Search

A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-52T, was isolated from the rhizospheric soil of a banana plant. Colonies grew at 10–35 °C (optimum, 28 °C), pH 6.0–9.5 (optimum, pH 7.0–7.5), and in the presence of 0–1.0 % NaCl (optimum 0 %). The strain was positive for catalase and oxidase tests, as well as hydrolysis of gelatin, casein, starch and Tween 20. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-52T clustered together within the genus Massilia . Strain MAHUQ-52T was closely related to Massilia soli R798T (98.6 %) and Massilia polaris RP-1-19T (98.3 %). The novel strain MAHUQ-52T has a draft genome size of 4 677 454 bp (25 contigs), annotated with 4193 protein-coding genes, 64 tRNA and 19 rRNA genes. The genomic DNA G+C content was 63.0 %. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAHUQ-52T and closely related type strains were ≤88.4 and 35.8 %, respectively. The only respiratory quinone was ubiquinone-8. The major fatty acids were identified as C16 : 0 and summed feature 3 (C15 : 0 iso 2-OH and/or C16 : 1 ω7c). Strain MAHUQ-52T contained phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as the major polar lipids. On the basis of dDDH and ANI values, as well as genotypic, chemotaxonomic and physiological data, strain MAHUQ-52T represents a novel species within the genus Massilia , for which the name Massilia agrisoli sp. nov. is proposed, with MAHUQ-52T (=KACC 21999T=CGMCC 1.18577T) as the type strain.

A Gram-stain negative, aerobic, rod-shaped and creamy pink-coloured bacterium, designated MAHUQ-68T, was isolated from rhizospheric soil of a jujube tree. Colonies grew at 10–40 °C (optimum, 28 °C), pH 6.0–9.0 (optimum pH, 7.0) and in the presence of 0–1.5 % NaCl (optimum 0–0.5 %). Positive for both catalase and oxidase activity. Strain MAHUQ-68T hydrolysed casein, starch, aesculin and l-tyrosine. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-68T clustered together within the genus Solitalea . The closest members were Solitalea longa HR-AVT (98.8 % sequence similarity), Solitalea canadensis DSM 3403T (96.9 %) and Solitalea koreensis R2A36-4T (94.0 %). The genome of strain MAHUQ-68 T was 4 250 173 bp long with 68 scaffolds and 3 570 protein-coding genes. The genomic DNA G+C content of the type strain was 38.0 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain MAHUQ-68T and its closest relatives were 72.0–81.4% and 19.8–24.3 %, respectively. The major cellular fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The main respiratory quinone was menaquinone-7. The polar lipids comprised phosphatidylethanolamine, an unidentified aminolipid and four unidentified lipids. Based on these data, strain MAHUQ-68T represents a novel species in the genus Solitalea , for which the name Solitalea agri sp. nov. is proposed. The type strain is MAHUQ-68T (=KACC 22249T=CGMCC 1.19062T).

A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAHUQ-58T, was isolated from soil sample of a rice field. The colonies were observed to be light pink-coloured, smooth, spherical and 0.6–1.0 mm in diameter when grown on nutrient agar (NA) medium for 2 days. Strain MAHUQ-58T was found to be able to grow at 15–40 °C, at pH 5.5–10.0 and with 0–1.0 % NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria–Bertani agar, NA, MacConkey agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of Tween 20 and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Pseudomonas and to be closely related to Pseudomonas oryzae WM-3T (98.9 % similarity), Pseudomonas linyingensis LYBRD3-7T (97.7 %), Pseudomonas sagittaria JCM 18195 T (97.6 %) and Pseudomonas guangdongensis SgZ-6T (97.2 %). The novel strain MAHUQ-58T has a draft genome size of 4 536 129 bp (46 contigs), annotated with 4064 protein-coding genes, 60 tRNA genes and four rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAHUQ-58T and four closely related type strains were in the range of 85.5–89.5 % and 29.5–38.0 %, respectively. The genomic DNA G+C content was determined to be 67.0 mol%. The predominant isoprenoid quinone was ubiquinone 9. The major fatty acids were identified as C16:0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). On the basis of dDDH and ANI values, genotypic results, and chemotaxonomic and physiological data, strain MAHUQ-58T represents a novel species within the genus Pseudomonas , for which the name Pseudomonas oryzagri sp. nov. is proposed, with MAHUQ-58T (=KACC 22005T=CGMCC 1.18518T) as the type strain.

A ginsenoside Rg2-producing, Gram stain-negative, aerobic, catalase and oxidase-positive, rod-shaped, non-motile and orange pigmented novel bacterium designated strain MAH-28 T was isolated from soil sample of a grape garden. Strain MAH-28 T hydrolyzed aesculin, casein and DNA. Flexirubin-type pigments are present. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MAH-28 T formed a cluster within the genus Chitinophaga and the most close relatives were Chitinophaga alhagiae T22T (98.9% 16S rRNA gene sequence similarity), Chitinophaga humicola Ktm-2 T (98.8%), Chitinophaga barathri YLT18T (98.3%) and Chitinophaga lutea ZY74T (97.4%). The novel strain MAH-28 T has a draft genome size of 6,043,180 bp (14 contigs), annotated with 4,863 protein-coding genes, 53 tRNA and 6 rRNA genes. The ANI and dDDH values between strain MAH-28 T and the closely related type strains were in the range of 76.0–83.4% and 20.3–26.7%, respectively. The novel strain MAH-28 T was able to synthesize ginsenoside Rg2 from major ginsenoside Re. The genome annotation revealed 152 carbohydrate genes which may involve with the synthesis of ginsenoside Rg2. The respiratory quinone of strain MAH-28 T was MK-7 and the dominant cellular fatty acids were C15:0 iso, C16:1 ω5c and C17:0 iso 3-OH. The DNA G + C content of strain MAH-28 T was 53.3 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic studies, strain MAH-28 T represents a new member of genus Chitinophaga for which the name Chitinophaga chungangae sp. nov. is proposed with type strain MAH-28 T (= KACC 19968 T = CGMCC 1.16605 T).

A novel, pink-pigmented, Gram-stain-positive, aerobic, motile, rod-shaped and ginsenoside-converting bacterium, designated strain MAHUQ-46T, was isolated from soil of a forest. Strain MAHUQ-46T grew in the pH range 6.0–9.0 (optimum, 7.5), at temperatures between 10 and 37 °C (optimum, 30 °C) and at 0–3% (w/v) NaCl (optimum, 0.5%). 16S rRNA gene sequence analysis showed that strain MAHUQ-46T was closely related to Paenibacillus pinihumi S23T (97.3% similarity), followed by Paenibacillus elymi KUDC6143T (96.7%). The draft genome of strain MAHUQ-46T had a total length of 5,367,904 base pairs. A total of 4,857 genes were identified, in which 4,629 were protein-coding genes and 137 were RNA genes. The genome annotation of MAHUQ-46T showed 172 carbohydrate genes, some of them may be responsible for the biosynthesis of ginsenoside Rd from major ginsenoside Rb1. The DNA G + C content was 48.4 mol% and the major quinone was MK-7. Main fatty acids of strain MAHUQ-46T were C15: 0 anteiso, C16: 0 and C17: 0 anteiso. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyl-N-methylethanolamine, two unidentified aminophospholipids and five unidentified phospholipids. Diagnostic diamino acid of peptidoglycan was meso-diaminopimelic acid. The novel strain MAHUQ-46T was able to rapidly synthesize ginsenoside Rd from major ginsenoside Rb1. The synthesized ginsenoside was confirmed by TLC and HPLC analysis. According to the phenotypic, genetic and chemotaxonomic evidence, strain MAHUQ-46T was clearly distinguishable from validly published species of genus Paenibacillus and should, therefore, be categorized as a novel species for which the name Paenibacillus roseus sp. nov. is proposed. The type strain is MAHUQ-46T (= KACC 21242T = CGMCC 1.17353T).

A Gram-stain-negative, aerobic, non-motile and rod- or coccoid-shaped novel bacterial strain, designated MAH-25T, was isolated from soil sampled in a pine garden. The colonies were observed to be light pink-coloured, smooth, spherical and 1–2 mm in diameter when grown on nutrient agar for 2 days. Strain MAH-25T was found to be able to grow at 15–35 °C, at pH 5.0–8.0 and at 0–2.0 % NaCl. Cell growth occurred on Reasoner's 2A agar and nutrient agar. The strain was found to be positive in both oxidase and catalase tests. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Ramlibacter and closely related to Ramlibacter solisilvae 5-10T (98.0 % similarity), Ramlibacter henchirensis TMB834T (97.7 %), Ramlibacter tataouinensis TTB310T (97.6 %) and Ramlibacter rhizophilus YS3.2.7T (97.3 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-25T and the four closely related type strains were in the range of 78.8–81.3 % and 22.3–24.1 %, respectively. The novel strain MAH-25T has a draft genome size of 5 505 957 bp (11 contigs), annotated with 5210 protein-coding genes, 46 tRNA and three rRNA genes. The genomic DNA G+C content was determined to be 70.3 mol%. The predominant isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were identified as C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of DNA–DNA hybridization, genotypic analysis, chemotaxonomic and physiological data, strain MAH-25T represents a novel species within the genus Ramlibacter , for which the name Ramlibacter pinisoli sp. nov. is proposed, with MAH-25T (=KACC 19839T=CGMCC1.13660T) as the type strain.

A novel bacterial strain, designated MAH-20T, was isolated from a soil sample of a tomato garden. Cells of strain MAH-20T were Gram-stain negative, aerobic, motile, and rod-shaped. The colonies were light brown colored, smooth, spherical, and 0.2–0.7 mm in diameter when grown on Luria–Bertani agar for 2 days. Strain MAH-20T grows at 15–40 °C (optimum growth temperature 30–32 °C), at pH 5.0–10.0 (optimum growth pH 7.0) and at 0–2.0% NaCl. The strain showed positive activity for both oxidase and catalase tests. Cells were able to hydrolyze starch, DNA, urea, gelatin, L-arginine, and Tween 20. According to the 16S rRNA gene sequence similarity, the strain MAH-20T was identified as a new member of the genus Sphingomonas and had the close sequence similarity with Sphingomonas changbaiensis V2M44T (98.9%) and Sphingomonas tabacisoli X1-8T (98.1%). The genomic ANI value between strain MAH-20T and S. changbaiensis NBRC 104936T was 84.4%. The novel strain MAH-20T has a draft genome size of 3,350,026 bp (25 contigs), annotated with 3210 protein-coding genes, 46 tRNA, and 3 rRNA genes. The genomic DNA G + C content of isolate was 67.3 mol%, the predominant quinone was ubiquinone 10 and the major fatty acids were C16:0, C17:1 ω6c and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). On the basis of DNA-DNA hybridization results, phenotypic, genotypic, and chemotaxonomic data, the isolated strain MAH-20T represents a novel species, for which the name Sphingomonas horti sp. nov. is proposed, with MAH-20T as the type strain (= KACC 19746T = CGMCC1.13658T).

A novel bacterial strain, designated MAH-6T, was isolated from a garden soil sample. Cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. The colonies were light yellow, smooth, circular and 0.6–1.2 mm in diameter when grown on nutrient agar for 3 days. Strain MAH-6T grew at 15–35 °C, at pH 5.0–7.0 and with 0–0.5 % NaCl. Cell growth occurred on nutrient agar and Reasoner's 2A (R2A) agar. The strain was positive for both catalase and oxidase tests. Cells were able to hydrolyse starch, aesculin, Tween 20 and Tween 80. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingomonas and was most closely related to Sphingomonas polyaromaticivorans B2-7T (98.2 % sequence similarity), Sphingomonas oligoaromativorans SY-6T (96.9 %) and Sphingomonas morindae NBD5T (96.6 %). The novel strain MAH-6T has a draft genome size of 4 370 740 bp (28 contigs), annotated with 4199 protein-coding genes, 46 tRNA and three rRNA genes. The genomic DNA G+C content of the strain was determined to be 66.2 mol% and the predominant isoprenoid quinone is Q-10. The major fatty acids were identified as summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c), C14 : 0 2OH and C16 : 0. The main polar lipids were phosphatidylcholine, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on the results of phenotypic, genotypic, chemotaxonomic and DNA–DNA hybridization studies, strain MAH-6T represents a novel species, for which the name Sphingomonas chungangi sp. nov. is proposed, with MAH-6T as the type strain (=KACC 19292T=CGMCC1.13654T).

The present study highlights the biological synthesis of silver nanoparticles (AgNPs) using Sphingobium sp. MAH-11 and also their antibacterial mechanisms against drug-resistant pathogenic microorg...

A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAH-13T, was isolated from a soil sample. The colonies were observed to be yellow-coloured, smooth, spherical and 1.8–3.0 mm in diameter when grown on nutrient agar medium for 2 days. Strain MAH-13T was found to be able to grow at 20–40 °C, at pH 5.0–10.0 and with 0–1.0% NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria–Bertani agar, nutrient agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of casein, starch, DNA and l-tyrosine. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Frateuria and to be closely related to Frateuria terrea DSM 26515T (98.2% similarity), Dyella thiooxydans ATSB10T (98.2 %), Frateuria defendens HyOGT (97.9 %), Rhodanobacter glycinis MO64T (97.8 %) and Frateuria aurantia DSM 6220T (97.8 %). The novel strain MAH-13T has a draft genome size of 3 682 848 bp (40 contigs), annotated with 3172 protein-coding genes, 49 tRNA genes and three rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAH-13T and five closely related type strains were in the range of 73.7–85.5 % and 20.7–30.1%, respectively. The genomic DNA G+C content was determined to be 68.0 mol%. The predominant isoprenoid quinone was ubiquinone 8. The major fatty acids were identified as iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17 : 1 ω9c and/or C16:0 10-methyl). On the basis of dDDH and ANI values, genotypic analysis, and chemotaxonomic and physiological data, strain MAH-13T represents a novel species within the genus Frateuria , for which the name Frateuria flava sp. nov. is proposed, with MAH-13T (=KACC 19743T=CGMCC 1.13655T) as the type strain.

A Gram-stain-negative, aerobic and rod-shaped novel bacterial strain, designated MAH-26T, was isolated from rhizospheric soil of a pine tree. The colonies were orange coloured, smooth, spherical and 0.7–1.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-26T was able to grow at 10–40 °C, at pH 6.0–9.0 and with 0–1.0 % NaCl. Cell growth occurred on nutrient agar, R2A agar, tryptone soya agar and Luria–Bertani agar. The strain gave positive results in oxidase and catalase tests. Strain MAH-26T was closely related to Flavihumibacter sediminis CJ663T and Parasegetibacter terrae SGM2-10T with a low 16S rRNA gene sequence similarity (92.8 and 92.9 %, respectively) and phylogenetic analysis indicated that the strain formed a distinct phylogenetic lineage from the members of the closely related genera of the family Chitinophagaceae . Strain MAH-26T has a draft genome size of 6 857 405 bp, annotated with 5173 protein-coding genes, 50 tRNA and two rRNA genes. The genomic DNA G+C content was 41.5 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of phylogenetic inference and phenotypic, chemotaxonomic and molecular properties, strain MAH-26T represents a novel species of a novel genus of the family Chitinophagaceae , for which the name Pinibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain of Pinibacter aurantiacus is MAH-26T (=KACC 19749T=CGMCC 1.13701T).

The present study describes the isolation and characterization of novel bacterial species Arthrobacter bangladeshi sp. nov., applied for the green synthesis of AgNPs, and investigates its antibacterial efficacy against drug-resistant pathogenic Salmonella Typhimurium and Yersinia enterocolitica. Novel strain MAHUQ-56T is Gram-positive, aerobic, non-motile, and rod-shaped. Colonies were spherical and milky white. The strain showed positive activity for catalase and nitrate reductase, and the hydrolysis of starch, L-tyrosine, casein, and Tween 20. On the basis of the 16S rRNA gene sequence, strain MAHUQ-56T belongs to the Arthrobacter genus and is most closely related to Arthrobacter pokkalii P3B162T (98.6%). Arthrobacter bangladeshi MAHUQ-56T has a genome 4,566,112 bp long (26 contigs) with 4125 protein-coding genes, 51 tRNA and 6 rRNA genes. The culture supernatant of Arthrobacter bangladeshi MAHUQ-56T was used for the easy and green synthesis of AgNPs. Synthesized AgNPs were characterized by UV–vis spectroscopy, FE-TEM, XRD, DLS, and FT-IR. Synthesized AgNPs were spherical and 12–50 nm in size. FT-IR analysis revealed various biomolecules that may be involved in the synthesis process. Synthesized AgNPs showed strong antibacterial activity against multidrug-resistant pathogenic S. typhimurium and Y. enterocolitica. MIC values of the synthesized AgNPs against S. typhimurium and Y. enterocolitica were 6.2 and 3.1 ug/mL, respectively. The MBC of synthesized AgNPs for both pathogens was 12.5 ug/mL. FE-SEM analysis revealed the morphological and structural alterations, and damage of pathogens treated by AgNPs. These changes might disturb normal cellular functions, which ultimately leads to the death of cells.

A Gram-stain-negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-29T, was isolated from rhizospheric soil of a persimmon tree. The colonies were light pink coloured, smooth, spherical and 0.1–0.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-29T was able to grow at 20–37 °C, at pH 5.0–8.5 and at 0–2.0 % NaCl. Cell growth occurred on nutrient agar and R2A agar. The strain was positive in both oxidase and catalase tests. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Niastella and was closely related to Niastella vici DJ57T (97.7 % similarity), Niastella koreensis GR20-10T (97.1 %) and Niastella yeongjuensis GR20-13T (97.0 %). Strain MAH-29T has a draft genome size of 8 876 333 bp (31 contigs), annotated with 6920 protein-coding genes, 61 tRNA and four rRNA genes. The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-29T and three closely related type strains were in the range of 78.2–83.2 % and 22.1–27.0 %, respectively. The genomic DNA G+C content was 43.8 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C15:0, iso-C15:1 G and iso-C17:0 3OH. On the basis of DNA–DNA hybridization results, genotypic analysis and chemotaxonomic and physiological data, strain MAH-29T represents a novel species within the genus Niastella , for which the name Niastella soli sp. nov. is proposed, with MAH-29T (=KACC 19969T=CGMCC 1.16606T) as the type strain.

A Gram-stain negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-3T, was isolated from soil sample of a rice field. The colonies were orange pigmented, smooth, circular and 0.4–0.9 mm in diameter when grown on R2A agar for 3 days. Strain MAH-3T was found to grow at 10–40 °C (optimum 30 °C), pH 6.0–8.0 (optimum 7.0) and in the presence of 0–1.0% NaCl (optimum 0%). Cell growth occurs on R2A agar and Luria–Bertani agar, but not on nutrient agar, tryptone soya agar and MacConkey agar. Cells were positive for catalase test but negative for oxidase test. Cells were able to hydrolyze casein, gelatin, DNA and Tween 80. 16S rRNA gene sequence analysis revealed that strain MAH-3T was most closely related to the genus Fluviicola and exhibited the highest sequence similarity to Fluviicola hefeinensis MYL-8T (97.4%), Fluviicola taffensis RW262T (96.2%) and Fluviicola kyonggii CA-1T (95.6%). Strain MAH-3T had a genome size of 4,271,694 bp and the genomic DNA G + C content was determined to be 41.7 mol%. The genome contained 19 contigs encoded by 3,664 protein-coding genes with 34 tRNA and 4 rRNA genes. The genomic ANI value between strain MAH-3T and one of the closely related type strains, F. taffensis DSM 16823T was 76.2%. The predominant isoprenoid quinone of isolated strain MAH-3T was menaquinone-6 (MK-6). The major fatty acids were identified as C15:0 iso, C15:0 2OH and C17:0 iso 3OH. On the basis of these phenotypic, genotypic and chemotaxonomic studies and DNA–DNA hybridization results, the isolated strain MAH-3T represents a novel species, for which the name Fluviicola chungangensis sp. nov. is proposed, with MAH-3T as the type strain (= KACC 19742T = CGMCC 1.13750T).

The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic functions. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 patients = 8, recovered humans = 7, and healthy people = 7) were collected, and underwent to RNAseq-based metagenomic investigation. Our RNAseq data mapped to 2281 bacterial species (including 1477, 919 and 676 in healthy, COVID-19 and recovered metagenomes, respectively) indicating a distinct microbiome dysbiosis. The COVID-19 and recovered samples included 67% and 77% opportunistic bacterial species, respectively compared to healthy controls. Notably, 79% commensal bacterial species found in healthy controls were not detected in COVID-19 and recovered people. Similar dysbiosis was also found in viral and archaeal fraction of the nasopharyngeal microbiomes. We also detected several altered metabolic pathways and functional genes in the progression and pathophysiology of COVID-19. The nasopharyngeal microbiome dysbiosis and their genomic features determined by our RNAseq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.

Background The SARS-CoV-2 primarily enters into the human body through nasopharyngeal tract (NT) and is the etiological agent of COVID-19. The microbiota of the NT may play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. To shed light on the effects and consequences of SARS-CoV-2 infection on microbiome diversity and composition, we conducted a high throughput RNA-Seq metagenomic investigation of 22 NT swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7). Results This study for the first time demonstrates the association of microbiome diversity and their concomitant genomic features in the NT of COVID-19 and Recovered patients compared to Healthy humans, and discusses the role of the altered microbiomes in the pathophysiology of the SARS-CoV-2 infections. Our RNA-Seq metagenomic analyses detected 2281 bacterial species (including 1477, 919 and 676 in samples of Healthy human, COVID-19 and Recovered patients, respectively) indicating a distinct microbiome dysbiosis (COVID-19>Recovered>Healthy). The samples from COVID-19 patients and Recovered individuals had inclusion of 67% (including Streptococcus salivarius, S. mitis, Neisseria subflava, Veillonella dispar, Acinetobacter junii, Prevotella melaninogenica etc.) and 77% (including Pseudomonas stutzeri, Staphylococcus capitis, S. epidermidis, P. mendocina, Moraxella osloensis, A. indicus, Escherichia coli etc.) opportunistic pathogenic bacteria, respectively compared to Healthy individuals. Notably, 79% commensal bacteria (e.g., Pseudomonas sp. LPH1, Brevundimonas sp. Bb-A, P. oleovorans, Pseudomonas sp. phDV1, Brevundimonas sp. DS20, Idiomarinaceae bacterium HL-53, Alishewanella sp. 205, Sphingobacterium psychroaquaticum etc.) were found in healthy individuals but not detected in COVID-19 patients and Recovered individuals. Similar dysbiosis was also found in viral and archaeal fraction of the microbiomes. Although, 55 viral and 48 archaeal genera were detected, only 16% viral and 27% archaeal genera were shared across three metagenomes. We also detected altered metabolic pathways and functional genes including resistance to antibiotics and toxic compounds in the pathophysiology of COVID-19.Conclusions The nasopharyngeal microbiome dysbiosis and their genomic features in COVID-19, Recovered and Healthy individuals determined by our RNA-Seq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.

It is essential to develop and discover alternative eco-friendly antibacterial agents due to the emergence of multi-drug-resistant microorganisms. In this study, we isolated and characterized a novel bacterium named Terrabacter humi MAHUQ-38T, utilized for the eco-friendly synthesis of silver nanoparticles (AgNPs) and the synthesized AgNPs were used to control multi-drug-resistant microorganisms. The novel strain was Gram stain positive, strictly aerobic, milky white colored, rod shaped and non-motile. The optimal growth temperature, pH and NaCl concentration were 30 &deg, C, 6.5 and 0%, respectively. Based on 16S rRNA gene sequence, strain MAHUQ-38T belongs to the genus Terrabacter and is most closely related to several Terrabacter type strains (98.2%&ndash, 98.8%). Terrabacter humi MAHUQ-38T had a genome of 5,156,829 bp long (19 contigs) with 4555 protein-coding genes, 48 tRNA and 5 rRNA genes. The culture supernatant of strain MAHUQ-38T was used for the eco-friendly and facile synthesis of AgNPs. The transmission electron microscopy (TEM) image showed the spherical shape of AgNPs with a size of 6 to 24 nm, and the Fourier transform infrared (FTIR) analysis revealed the functional groups responsible for the synthesis of AgNPs. The synthesized AgNPs exhibited strong anti-bacterial activity against multi-drug-resistant pathogens, Escherichia coli and Pseudomonas aeruginosa. Minimal inhibitory/bactericidal concentrations against E. coli and P. aeruginosa were 6.25/50 and 12.5/50 &mu, g/mL, respectively. The AgNPs altered the cell morphology and damaged the cell membrane of pathogens. This study encourages the use of Terrabacter humi for the ecofriendly synthesis of AgNPs to control multi-drug-resistant microorganisms.

A Gram-stain-negative, strictly aerobic, cream yellow colored, non-motile, rod-shaped bacterial strain, designated MAH-1T was isolated from rhizospheric soil of Coriandrum sativum. A polyphasic taxonomic study was performed on the isolated strain. Optimal growth occurred at 28–30 °C, pH 6.5 and 0% NaCl. The strain showed activity for both catalase and oxidase tests. Cell growth occurs on R2A agar, nutrient agar and Luria–Bertani agar. Cells were able to hydrolyze starch, aesculin, gelatin, and Tween 20. Alignment of 16S rRNA gene sequences indicated that strain MAH-1T was associated with the genus Flavobacterium and was most closely related to Flavobacterium longum YIT 12745T (94.5% sequence similarity) and Flavobacterium caeni LM5T (93.0%). Strain MAH-1T had a genome size of 3,975,600 bp. Genome contained 67 contigs encoded by 3,522 protein-coding genes with 38 tRNA and 6 rRNA genes. The genomic DNA G + C contents of strain MAH-1T was 47.1 mol %. The genomic ANI and dDDH values between strain MAH-1T and one of the close relatives F. caeni LM5T were 72.2 and 18.8%, respectively. The major fatty acids were C15:0 iso, C16:0 iso and C15:0 anteiso. The predominant respiratory quinone was menaquinone 6 (MK-6). Based on physiological, biochemical and phylogenetic data for this isolate, it was confirmed that strain MAH-1T was affiliated to the genus Flavobacterium and represented a novel species, for which the name Flavobacterium agri sp. nov. is proposed. The type strain is MAH-1T (= KACC 19300T = CGMCC 1.16617T).

A Gram-stain positive, aerobic, motile, rod-shaped, and ginsenoside Rd producing novel bacterial strain, designated as MAH-16T, was isolated from soil sample of a vegetable garden and was characterized by using a polyphasic approach. The colonies were beige color, smooth, circular, and 0.3–0.7 mm in diameter when grown on tryptone soya agar for 3 days. Strain MAH-16T can grow at 20–40 °C temperature, at pH 5.0–7.0 and at 0–1% NaCl. Cell growth occurs on nutrient agar, R2A agar, tryptone soya agar, and Luria–Bertani agar but not on MacConkey agar. The strain was positive for both catalase and oxidase test. The novel strain rapidly synthesized ginsenoside Rd from major ginsenoside Rb1. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Paenibacillus and was most closely related to Paenibacillus barengoltzii SAFN-016T (97.1%), Paenibacillus faecis 656.84T (96.7%), and Paenibacillus konsidensis LBYT (96.2%). In DNA–DNA hybridization tests, the DNA relatedness between strain MAH-16T and its closest phylogenetic neighbor was below 45.0%. The genomic DNA G + C content of isolated strain was determined to be 52.0 mol% and the predominant isoprenoid quinine was menaquinone-7 (MK-7). The major fatty acids were identified as anteiso-C15:0. The genetic characteristics in combination with chemotaxonomic and physiological data demonstrated that strain MAH-16T represented a novel species within the genus Paenibacillus, for which the name Paenibacillus horti sp. nov. is proposed, with MAH-16T as the type strain (=KACC 19299T = CGMCC1.16487T).

A novel bacterial strain THG-PC4T was isolated from soil sample of rice field and was characterized by using a polyphasic approach. Cells were Gram-negative, bright yellow colored, nonmotile and rod shaped. The strain was aerobic and catalase positive, optimum growth temperature, and pH were 28 °C and 7, respectively. On the basis of 16S rRNA gene sequence analysis, strain THG-PC4T belongs to the genus Lysobacter and is most closely related to Lysobacter fragariae KCTC 42236T, followed by Lysobacter oryzae KCTC 22249T, Lysobacter tyrosinelyticus KCTC 42235T, Lysobacter terrae KACC 17646T, Lysobacter yangpyeongensis KACC 11407T, Lysobacter rhizosphaerae KCTC 42237T and Lysobacter niabensis KACC 11587T. In DNA–DNA hybridization tests, the DNA relatedness between strain THG-PC4T and its closest phylogenetic neighbors was below 45 %. The DNA G + C content was 66.6 mol %, and the predominant respiratory quinone was ubiquinone-8. Flexirubin-type pigments were found to be present. The major cellular fatty acids were iso-C16:0, iso-C17:1 ω9c, iso-C17:0 and iso-C11:0 3OH. The predominant polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA–DNA hybridization, genotypic, chemotaxonomic and physiological data demonstrated that strain THG-PC4T represented a novel species within the genus Lysobacter, for which the name Lysobcater humi is proposed. The type strain is THG-PC4T (=KACC 18284T = CCTCC AB 2015292T).

A novel bacterial strain THG-SL1(T) was isolated from a soil sample of Cucurbita maxima garden and was characterized by using a polyphasic approach. Cells were Gram-reaction-positive, non-motile and rod-shaped. The strain was aerobic, catalase positive and weakly positive for oxidase. Phylogenetic analysis based on 16S rRNA gene sequence analysis but it shared highest similarity with Microbacterium ginsengisoli KCTC 19189(T) (96.6 %), indicating that strain THG-SL1(T) belongs to the genus Microbacterium. The DNA G + C content of the isolate was 68.9 mol %. The major fatty acids were anteiso-C15: 0 (39.7 %), anteiso-C17: 0 (24.4 %) and iso-C16: 0 (18.5 %). The major polar lipids of strain THG-SL1(T) were phosphatidylglycerol (PG) and an unidentified glycolipid (GL). The predominant respiratory isoprenoid quinones were menaquinone-11 and menaquinone-12. The diamino acid in the cell-wall peptidoglycan was ornithine. Based on the results of polyphasic characterization, strain THG-SL1(T) represented a novel species within the genus Microbacterium, for which the name Microbacterium horti sp. nov. is proposed. The type strain is THG-SL1(T) (=KACC 18286(T)=CCTCC AB 2015117(T)).

A Gram-stain negative, aerobic, non-motile and rod-shaped novel bacterial strain, designated as MAH-5T, was isolated from a road-side soil sample and was characterised by using a polyphasic taxonomic approach. The colonies were observed to be yellowish orange in colour, smooth, circular and 0.3–0.7 mm in diameter when grown on nutrient agar for 2 days. Strain MAH-5T was found to be able to grow at 15–35 °C and at pH 4.0–8.0. The strain was observed to be positive for both the catalase and oxidase tests. Cells were found to be able to hydrolyse aesculin, gelatin and starch. By 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Mucilaginibacter and to be closely related to Mucilaginibacter panaciglaebae BXN5-31T (98.35%), Mucilaginibacter soyangensis HME6664T (97.82%), Mucilaginibacter antarcticus S14-88T (97.49%) and Mucilaginibacter ximonensis XM-003T (97.06%). In DNA–DNA hybridization tests, the DNA relatedness values between strain MAH-5T and its close phylogenetic neighbors were below 45.0%. The genomic DNA G + C content of strain MAH-5T was determined to be 41.5 mol% and the predominant isoprenoid quinine was identified as MK-7. The major fatty acids were identified as C15:0 iso and summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c). The genetic characteristics, in combination with chemotaxonomic and physiological data, demonstrated that the isolated strain MAH-5T represents a novel species within the genus Mucilaginibacter, for which the name Mucilaginibacter formosus sp. nov. is proposed, with MAH-5T as the type strain (= KACC 19291T = CGMCC1.16489T).

A yellow pigmented, Gram-staining negative, motile and rod-shaped novel bacterial strain, designated MAH-14T was isolated from rhizospheric soil and was characterized using a polyphasic approach. The isolated strain was aerobic, oxidase and catalase were positive, optimum growth temperature and pH were 28–30 °C and 6.5, respectively. The novel strain is able to hydrolyze casein, starch, esculin, gelatin, l-tyrosine, DNA, tween 80, tween 20, l-arginine and 4-nitrophenyl-BD-galactopyranoside. On the basis of 16S rRNA gene sequence analysis, strain MAH-14T belongs to the genus Luteibacter and is most closely related to Luteibacter yeojuensis R2A16-10T (98.5%), Luteibacter anthropi CCUG 25036T (98.4%) and Luteibacter rhizovicinus LJ96T (98.3%). In DNA–DNA hybridization experiments, the DNA relatedness between strain MAH-14T and its closest phylogenetic neighbor was below 45.0%. The predominant respiratory quinone and the DNA G + C content of the novel strain were ubiquinone-8 and 63.5 mol%, respectively. The novel strain MAH-14T is able to produce flexirubin-type pigments. The major cellular fatty acids were C15:0 iso, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 9 (C17:1 iso ω9c and/or C16:0 10-methyl). The DNA–DNA hybridization results and results of the genotypic analysis in combination with chemotaxonomic and physiological data revealed that strain MAH-14T represented a novel species within the genus Luteibacter, for which the name Luteibacter pinisoli, is proposed. The type strain is MAH-14T (= KACC 19298T = CGMCC 1.16227T).

A Gram-stain-negative, aerobic, motile and rod-shaped strain, THG-DN7.3T, was isolated from a waterfall. Strain THG-DN7.3T grew well at 18–28 °C and at pH 6.0–7.5 on Reasoner's 2A agar. Based on 16S rRNA gene sequence comparisons, strain THG-DN7.3T was most closely related to Undibacterium jejuense JS4-4T (97.3 % 16S rRNA gene sequence similarity) and Undibacterium seohonense SHS5-24T (96.5 %). The G+C content of the genomic DNA was 57.4 mol%. The mean DNA–DNA relatedness of strain THG-DN7.3T with U. jejuense KACC 12607T was 40 ± 1 % (reciprocal 50 ± 2.1 %). The major cellular fatty acids of strain THG-DN7.3T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (47.4 %), C16 : 0 (30.4 %), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) (6.8 %) and C12 : 0 (6.2 %). The predominant isoprenoid quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The results of the DNA–DNA hybridization and genotypic analysis, in combination with chemotaxonomic and physiological data, demonstrated that strain THG-DN7.3T represents a novel species of the genus Undibacterium, for which the name Undibacterium aquatile sp. nov. is proposed. The type strain is THG-DN7.3T ( = KCTC 42243T = CCTCC AB 2015119T).

A novel bacterial strain THG-MM13(T) was isolated from rhizospheric soil sample and was characterized by using a polyphasic approach. Cells were Gram-reaction-negative, non-motile and rod-shaped. The strain was aerobic, catalase and oxidase positive, and optimum growth temperature and pH were 28 °C and 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain THG-MM13(T) (KM598260) belongs to the genus Pseudoxanthomonas and is most closely related to Pseudoxanthomonas wuyuanensis KCTC 23877(T) (97.4 %) (JN247803), followed by Pseudoxanthomonas koreensis KCTC 12208(T) (96.7 %) (AY550263) and Pseudoxanthomonas yeongjuensis KACC 11580(T) (96.7 %) (DQ438977). The DNA G + C content was 63.7 mol%, and the predominant respiratory quinone was ubiquinone-8. The major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were iso-C15:0 (31.3 %) and iso-C16:0 (19.3 %). The DNA-DNA relatedness value between strain THG-MM13(T) and P. wuyuanensis KCTC 23877(T) was below 50 %. The DNA-DNA hybridization result and results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain THG-MM13(T) represented a novel species within the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas humi is proposed. The type strain is THG-MM13(T) (=KACC 18280(T) = CCTCC AB 2015122(T)).

A novel bacterial strain, designated THG-PC7T, was isolated from fallow farmland soil in Yongin, South Korea. Cells of strain THG-PC7Twere Gram-stain-negative, dark yellow, aerobic, rod-shaped and had gliding motility. Strain THG-PC7Tgrew optimally at 25–35 °C, at pH 7 and in the absence of NaCl. Comparative 16S rRNA gene sequence analysis identified strain THG-PC7Tas belonging to the genusLysobacter, exhibiting highest sequence similarity withLysobacter ximonensisKCTC 22336T(98.7 %) followed byLysobacter niastensisKACC 11588T(95.7 %). In DNA–DNA hybridization tests, DNA relatedness between strain THG-PC7Tand its closest phylogenetic neighbourL. ximonensiswas below 25 %. The DNA G+C content of the novel isolate was determined to be 62.5 mol%. Flexirubin-type pigments were found to be present. The major cellular fatty acids were determined to be iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0and iso-C17 : 1ω9c. The major respiratory quinone was identified as ubiquonone-8 (Q8). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospolipid. On the basis of results from DNA–DNA hybridization and the polyphasic data, strain THG-PC7Trepresents a novel species of the genusLysobacter, for which the nameLysobacter novalissp. nov. is proposed. The type strain is THG-PC7T( = KACC 18276T = CCTCC AB 2014319T).

A novel bacterial strain, THG-sc1(T), was isolated from a soil sample of a cucumber garden and was characterised by using a polyphasic approach. Cells were observed to be Gram-stain negative, non-motile and rod-shaped. The strain was found to be aerobic, catalase and oxidase positive, esculin and starch negative, and to have an optimum growth temperature and pH of 28 °C and 7.5, respectively. On the basis of 16S rRNA gene sequence analysis, strain THG-sc1(T) was found to belong to the genus Sphingosinicella and to be closely related to Sphingosinicella vermicomposti KCTC 22446(T), followed by Sphingosinicella xenopeptidilytica DSM 17130(T) and Sphingosinicella microcystinivorans KCTC 12019(T). The DNA G+C content was determined to be 60.8 mol% and the predominant respiratory quinone was identified as ubiquinone-10. The major polyamine was found to be sym-homospermidine. The major polar lipids were identified as sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid. The major fatty acids were identified as C(18:1)ω7c, C(16:0) and summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH, as defined by MIDI). The results of the genotypic analysis, in combination with chemotaxonomic and physiological data, demonstrated that strain THG-sc1(T) represents a novel species within the genus Sphingosinicella, for which the name Sphingosinicella cucumeris is proposed. The type strain is THG-sc1(T) (=KACC 18279(T) = CCTCC AB 2015120(T)).

A Gram-reaction-negative, non-motile and rod-shaped bacterium, designated as THG-DN3.6(T), was isolated from an ancient tree trunk from Republic of Korea. On the basis of 16S rRNA gene sequence analysis, strain THG-DN3.6(T) was shown to belong to the genus Chryseobacterium and the highest similarity to Chryseobacterium indoltheticum LMG 4025(T) (97.2%) and the closest phylogenetic relatives were Chryseobacterium scophthalmum (96.8%), Chryseobacterium piscium (96.7%) and Chryseobacterium balustinum KCTC 2903(T) (96.3%). The DNA G + C content of the isolate was 33.2 mol%. The predominant isoprenoid quinone was menaquinone-6. The major fatty acids were iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω7t and/or iso-C15:0 2-OH), iso-C17:1 ω9c and iso-C17:0 3-OH. The major polar lipids of strain THG-DN3.6(T) were phosphatidylethanolamine. The mean DNA-DNA relatedness of strain THG-DN3.6(T) to C. indoltheticum LMG 4025(T) was 52 ± 0.5%. Based on the results of polyphasic characterization, strain THG-DN3.6(T) represented a novel species within the genus Chryseobacterium, for which the name Chryseobacterium formosus sp. nov. is proposed. The type strain is THG-DN3.6(T) (=KCTC 42606 = CCTCC AB 2015118). The NCBI GenBank accession number for the 16S rRNA gene sequence of strain THG-DN3.6(T) is KM035938.

A novel Gram-negative, aerobic, yellow-pigmented, non-motile and rod-shaped bacterium, designated as THG-SM1(T), was isolated from field soil collected from Suwon, South Korea. The strain was found to grow optimally at 28 °C, at pH 7.0 and in the absence of NaCl. Based on 16S rRNA gene sequence similarities, strain THG-SM1(T) belongs to the genus Flavobacterium and is most closely related to Flavobacterium terrae KACC 11731(T), followed by Flavobacterium columnare KACC 11683(T) and Flavobacterium enshiense KCTC 23775(T). The DNA G+C content of the novel isolate was determined to be 38.5 mol%. In DNA-DNA hybridization tests, the DNA relatedness between strain THG-SM1(T) and its closest phylogenetic neighbour F. terrae was below 50 %. Flexirubin-type pigments were found to be present. The major polar lipid and isoprenoid quinone were phosphatidylethanolamine and menaquinone 6 (MK-6), respectively. The main cellular fatty acids were identified as iso-C15:1G, iso-C15:0 3OH, iso-C16:0 and iso-C15:0. The DNA-DNA hybridization result and differentiating chemotaxonomic and phenotypic characteristics showed that strain THG-SM1(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium vireti sp. nov. is proposed. The type strain is THG-SM1(T) (=KACC 18371(T) = CCTCC AB2014312(T)).

A novel bacterial strain MAH-10T was isolated from soil sample of a Chinese cabbage garden, Republic of Korea and was characterized using a polyphasic approach. Cells were Gram-staining negative, rod-shaped, yellowish orange colored, and motile. The strain was aerobic, catalase and oxidase are positive, and optimum growth temperature and pH were 28 °C and 6.5, respectively. Flexirubin-type pigments were found to be present. On the basis of 16S rRNA gene sequence analysis, strain MAH-10T belongs to the genus Flavobacterium and is most closely related to Flavobacterium tyrosinilyticum KCTC 42726T (98.7%). On the basis of phylogenetic tree, other closely related species are Flavobacterium banpakuense KACC 14225T (98.3%) and Flavobacterium chungbukense KACC 15048T (97.6%). In DNA–DNA hybridization tests, the DNA relatedness between strain MAH-10T and its closest phylogenetic neighbor was below 45.0%. The DNA G+C content was 37.2 mol% and the predominant respiratory quinone was menaquinone-6. The major cellular fatty acids were C15:0 iso, C16:0, and summed feature 3 (C16:1ω7c and/or C16:1ω6c). On the basis of DNA–DNA hybridization results and genotypic, chemotaxonomic, and physiological data analysis, it is demonstrated that strain MAH-10T represented a novel species within the genus Flavobacterium, for which the name Flavobacterium chungangensis is proposed. The type strain is MAH-10T (=KACC 19296T=CGMCC 1.16226T). The NCBI GenBank accession number for the 16S rRNA gene sequence of strain MAH-10T is KY964277 and the digital protologue database (DPD) Taxon Number of strain MAH-10T is TA00296.

A bacterial isolate, designated strain THG-MM1T, was isolated from soil in Yongin region, Republic of Korea. Strain THG-MM1T was Gram-stain-negative, aerobic, non-motile and rod-shaped. Based on 16S rRNA gene sequence comparisons, strain THG-MM1T was most closely related to Devosia insulae DS-56T (96.5 % 16S rRNA gene sequence similarity), followed by Devosia yakushimensis Yak96BT (95.7 %) and Devosia albogilva IPL15T (95.2 %). The G+C content of the genomic DNA was 63.7 mol%. The major cellular fatty acids were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C18 : 0. The predominant isoprenoid quinone was ubiquinone-10 (Q-10). The major polar lipids were phosphatidylglycerol and an unidentified lipid. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain THG-MM1T represents a novel species of the genus Devosia, for which the name Devosia humi sp. nov. is proposed, with strain THG-MM1T ( = KACC 18281T = CCTCC AB 2015121T) as the type strain.

A yellowish colored, Gram-staining negative, strictly aerobic, motile, rod-shaped bacterium, designated THG-SQE7T, was isolated from reed pond water in Shangqiu, PR China. Comparative 16S rRNA gene sequence analysis indicated that strain THG-SQE7T is most closely related to Hydrogenophaga pseudoflava ATCC 33668T (98.4 %), followed by Hydrogenophaga bisanensis K102T (97.6 %) and Hydrogenophaga flava CCUG 1658T (97.6 %). DNA–DNA hybridization showed 53.5, 36.0 and 22.5 % DNA re-association with H. pseudoflava KCTC 2348T, H. bisanensis KCTC 12980T and H. flava KCTC 1648T, respectively. Chemotaxonomic data revealed that strain THG-SQE7T possesses ubiquinone-8 as the only isoprenoid quinone, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and C18:1 ω7c as the major fatty acids. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was determined to be 63.7 mol%. These data corroborated the affiliation of strain THG-SQE7T to the genus Hydrogenophaga. Thus, the isolate represents a novel species, for which the name Hydrogenophaga luteola sp. nov. is proposed, with THG-SQE7T as the type strain (=KCTC 42501T = CCTCC AB 2014314T = JCM 30433T).

A bacterial strain, designated as THG-SKA3(T), was isolated from field soil of Kyung Hee University, South Korea. Cells of the isolate were observed to be Gram-negative, aerobic, rod-shaped and motile by gliding. The strain was found to grow optimally at 28 °C, at pH 7 and in absence of NaCl. Based on 16S rRNA gene sequence comparisons, strain THG-SKA3(T) shared highest sequence similarity with Lysobacter niastensis KACC 11588(T) followed by Lysobacter panacisoli KACC 17502(T), Lysobacter enzymogenes LMG 8762(T) and Lysobacter oryzae KCTC 22249(T). The G+C content of THG-SKA3(T) was determined to be 68.9 mol%. The DNA-DNA relatedness values between strain THG-SKA3(T) and its closest phylogenetic neighbors were below 25.0 %.The major polar lipids of strain THG-SKA3(T) were determined to be diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was identified as ubiquinone 8 (Q-8). The major cellular fatty acids were identified as branched chain iso-C15:0, iso-C16:0 and unsaturated iso-C17:1 ω9c. On the basis of polyphasic data presented, it is evident that strain THG-SKA3(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter agri sp. nov. (type strain THG-SKA3(T) = KACC 18283(T) = CSCTCC AB 2015126(T)) is proposed.

A yellow-colored, Gram-negative, strictly aerobic, non-motile, rod-shaped bacterium, designated THG-MM5(T), was isolated from road soil in Yongin-si, Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence, strain THG-MM5(T) was moderately related to Sphingomonas sediminicola KACC 15039(T) (96.1%), Sphingomonas ginsengisoli KACC 16858(T) (96.1%) and Sphingomonas jaspsi KACC 13230(T) (96.0%). Chemotaxonomic data revealed that strain THG-MM5(T) possesses ubiquinone-10 as the only respiratory quinone, sym-homospermidine as the major polyamine and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C18:1 ω7c and C16:0 as the major fatty acids. The polar lipid profile included sphingoglycolipid. The DNA G + C content was 60.7 mol%. These data, together with phenotypic characterization, corroborated the affiliation of strain THG-MM5(T) to the genus Sphingomonas. Thus, the isolate represents a novel species, for which the name Sphingomonas flavus sp. nov. is proposed, with THG-MM5(T) as the type strain (=KACC 18277(T) = CCTCC AB 2014320(T)).