Exploring the Distinct Distribution of Archaeal Communities in Sites Contaminated with Explosives.

Most of the research on bioremediation and estimation of microbial diversity in waste contaminated sites is focused on the domain Bacteria, whereas details on the relevance of Archaea are still lacking. The present study examined the archaeal diversity and predicted metabolic pathways in two discrete sites (SITE1 and SITE2) contaminated with explosives (RDX and HMX) by amplicon-targeted sequencing of 16S rRNA genes. In total, 14 soil samples were processed, and 35,758 OTUs were observed, among which 981 OTUs were classified as Archaea, representing ~2.7% of the total microbial diversity in our samples. The majority of OTUs belonged to phyla Euryarchaeota (~49%), Crenarchaeota (~24%), and Thaumarchaeota (~23%), while the remaining (~4%) OTUs were affiliated to Candidatus Parvarchaeota, Candidatus Aenigmarchaeota, and Candidatus Diapherotrites. The comparative studies between explosives contaminated and agricultural soil samples (with no history of explosives contamination) displayed significant differences between the compositions of the archaeal communities. Further, the metabolic pathways pertaining to xenobiotic degradation were presumably more abundant in the contaminated sites. Our data provide a first comprehensive report of archaeal communities in explosives contaminated sites and their putative degradation role in such ecosystems which have been as yet unexplored.

Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach.

In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.

An insight into the genome of extensively drug-resistant and uropathogenic Citrobacter werkmanii.

OBJECTIVE: Carbapenemase-producing bacteria pose a serious public-health threat. This study was performed to understand the emergence and genetic features of NDM-producers in hospital setting. METHODS: Samples were collected from a tertiary-care hospital. Isolate identification was performed by 16S rRNA sequencing. The genome of Citrobacter werkmanii (AK-8) was sequenced on an Illumina NextSeq 500 platform. Resistance determinants and pathogenicity islands were determined by ResFinder and PathogenFinder, respectively. MLST, two-component systems and transcription factors were identified by P2RP server, whilst variant calling and insertion sequence (IS) elements were determined by Galaxy and ISfinder, respectively. The genome of AK-8 was compared with uropathogenic Escherichia coli strain 536. RESULTS: This is the first report on whole-genome analysis of extensively drug-resistant NDM-6-producing uropathogenic C. werkmanii ST-104. Resistance genes for all antibiotics except colistin, fosfomycin, fusidic- acid, nitroimidazole, oxazolidinones, tetracycline and glycopeptides were detected in this strain. Genome analysis of AK-8 led to the identification of the BaeSR two-component system regulating production of multidrug efflux proteins. Virulence was regulated by CpxRA, ZraRS, RstAB, UhpAB, AcrAB, RcsBc and UvrY, whereas Bar-UvrY was found to control carbon metabolism, flagellum biosynthesis and biofilm formation. The AK-8 genome encodes 21 chemoreceptors involved in colonisation and pathogenesis. Fur family transcriptional regulator, cAMP receptor protein and RpoS were found to increase the virulence of AK-8. ntBLAST analysis showed 69.60% genetic identity with E. coli 536 as an adaptive feature for survival. CONCLUSION: The emergence of extensively drug-resistant pathogenic C. werkmanii is alarming and it should not be ignored as commensal.

Draft Genome Sequence of a Bioflocculant-Producing Bacterium, Citrobacter freundii IFO 13545.

Here, we report the 5.2-Mb genome sequence of a bioflocculant-producing bacterial strain, Citrobacter freundii IFO 13545, which consists of 5,209,670 bp with a G+C content of 51.5% and 4,853 predicted coding sequences (CDSs). The genes related to the biosynthetic pathway of the bioflocculant were localized on the genome map.

Indiicoccus explosivorum gen. nov., sp. nov., isolated from an explosives waste contaminated site.

A pink-pigmented, Gram-stain-positive, aerobic, coccoid-shaped bacterial strain, designated as S5-TSA-19T, was isolated from an explosives contaminated site in Panchkula, Haryana, India. The 16S rRNA gene sequencing blast analysis indicated that the strain is a member of the family Planococcaceae with the highest sequence similarity to Planomicrobium soli XN13T (96.1 %), followed by Planococcus maitriensis S1T (95.6 %), Planococcus plakortidis DSM 23997T (95.6 %), Planomicrobium flavidum ISL-41T (95.6 %), Planococcus rifietoensis M8T (95.5 %), Planococcus salinus LCB217T (95.5 %) and Planococcus maritimus DSM 17275T (95.5 %). Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences (based on a conserved set of 400 proteins) retrieved the strain in a distinct branch indicating a separate lineage within the family Planococcaceae. Strain S5-TSA-19T had a distinctive chemotaxonomic pattern comprising A4α type peptidoglycan based on l-Lys-d-Asp, iso-C15 : 0 as the major fatty acid, absence of phosphatidylethanolamine as a major lipid and MK-7 and MK-6 as the major menaquinones, differentiating it from the genera Planococcus and Planomicrobium, thus supporting the findings of molecular phylogeny. Further, strain S5-TSA-19T was able to biotransform hexahydro-1,3,5,-trinitro-1,2,5-triazine (RDX) into nitrite derivatives under aerobic conditions in 2-4 days, whereas the closest reference strains did not possess this property. On the basis of polyphasic taxonomic characterization and a phylogenomics approach, strain S5-TSA-19T is proposed as the type strain of a novel species in a novel genus for which the name Indiicoccus explosivorum gen. nov., sp. nov. is proposed (=JCM 31737T=KCTC 33871T=MTCC 12608T).

Genomic analysis of Indian strains of Salmonella enterica subsp. enterica serovar Typhi indicates novel genetic repertoire for pathogenicity and adaptations.

In the era of emerging antibiotic resistance, Salmonella enterica subsp. enterica serovar Typhi the causative agent of typhoid, is a threat for healthcare systems in developing countries especially India, where the disease is highly endemic. Genetic diversity among different strains may be the cause of variable severity of disease in different regions of the world. To explore this genetic diversity, genome annotation by rapid annotation using subsystem technology (RAST) was carried out for genomes of four Salmonella Typhi strains from two distinct areas available in the public domain. Two clinical strains were from India (P-stx-12 and E02-1180) and the other two strains considered as reference strains were from the endemic regions of Papua New Guinea (UJ308A and UJ816A). We report that Indian clinical strains possess several similar genes responsible for virulence and pathogenicity as those present in the reference strains. Interestingly, Indian clinical strains also possess 34 additional potential virulence genes that are absent in the reference strains, suggesting the more dreadful nature of Indian clinical strains as compared to those causing endemic typhoid. Indian strains contained genes coding for; Colicin V and bacteriocin production; multidrug resistance efflux pumps; ABC transporters; Type III and Type VI secretion systems, siderophore aerobactin, pathogenicity islands and Vi polysaccharide biosynthesis and transport. These unique genes are also reported in the genomes of other six clinical strains of India analyzed through RAST and IslandViewer 4 for validation purpose. This study highlights the presence of potential genes as molecular targets to overcome the future endemic outbreaks in India.

Taxonomic insights into the phylogeny of Bacillus badius and proposal for its reclassification to the genus Pseudobacillus as Pseudobacillus badius comb. nov. and reclassification of Bacillus wudalianchiensis Liu et al., 2017 as Pseudobacillus wudalianchiensis comb. nov.

The species Bacillus badius is one of the oldest members of the genus Bacillus isolated from faeces of children and was classified based on its ability to form endospores [8]. In 16S rRNA gene sequence and phylogenetic analysis, Bacillus badius DSM 23T shared low similarity (93.0%) and distant relationship with B. subtilis, the type species of the genus Bacillus indicating that it does not belong to this genus. Additional strains of the species, B. badius DSM 5610, DSM 30822 and B. encimensis SGD-V-25 (which has been recently reclassified as a member of this species) were included in the study to consider intraspecies diversity. Detailed molecular phylogenetic and comparative genome analysis clearly showed that the strains of B. badius were consistently retrieved outside the cluster of Bacillus sensu stricto and also distantly related to the genera Domibacillus and Quasibacillus. Further, the data from biochemical reactions (inability to ferment most carbohydrates), polar lipids profile (presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an aminophosphoglycolipid) and fatty acids supported the molecular analysis. Thus the four B. badius strains; DSM 23T, DSM 5610, DSM 30822 and SGD-V-25 displayed sufficient demarcating phenotypic characteristics that warrant their classification as members of a novel genus and single species, for which the name Pseudobacillus badius gen. nov. comb. nov. is proposed with Pseudobacillus badius DSM 23T (= ATCC 14574T) as the type strain. Additionally, based on our findings from phenotypic, chemotaxonomic and genotypic parameters, Bacillus wudalianchiensis DSM 100757T was reclassified as Pseudobacillus wudalianchiensis comb. nov.

A genomic analysis of Mycobacterium immunogenum strain CD11_6 and its potential role in the activation of T cells against Mycobacterium tuberculosis.

BACKGROUND: Mycobacterium tuberculosis (Mtb) is an etiological agent of tuberculosis (TB). Tuberculosis is a mounting problem worldwide. The only available vaccine BCG protects the childhood but not adulthood form of TB. Therefore, efforts are made continuously to improve the efficacy of BCG by supplementing it with other therapies. Consequently, we explored the possibility of employing Mycobacterium immunogenum (Mi) to improve BCG potential to protect against Mtb. RESULTS: We report here the genome mining, comparative genomics, immunological and protection studies employing strain CD11_6 of Mi. Mycobacterium immunogenum was isolated from duodenal mucosa of a celiac disease patient. The strain was whole genome sequenced and annotated for identification of virulent genes and other traits that may make it suitable as a potential vaccine candidate. Virulence profile of Mi was mapped and compared with two other reference genomes i.e. virulent Mtb strain H37Rv and vaccine strain Mycobacterium bovis (Mb) AFF2122/97. This comparative analysis revealed that Mi is less virulent, as compared to Mb and Mtb, and contains comparable number of genes encoding for the antigenic proteins that predict it as a probable vaccine candidate. Interestingly, the animals vaccinated with Mi showed significant augmentation in the generation of memory T cells and reduction in the Mtb burden. CONCLUSION: The study signifies that Mi has a potential to protect against Mtb and therefore can be a future vaccine candidate against TB.

Structural characterization and antioxidant potential of a novel anionic exopolysaccharide produced by marine Microbacterium aurantiacum FSW-25.

An exopolysaccharide (EPS) producing strain FSW-25 was isolated from the Rasthakaadu beach Kanyakumari, Tamil Nadu India. Based on polyphasic taxonomy, the strain FSW-25 was assigned to the genus Microbacterium and found to be the closest relative of the species aurantiacum. Large quantity of EPS (7.81 g/l) was secreted by the strain upon fermentation using Reasoner's 2A medium enriched with 2.5% glucose and was designated as Mi-25. FT-IR spectrum revealed presence of hydroxyl, carbonyl, carboxyl, methyl and sulfate functional groups in purified EPS. The EPS Mi-25 has a molecular weight of 7.0 × 106 Da and mainly comprises of glucuronic acid followed by glucose, mannose and fucose. Rheological study revealed that Mi-25 possesses significant viscosity with pseudoplastic nature. Interestingly, it was observed that the EPS Mi-25 has higher antioxidant activity as compared to xanthan. The characteristics of EPS Mi-25 suggested that, it can be used as a potential antioxidant with viscosifier properties in diverse industrial sectors.

Paenibacillus xerothermodurans sp. nov., an extremely dry heat resistant spore forming bacterium isolated from the soil of Cape Canaveral, Florida.

A Gram-stain-positive, motile, endospore-producing, facultative anaerobic bacterial strain, designated ATCC 27380T, was isolated from heat-stressed soil of Cape Canaveral, Florida, USA. Growth was observed at 20-42 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum pH 7.0) and in the presence of 0.5-3 % NaCl (optimum 0.5 %). The cell wall contained meso-diaminopimelic acid as the diagnostic amino acid and the isoprenoid quinone was MK-7. The polar lipids present were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and one unknown phospholipid. The main fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Phylogenetic analysis based on 16S rRNA gene sequencing affiliated strain ATCC 27380T to the genus Paenibacillus, and showed the highest sequence similarity to Paenibacillus rigui JCM 16352T (97.0 %). The other closely related type strains exhibited 16S rRNA gene sequence similarity values below 95.9 %. The draft genome of ATCC 27380T had a size of 4,361,187 bases, with a G+C content of 51.0 %. The average nucleotide identity and in silico DNA-DNA hybridization values between strain ATCC 27380T and P. rigui JCM 16352T were 72.5% and 18.5 %, respectively, which were below the threshold suggested for species differentiation (96% and 70 %, respectively). The average amino acid identity between strain ATCC 27380T and P. rigui JCM 16352T was 68.72 %, which was above the suggested genus level demarcation of 65 %. Based on phenotypic, genotypic and chemotaxonomic data, strain ATCC 27380T represents a novel species in the genus Paenibacillus, for which the name Paenibacillusxerothermodurans sp. nov. (=DSM 520T=NRRL NRS-1629T=ATCC 27380T) is proposed.

Acidovorax kalamii sp. nov., isolated from a water sample of the river Ganges.

A Gram-stain-negative, rod-shaped, aerobic, straw yellow, motile strain, designated KNDSW-TSA6T, belonging to the genus Acidovorax, was isolated from a water sample of the river Ganges, downstream of the city of Kanpur, Uttar Pradesh, India. Cells were aerobic, non-endospore-forming and motile with single polar flagella. It differed from its phylogenetically related strains by phenotypic characteristics such as hydrolysis of urea, gelatin, casein and DNA, and the catalase reaction. The major fatty acids were C16 : 1ω7c/C16 : 1ω6c, C16 : 0 and C18 : 1ω7c/C18 : 1ω6c. Phylogenetic analysis based on 16S rRNA and housekeeping genes (gyrb, recA and rpoB gene sequences), confirmed its placement within the genus Acidovorax as a novel species. Strain KNDSW-TSA6T showed highest 16S rRNA sequence similarity to Acidovorax soli BL21T (98.9 %), Acidovorax delafieldii ATCC 17505T (98.8 %), Acidovorax temperans CCUG 11779T (98.2 %), Acidovorax caeni R-24608T (97.9 %) and Acidovorax radicis N35T (97.6 %). The digital DNA-DNA hybridization and average nucleotide identity values calculated from whole genome sequences between strain KNDSW-TSA6T and the two most closely related strains A. soli BL21T and A. delafieldii ATCC 17505T were below the threshold values of 70 and 95 % respectively. Thus, the data from the polyphasic taxonomic analysis clearly indicates that strain KNDSW-TSA6T represents a novel species, for which the name Acidovorax kalamii sp. nov. is proposed. The type strain is Acidovorax kalamii (=MTCC 12652T=KCTC 52819T=VTCC-B-910010T).

Genome sequence and comparative genomic analysis of a clinically important strain CD11-4 of Janibacter melonis isolated from celiac disease patient.

BACKGROUND: Janibacter melonis and other member of this genus are known to cause bacteremia and serious clinical comorbidities, but there is no study reporting about pathogenicity attributes of J. melonis. Janibacter terrae is known to cause lethal infection. Reporting the genome of J. melonis CD11-4 and comparative genomics with other members of genus has provided some novel insights that can enable us to understand the mechanisms responsible for its pathogenicity in humans. RESULTS: Comparative genomic analysis by Rapid Annotation Server and Technology revealed the presence of similar virulence determinant genes in both J. terrae NBRC 107853T and J. melonis CD11-4. Like J. terrae NBRC 107853T, J. melonis CD11-4 contained two genes responsible for resistance against ß-lactam class of antibiotics and two genes for resistance against fluoroquinolones. Interestingly, J. melonis CD11-4 contained a unique gene coding for multidrug resistance efflux pumps unlike all other members of this genus. It also contained two genes involved in Toxin-antitoxin Systems that were absent in J. terrae NBRC 107853T but were present in some other members of genus. CONCLUSIONS: Genome annotations of J. melonis CD11-4 revealed that it contained similar or more virulence repertoire like J. terrae NBRC 107853T. Like other gut pathogens, J. melonis possesses key virulence determinant genes for antibiotic resistance, invasion, adhesion, biofilm formation, iron acquisition and to cope with stress response, thereby indicating that strain J. melonis CD11-4 could be a gut pathogen.

Chryseobacterium glaciei sp. nov., isolated from the surface of a glacier in the Indian trans-Himalayas.

A novel bacterial strain, IHBB 10212T, of the genus Chryseobacterium was isolated from a glacier near the Kunzum Pass located in the Lahaul-Spiti in the North-Western Himalayas of India. The cells were Gram-negative, aerobic, non-sporulating, single rods, lacked flagella, and formed yellow to orange pigmented colonies. The strain utilized maltose, trehalose, sucrose, gentibiose, glucose, mannose, fructose, mannitol, arabitol and salicin for growth. Flexirubin-type pigments were produced by strain IHBB 10212T. The 16S rRNA gene sequence analysis showed relatedness of strain IHBB 10212T to Chryseobacterium polytrichastri DSM 26899T (97.43 %), Chryseobacterium greenlandense CIP 110007T (97.29 %) and Chryseobacterium aquaticum KCTC 12483T (96.80 %). Iso-C15 : 0 and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) constituted the major cellular fatty acids. The polar lipids present were six unidentified aminolipids, one unidentified phospholipid and three unidentified lipids. MK-6 was identified as the major quinone. The DNA G+C content was 34.08  mol%. Digital DNA-DNA hybridization of strain IHBB 10212T with C. polytrichastri, C. greenlandense and C. aquaticum showed values far below the prescribed thresholds of 95 % for average nucleotide identity and 70 % for the Genome-to-Genome Distance Calculator for species delineation. Based on its differences from validly published Chryseobacterium species, strain IHBB 10212T is identified as a new species, for which the proposed name is Chryseobacterium glaciei sp. nov., with IHBB 10212T as the type strain (=MTCC 12457T=JCM 31156T=KACC 19170T).

Biosynthetic Pathway and Genes of Chitin/Chitosan-Like Bioflocculant in the Genus Citrobacter.

Chitin/chitosan, one of the most abundant polysaccharides in nature, is industrially produced as a powder or flake form from the exoskeletons of crustaceans such as crabs and shrimps. Intriguingly, many bacterial strains in the genus Citrobacter secrete a soluble chitin/chitosan-like polysaccharide into the culture medium during growth in acetate. Because this polysaccharide shows strong flocculation activity for suspended solids in water, it can be used as a bioflocculant (BF). The BF synthetic pathway of C. freundii IFO 13545 is expected from known bacterial metabolic pathways to be as follows: acetate is metabolized in the TCA cycle and the glyoxylate shunt via acetyl-CoA. Next, fructose 6-phosphate is generated from the intermediates of the TCA cycle through gluconeogenesis and enters into the hexosamine synthetic pathway to form UDP-N-acetylglucosamine, which is used as a direct precursor to extend the BF polysaccharide chain. We conducted the draft genome sequencing of IFO 13545 and identified all of the candidate genes corresponding to the enzymes in this pathway in the 5420-kb genome sequence. Disruption of the genes encoding acetyl-CoA synthetase and isocitrate lyase by homologous recombination resulted in little or no growth on acetate, indicating that the cell growth depends on acetate assimilation via the glyoxylate shunt. Disruption of the gene encoding glucosamine 6-phosphate synthase, a key enzyme for the hexosamine synthetic pathway, caused a significant decrease in flocculation activity, demonstrating that this pathway is primarily used for the BF biosynthesis. A gene cluster necessary for the polymerization and secretion of BF, named bfpABCD, was also identified for the first time. In addition, quantitative RT-PCR analysis of several key genes in the expected pathway was conducted to know their expression in acetate assimilation and BF biosynthesis. Based on the data obtained in this study, an overview of the BF synthetic pathway is discussed.

Pseudomonas fluvialis sp. nov., a novel member of the genus Pseudomonas isolated from the river Ganges, India.

A bacterial strain, designated ASS-1T, was isolated and identified from a sediment sample of the river Ganges, Allahabad, India. The strain was Gram-stain-negative, formed straw-yellow pigmented colonies, was strictly aerobic, motile with a single polar flagellum, and positive for oxidase and catalase. The major fatty acids were C16 : 1ω7c/ 16 : 1 C16 : 1ω6c, C18 : 1ω7c and C16 : 0. Sequence analysis based on the 16S rRNA gene revealed that strain ASS-1T showed high similarity to Pseudomonas guguanensis CC-G9AT (98.2 %), Pseudomonas alcaligenes ATCC 14909T (98.2 %), Pseudomonas oleovorans DSM 1045T (98.1 %), Pseudomonas indolxydans IPL-1T (98.1 %) and Pseudomonas toyotomiensis HT-3T (98.0 %). Analysis of its rpoB and rpoD housekeeping genes confirmed its phylogenetic affiliation and showed identities lower than 93 % with respect to the closest relatives. Phylogenetic analysis based on the 16S rRNA, rpoB, rpoD genes and the whole genome assigned it to the genus Pseudomonas. The results of digital DNA-DNA hybridization based on the genome-to-genome distance calculator and average nucleotide identity revealed low genome relatedness to its close phylogenetic neighbours (below the recommended thresholds of 70 and 95 %, respectively, for species delineation). Strain ASS-1T also differed from the related strains by some phenotypic characteristics, i.e. growth at pH 5.0 and 42 °C, starch and casein hydrolysis, and citrate utilization. Therefore, based on data obtained from phenotypic and genotypic analysis, it is evident that strain ASS-1T should be regarded as a novel species within the genus Pseudomonas, for which the name Pseudomonasfluvialis sp. nov. is proposed. The type strain is ASS-1T (=KCTC 52437T=CCM 8778T).

Fictibacillus aquaticus sp. nov., isolated from downstream river water.

A Gram-stain-positive, facultatively anaerobic bacterial strain, GDSW-R2A3T, was isolated from a downstream water sample collected from the river Ganges, India. Analysis of the 16S rRNA gene sequence of strain GDSW-R2A3T revealed its affiliation to the family Bacillaceae. Further analysis using a polyphasic approach revealed that strain GDSW-R2A3T was most closely related to the genus Fictibacillus. Analysis of the almost-complete (1488 bp) 16S rRNA gene sequence of strain GDSW-R2A3T revealed the highest level of sequence similarity with Fictibacillus phosphorivorans CCM 8426T (98.3 %) and Fictibacillus nanhaiensis KCTC 13712T (98.3 %) followed by Fictibacillus barbaricus DSM 14730T (98.0 %). The digital DNA-DNA hybridization and average nucleotide identity (ANI) values between strain GDSW-R2A3T and the most closely related taxon, F. phosphorivorans CCM 8426T, were 20.3 and 78.2 %, respectively. The DNA G+C content of the strain was 44.2 mol%. The cell-wall amino acid was meso-diaminopimelic acid. Polar lipids present were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three aminophospholipids, two phospholipids and one unidentified lipid; the major menaquinone was MK-7; iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0 were the major fatty acids. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it can be concluded that strain GDSW-R2A3T represents a novel species of the genus Fictibacillus, for which the name Fictibacillus aquaticus sp. nov. is proposed. The type strain is GDSW-R2A3T (=VTCC-B-910015T=CCM 8782T).

Thauera propionica sp. nov., isolated from downstream sediment sample of the river Ganges, Kanpur, India.

A Gram-stain-negative, non-endospore-producing, short-rod strain, KNDSS-Mac4T, was isolated from a downstream sediment sample of the river Ganges, Kanpur, India and studied by using the polyphasic taxonomic approach. 16S rRNA gene sequence analysis uncovered that the strain had similarity to species of the genus Thauera and formed a distinct phylogenetic cluster with Thauera humireducens KACC16524T. However, KNDSS-Mac4T showed closest phylogenetic affiliation to Thauera aminoaromatica DSM 14742T with 16S rRNA gene sequence similarity of 98.7 % followed by Thauera phenylacetica DSM 14743T (98.6 %), Thauera chlorobenzoica (98.2 %), T. humireducens KACC16524T (98.2 %), Thauera selenatis ATCC 55363T (98.2 %) and Thauera mechernichensis DSM 12266T (98.0 %). The digital DNA-DNA hybridization and average nucleotide identity values between strain KNDSS-Mac4T and the two most closely related taxa, T. aminoaromatica DSM 14742T and T. phenylacetica DSM 14743T, were 26.0, 26.7 and 84.0, 84.3 % respectively. Major lipids present were phosphatidylglycerol, three unknown aminophospholipids, phosphatidylmethylethanolamine, two unidentified lipids and Q-8 as the only ubiquonone. The major cellular fatty acids present were C16 : 1 ω6c/C16 : 1ω7c and C16 : 0. The DNA G+C content of strain KNDSS-Mac4T was 65.9 %. Based on data from phenotypic tests and the genotypic differences of strain KNDSS-Mac4T from its closest phylogenetic relatives, it is evident that this isolate should be regarded as a new species. It is proposed that strain KNDSS-Mac4T should be classified in the genus Thauera as a novel species, Thauerapropionica sp. nov. The type strain is KNDSS-Mac4T (=KCTC 52820T=VTCC-B-910017T).

Genome Sequence of Kocuria polaris Strain CD08_4, an Isolate from the Duodenal Mucosa of a Celiac Disease Patient.

We report here the 3.8-Mb genome sequence of Kocuria polaris strain CD08_4, an isolate from the duodenal mucosa of a celiac disease patient. The genome consists of specific virulence determinant genes, antibiotic resistance genes, genes for coping with oxidative stress, and genes responsible for iron acquisition and metabolism, suggestive of its pathogenic attributes.

Examination into the taxonomic position of Bacillus thermotolerans Yang et al., 2013, proposal for its reclassification into a new genus and species Quasibacillus thermotolerans gen. nov., comb. nov. and reclassification of B. encimensis Dastager et al., 2015 as a later heterotypic synonym of B. badius.

Two novel Gram-staining positive, rod-shaped, moderately halotolerant, endospore forming bacterial strains 5.5LF 38TD and 5.5LF 48TD were isolated and taxonomically characterized from a landfill in Chandigarh, India. The analysis of 16S rRNA gene sequences of the strains confirmed their closest identity to Bacillus thermotolerans SgZ-8T with 99.9% sequence similarity. A comparative phylogenetic analysis of strains 5.5LF 38TD, 5.5LF 48TD and B. thermotolerans SgZ-8T confirmed their separation into a novel genus with B. badius and genus Domibacillus as the closest phylogenetic relatives. The major fatty acids of the strains are iso-C15:0 and iso-C16:0 and MK-7 is the only quinone. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The digital DNA-DNA hybridization (DDH) and ortho average nucleotide identity (ANI) values calculated through whole genome sequences indicated that the three strains showed low relatedness with their phylogenetic neighbours. Based on evidences from phylogenomic analyses and polyphasic taxonomic characterization we propose reclassification of the species B. thermotolerans into a novel genus named Quasibacillus thermotolerans gen. nov., comb. nov with the type strain SgZ-8T (=CCTCC AB2012108T=KACC 16706T). Further our analyses also revealed that B. encimensis SGD-V-25T is a later heterotypic synonym of Bacillus badius DSM 23T.

Paenibacillus ihbetae sp. nov., a cold-adapted antimicrobial producing bacterium isolated from high altitude Suraj Tal Lake in the Indian trans-Himalayas.

The assessment of bacterial diversity and bioprospection of the high-altitude lake Suraj Tal microorganisms for potent antimicrobial activities revealed the presence of two Gram-stain-variable, endospore-forming, rod-shaped, aerobic bacteria, namely IHBB 9852T and IHBB 9951. Phylogenetic analysis based on 16S rRNA gene sequence showed the affiliation of strains IHBB 9852T and IHBB 9951 within the genus Paenibacillus, exhibiting the highest sequence similarity to Paenibacillus lactis DSM 15596T (97.8% and 97.7%) and less than 95.9% similarity to other species of the genus Paenibacillus. DNA-DNA relatedness among strains IHBB 9852T and IHBB 9951 was 90.2%, and with P. lactis DSM 15596T, was 52.7% and 52.4%, respectively. The novel strains contain anteiso-C15:0, iso-C15:0, C16:0 and iso-C16:0 as major fatty acids, and phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol were predominant polar lipids. The DNA G+C content for IHBB 9852T and IHBB 9951 was 52.1 and 52.2mol%. Based on the results of phenotypic and genomic characterisations, we concluded that strains IHBB 9852T and IHBB 9951 belong to a novel Paenibacillus species, for which the name Paenibacillus ihbetae sp. nov. is proposed. The type strain is IHBB 9852T (=MTCC 12459T=MCC 2795T=JCM 31131T=KACC 19072T; DPD TaxonNumber TA00046) and IHBB 9951 (=MTCC 12458=MCC 2794=JCM 31132=KACC 19073) is a reference strain.