A robust computational quest: Discovering potential hits to improve the treatment of pyrazinamide-resistant Mycobacterium tuberculosis.

The rise of pyrazinamide (PZA)-resistant strains of Mycobacterium tuberculosis (MTB) poses a major challenge to conventional tuberculosis (TB) treatments. PZA, a cornerstone of TB therapy, must be activated by the mycobacterial enzyme pyrazinamidase (PZase) to convert its active form, pyrazinoic acid, which targets the ribosomal protein S1. Resistance, often associated with mutations in the RpsA protein, complicates treatment and highlights a critical gap in the understanding of structural dynamics and mechanisms of resistance, particularly in the context of the G97D mutation. This study utilizes a novel integration of computational techniques, including multiscale biomolecular and molecular dynamics simulations, physicochemical and medicinal chemistry predictions, quantum computations and virtual screening from the ZINC and Chembridge databases, to elucidate the resistance mechanism and identify lead compounds that have the potential to improve treatment outcomes for PZA-resistant MTB, namely ZINC15913786, ZINC20735155, Chem10269711, Chem10279789 and Chem10295790. These computational methods offer a cost-effective, rapid alternative to traditional drug trials by bypassing the need for organic subjects while providing highly accurate insight into the binding sites and efficacy of new drug candidates. The need for rapid and appropriate drug development emphasizes the need for robust computational analysis to justify further validation through in vitro and in vivo experiments.

Nocardioides agri sp. nov., isolated from garden soil.

A novel bacterial strain, designated as MAH-18T, was isolated from soil sampled in a flower garden. Cells of strain MAH-18T were Gram-stain-positive, aerobic, motile, and rod-shaped. The colonies were beige in colour, smooth, and spherical when grown on Reasoner's 2A agar medium. Strain MAH-18T grew at 20-40 °C, pH 6.0-8.0, and 0-1.0 % NaCl. Cells were able to hydrolyse aesculin, gelatin, and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was determined to be a member of the genus Nocardioides and most closely related to Nocardioides pyridinolyticus OS4T (97.9 %), Nocardioides hankookensis DS-30T (97.9 %), Nocardioides aquiterrae GW-9T (97.6 %), Nocardioides soli mbc-2T (97.5 %), Nocardioides conyzicola HWE 2-02T (97.4 %), and Nocardioides mangrovi GBK3QG-3T (96.3 %). Strain MAH-18T has a draft genome size of 4 788 325 bp (eight contigs), 4572 protein-coding genes, 46 tRNA, and three rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-18T and the closest type strains were 81.5-83.4 % and 24.4-25.8 %, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAH-18T. The G+C content of the genomic DNA of strain was 72.2 mol% and the predominant isoprenoid quinone was MK-8 (H4). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and unknown phospholipids. The major cellular fatty acids were determined to be C16:0 iso and C17 : 1 ω6c. The DNA-DNA hybridization results and phenotypic, genotypic, and chemotaxonomic data demonstrated that strain MAH-18T represents a novel species, for which the name Nocardioides agri sp. nov. is proposed, with MAH-18T as the type strain (=KACC 19744T=CGMCC 1.13656T).

Isolation and characterization of Pinibacter soli sp. nov., and in silico genome mining of Pinibacter for biosynthetic gene cluster prediction.

A Gram-stain-negative, aerobic, rod-shaped, non-motile and non-flagellated novel bacterial strain, designated MAH-24T, was isolated from the rhizospheric soil of a pine garden. The colonies were observed to be orange-coloured, smooth, spherical and 0.4-0.8 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAH-24T was found to be able to grow at 10-35 °C, at pH 6.0-9.0 and in the presence of 0-1.0 % NaCl (w/v). The strain was found to be positive for the catalase and oxidase tests. The strain was positive for hydrolysis of aesculin and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Pinibacter and to be closely related to Pinibacter aurantiacus MAH-26T (99.2 % sequence similarity). The novel strain MAH-24T has a draft genome size of 5 918 133 bp (13 contigs), annotated with 4613 protein-coding genes, 47 tRNA and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAH-24T and the closest type strain P. aurantiacus MAH-26T were in the range of 85.3 and 29.9 %, respectively. In silico genome mining revealed that both novel strain MAH-24T and P. aurantiacus MAH-26T have a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 41.0 mol%. The predominant isoprenoid quinone was menaquinone-7. The major fatty acids were identified as C15:0 iso, C15:1 iso G and C17:0 iso 3OH. On the basis of dDDH, ANI, genotypic, chemotaxonomic and physiological data, strain MAH-24T represents a novel species within the genus Pinibacter, for which the name Pinibacter soli sp. nov. is proposed, with MAH-24T (=KACC 19747T=CGMCC 1.13659T) as the type strain.

Sphingomonas oryzagri sp. nov., isolated from a rice field.

A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-71T, was isolated from the soil of a rice field. The colonies were observed to be milky yellow-coloured, smooth, spherical and 0.1-0.4 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAHUQ-71T was found to be able to grow at 15-37 °C, pH 5.0-10.0 and with 0-3.0 % NaCl (w/v). The strain was found to be positive for the catalase test, but negative for the oxidase test. The strain was positive for hydrolysis of aesculin and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingomonas and to be closely related to Sphingomonas chungangi MAH-6T (98.5 % sequence similarity), Sphingomonas polyaromaticivorans B2-7T (98.4 %) and Sphingomonas oligoaromativorans SY-6T (96.6 %). Strain MAHUQ-71T has a draft genome size of 4 255 278 bp (10 contigs), annotated with 4098 protein-coding genes, 47 tRNA and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-71T and the closest type strain S. chungangi MAH-6T were in the range of 85.6 and 30.6 %, respectively. The genomic DNA G+C content was determined to be 66.7 mol%. The predominant isoprenoid quinone was ubiquinone 10. The major fatty acids were identified as summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C14 : 0 2OH. The main polar lipids were phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol and sphingoglycolipid. On the basis of dDDH and ANI values, as well as the results of genotypic, chemotaxonomic and physiological analyses, strain MAHUQ-71T represents a novel species within the genus Sphingomonas, for which the name Sphingomonas oryzagri sp. nov. is proposed, with MAHUQ-71T (=KACC 22252T=CGMCC 1.19065T) as the type strain.

Solitalea agri sp. nov., a new member of the genus Solitalea isolated from rhizospheric soil of a jujube tree.

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).

Sphingobium agri sp. nov., isolated from rhizospheric soil of eggplant.

A Gram-stain-negative, aerobic, short rod-shaped and motile bacterial strain, designated MAH-33T, was isolated from rhizospheric soil of eggplant. The colonies were observed to be yellow-coloured, smooth, spherical and 0.1-0.3 mm in diameter when grown on TSA agar medium for 2 days. Strain MAH-33T was found to be able to grow at 10-40 °C, at pH 5.0-10.0 and at 0-3.0 % NaCl (w/v). The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of tyrosine and aesculin. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingobium and to be closely related to Sphingobium quisquiliarum P25T (98.4 % similarity), Sphingobium mellinum WI4T (97.8 %), Sphingobium fuliginis TKPT (97.3 %) and Sphingobium herbicidovorans NBRC 16415T (96.9 %). The novel strain MAH-33T has a draft genome size of 3 908 768 bp (28 contigs), annotated with 3689 protein-coding genes, 45 tRNA and three rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-33T and closely related type strains were in the range of 79.8-81.6 % and 23.2-24.5 %, respectively. The genomic DNA G+C content was determined to be 62.2 %. The predominant isoprenoid quinone was ubiquinone 10. The major fatty acids were identified as C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipids identified in strain MAH-33T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine; one unknown phospholipid and one unknown lipid. On the basis of digital DNA-DNA hybridization, ANI value, genotypic analysis, chemotaxonomic and physiological data, strain MAH-33T represents a novel species within the genus Sphingobium, for which the name Sphingobium agri sp. nov. is proposed, with MAH-33T (=KACC 19973T = CGMCC 1.16609T) as the type strain.

Massilia agrisoli sp. nov., isolated from rhizospheric soil of banana.

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.

Emergence of SARS-CoV-2 variant of interest B.1.525 (Eta) in Bangladesh.

In the present study, we report the complete genome of five Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Bangladesh harboring mutations at Spike protein (E484K, Q677H, D614G, A67V, Q52R, Y144del, H69del, V70del, F888L) assigned to the B.1.525 lineage (Variant of interest). Mutations are also found in viral structural proteins other than spike region (E_L21F, M_I82F, N_A12G and N_T208I) and other mutations (NSP3_T1189I, NSP6_S106del, NSP6_F108del, NSP6_G107del, NSP12_P323F) from all of five B.1.525 SARS-CoV-2 variants of Bangladesh. We have also found four unique mutations from two of SARS-CoV-2 B.1.525 variant of Bangladesh. Among the four unique mutations two mutations (NS7a_L96H, NS7a_Y97D) obtained from strain BCSIR-NILMRC-718, one (NSP3_A1430V) from BCSIR-NILMRC-738 and two mutation including one spike protein mutation (NSP2_L444I, Spike_I68 M) present in BCSIR-AFIP-10 strain. The identification of new mutations will contribute to characterizing SARS-CoV-2, to continue tracking its spread and better understanding its biological and clinical features to take medical countermeasures and vaccines.

Genomic characterization of the dominating Beta, V2 variant carrying vaccinated (Oxford-AstraZeneca) and nonvaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole-genome approach.

Bangladesh is experiencing a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approaches. Screening for SARS-CoV-2 by reverse transcriptase polymerase chain reaction and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated = 10, nonvaccinated = 7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the coinfected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta, V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthily, the receptor binding domain (RBD) region of S protein of all the isolates harbored similar substitutions including K417N, E484K, and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F, and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS = 0.621). Furthermore, we found different bacterial coinfections like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and nonvaccinated patients in Bangladesh.

Pseudomonas oryzagri sp. nov., isolated from a rice field soil.

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.

Chitinophaga chungangae sp. nov., isolated from a Korean grape garden and its potential to biosynthesize ginsenoside Rg2.

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).

Flavobacterium agri sp. nov., a novel bacterial species isolated from rhizospheric soil of Coriandrum sativum.

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).

Sphingomonas horti sp. nov., a novel bacterial species isolated from soil of a tomato garden.

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).

Paenibacillus roseus sp. nov., a ginsenoside-transforming bacterium isolated from forest soil.

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).

Frateuria flava sp. nov., isolated from soil.

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.

Niastella soli sp. nov., isolated from rhizospheric soil of a persimmon tree.

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.

Pinibacter aurantiacus gen. nov., sp. nov., isolated from rhizospheric soil of a pine tree.

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).

Biosynthesis, Characterization and Antibacterial Application of Novel Silver Nanoparticles against Drug Resistant Pathogenic Klebsiella pneumoniae and Salmonella Enteritidis.

The present study highlights the biosynthesis of silver nanoparticles (AgNPs) using culture supernatant of Massilia sp. MAHUQ-52 as well as the antimicrobial application of synthesized AgNPs against multi-drug resistant pathogenic Klebsiella pneumoniae and Salmonella Enteritidis. Well-defined AgNPs formation occurred from the reaction mixture of cell-free supernatant and silver nitrate (AgNO3) solution within 48 h of incubation. UV-visible spectroscopy analysis showed a strong peak at 435 nm, which corresponds to the surface plasmon resonance of AgNPs. The synthesized AgNPs were characterized by FE-TEM, EDX, XRD, DLS and FT-IR. From FE-TEM analysis, it was found that most of the particles were spherical shape, and the size of synthesized nanoparticles (NPs) was 15-55 nm. EDX spectrum revealed a strong silver signal at 3 keV. XRD analysis determined the crystalline, pure, face-centered cubic AgNPs. FT-IR analysis identified various functional molecules that may be involved with the synthesis and stabilization of AgNPs. The antimicrobial activity of Massilia sp. MAHUQ-52 mediated synthesized AgNPs was determined using the disk diffusion method against K. pneumoniae and S. Enteritidis. Biosynthesized AgNPs showed strong antimicrobial activity against both K. pneumoniae and S. Enteritidis. The MICs of synthesized AgNPs against K. pneumoniae and S. Enteritidis were 12.5 and 25.0 µg/mL, respectively. The MBC of biosynthesized AgNPs against both pathogens was 50.0 µg/mL. From FE-SEM analysis, it was found that the AgNPs-treated cells showed morphological changes with irregular and damaged cell walls that culminated in cell death.

Fluviicola chungangensis sp. nov., a bacterium isolated from rice field.

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).

Sphingomonas chungangi sp. nov., a bacterium isolated from garden soil sample.

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).