Isolated from Tidal Flat Sediment.

Zhouia amylolytica AD3 was isolated from tidal flat sediment at Taean, South Korea. We report here the draft genome sequence of Z. amylolytica AD3, which is the first report of a genome sequence of the genus Zhouia The genomic information will provide a better understanding of the physiology, adaptation, and evolution of Zhouia species.

Complete genome sequence of Sphingorhabdus sp. M41, a versatile hydrocarbon degrader, isolated from crude oil-contaminated costal sediment.

Sphingorhabdus sp. M41, capable of degrading aliphatic and aromatic hydrocarbons, was isolated from crude oil-contaminated costal sediment by an enrichment culture and its complete genome was sequenced. The genome of strain M41 has a chromosome with a size of 3,324,420bp, including 44 tRNAs, 6 rRNAs, and 3118 protein-coding genes. In addition, many potential genes responsible for the biodegradation of aliphatic and aromatic hydrocarbons were identified from the genome. This is the first complete genome of the genus Sphingorhabdus, which will provide insights into the bioremediation of crude oil-contaminated costal sediment by strain M41.