Nachimuthu Senthil Kumar

First report of bacterial community from a Bat Guano using Illumina next-generation sequencing

V4 hypervariable region of 16S rDNA was analyzed for identifying the bacterial communities present in Bat Guano from the unexplored cave — Pnahkyndeng, Meghalaya, Northeast India. Metagenome comprised of 585,434 raw Illumina sequences with a 59.59% G+C content. A total of 416,490 preprocessed reads were clustered into 1282 OTUs (operational taxonomical units) comprising of 18 bacterial phyla. The taxonomic profile showed that the guano bacterial community is dominated by Chloroflexi, Actinobacteria and Crenarchaeota which account for 70.73% of all sequence reads and 43.83% of all OTUs. Metagenome sequence data are available at NCBI under the accession no. SRP051094. This study is the first to characterize Bat Guano bacterial community using next-generation sequencing approach.

Investigations on microbial diversity of Jakrem hot spring, Meghalaya, India using cultivation-independent approach

Jakrem hot water spring is located in the West Khasi Hill District of the state of Meghalaya, and is one of the most popular hot springs of the state. There is a populist belief among the inhabitants and people that the hot spring water has got curative properties against various skin ailments. This is the first report on V3 hyper-variable region of 16S rDNA metagenome sequence employing Illumina platform to profile the microbial community of this less known hot spring from Meghalaya, India. Metagenome comprised of 10, 74,120 raw sequences with a sequence length of 151 bp and 56.35% G + C content. Metagenome sequence information is now available at NCBI, SRA database accession no. SRP056897. A total of 8, 77, 364 pre-processed reads were clustered into 694 OTUs (operational taxonomical units) comprising of 14 bacterial phyla including unknown phylum demonstrating 49 families. Hot spring bacterial community is dominated by Firmicutes (61.60%), Chloroflexi (21.37%), Cyanobacteria (12.96%) and unclassified bacteria (1.2%) respectively.

Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle

BackgroundBacteria present in cave often survive by modifying their metabolic pathway or other mechanism. Understanding these adopted bacteria and their survival strategy inside the cave is an important aspect of microbial ecology. Present study focuses on the bacterial community and geochemistry in five caves of Mizoram, Northeast India. The objective of this study was to explore the taxonomic composition and presumed functional diversity of cave sediment metagenomes using paired end Illumina sequencing using V3 region of 16S rRNA gene and bioinformatics pipeline.ResultsActinobacteria, Proteobacteria, Verrucomicrobia and Acidobacteria were the major phyla in all the five cave sediment samples. Among the five caves the highest diversity is found in Lamsialpuk with a Shannon index 12.5 and the lowest in Bukpuk (Shannon index 8.22). In addition, imputed metagenomic approach was used to predict the functional role of microbial community in biogeochemical cycling in the cave environments. Functional module showed high representation of genes involved in Amino Acid Metabolism in (20.9%) and Carbohydrate Metabolism (20.4%) in the KEGG pathways. Genes responsible for carbon degradation, carbon fixation, methane metabolism, nitrification, nitrate reduction and ammonia assimilation were also predicted in the present study.ConclusionThe cave sediments of the biodiversity hotspot region possessing a oligotrophic environment harbours high phylogenetic diversity dominated by Actinobacteria and Proteobacteria. Among the geochemical factors, ferric oxide was correlated with increased microbial diversity. In-silico analysis detected genes involved in carbon, nitrogen, methane metabolism and complex metabolic pathways responsible for the survival of the bacterial community in nutrient limited cave environments. Present study with Paired end Illumina sequencing along with bioinformatics analysis revealed the essential ecological role of the cave bacterial communities. These results will be useful in documenting the biospeleology of this region and systematic understanding of bacterial communities in natural sediment environments as well.

Coextraction and PCR Based Analysis of Nucleic Acids From Formalin-Fixed Paraffin-Embedded Specimens

Retrospective studies of archived human specimens, with known clinical follow‐up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin‐fixed paraffin embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. Our optimized co‐extraction approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies because of the high importance and less availability of clinical FFPE specimen.

Characterization of Bacillus thuringiensis isolates and their differential toxicity against Helicoverpa armigera populations

Bacillus thuringiensis isolates were characterized in rhizospheric cotton soils by using acetate selection process from eight different locations in South India. The fact that B. thuringiensis indices were higher in proportion in soil samples taken from Tamil Nadu and Karnataka than from Andhra Pradesh, indicates the abundance of B. thuringiensis populations in the cotton rhizosphere. Biochemical typing of the isolates designated eight local isolates (BtNg13, BtCo1, BtHyb7, BtAm2, BtRm5, BtWr3, BtPl 4, BtN 9), which belong to subspecies kurstaki, the most prevalent subspecies. Toxicity assays on American boll worm larval (F1) populations collected from the Andhra Pradesh, Bangalore and Coimbatore regions, with a susceptible insect strain against different isolates of B. thuringiensis kurstaki spore‐crystal mix, revealed distinct susceptibility patterns and specificity. The highest susceptibility was observed in the F1 populations of Coimbatore, followed by Bangalore and Hyderabad populations, in comparison with the susceptible insect strain. Significant differences were observed (p < 0.0005 and CD = 5.3975) among Btk local isolates, H. armigera biotypes, Btk spore‐crystal mix concentration and their interactions, through the Multifactorial ANOVA analysis. The toxicity of local B. thuringiensis isolates was higher than that of HD‐1 (reference B.t.k strain). Indigenous Btk isolates have an enormous potential for the management of H. armigera in terms of development of resistance to HD‐1. The present study would serve as a baseline data for future resistance monitoring of B. thuringiensis strains in H. armigera in Southern India. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Protocol for Optimal Quality and Quantity Pollen DNA Isolation from Honey Samples

The present study illustrates an optimized sample preparation method for an efficient DNA isolation from low quantities of honey samples. A conventional PCR-based method was validated, which potentially enables characterization of plant species from as low as 3 ml bee-honey samples. In the present study, an anionic detergent was used to lyse the hard outer pollen shell, and DTT was used for isolation of thiolated DNA, as it might facilitate protein digestion and assists in releasing the DNA into solution, as well as reduce cross-links between DNA and other biomolecules. Optimization of both the quantity of honey sample and time duration for DNA isolation was done during development of this method. With the use of this method, chloroplast DNA was successfully PCR amplified and sequenced from honey DNA samples.

Xenobiotic Pathway Gene Polymorphisms Associated with Gastric Cancer in High Risk Mizo-Mongoloid Population, Northeast India

The aim of this study was to evaluate the risk of gastric cancer associated with individual or combined glutathione S‐transferases (GSTs) polymorphism and their interaction with environmental factors.

Complete mitochondrial genome of Chocolate Pansy, Junonia iphita (Lepidoptera: Nymphalidae: Nymphalinae).

Abstract The complete mitochondrial genome of Junonia iphita was determined to be 15,433 bp in length, including 37 typical mitochondrial genes and an AT-rich region. All the protein coding genes (PCGs) are initiated by typical ATN codons, except cox1 gene that is by CGA codon. Eight genes use complete termination codon (TAA), whereas the cox1, cox2 and nad5 genes end with single T; nad4 and nad1 ends with stop codon TA. All the tRNA show secondary cloverleaf structures except trnS1 (AGN). The A + T rich region is 546 bp in length containing ATAGA motif followed by a 18 bp poly-T stretch, two microsatellite-like (TA)9 elements and 8 bp poly-A stretch immediately upstream of trnM gene.

Bacterial diversity of Murlen National Park located in Indo-Burman Biodiversity hotspot region: A metagenomic approach.

Paired end Illumina Mi-Seq sequencing of 16S rRNA gene amplicon was carried out to study the bacterial community in the soil of Murlen National Park located in Indo-Burman Biodiversity hotspot region. Metagenome consisted of 302,416 reads with 151.81 Mb data and G + C content of 56.48%. More than 85% sequence was having a Phred score >=Q30 and individual sequence length was 251 bp. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. SRP057136. Community metagenomics revealed a total of 1802 species belonging to 29 different phyla dominated by Acidobacteria (39.45%), Proteobacteria (26.95%) and Planctomycetes (7.81%). Our data detected a wide group of bacterial community which will be useful in further isolating and characterizing the economic importance of bacteria from this region.

Illumina-based analysis of bacterial community in Khuangcherapuk cave of Mizoram, Northeast India

Bacterial community of the Khuangcherapuk cave sediment was assessed by Illumina amplicon sequencing. The metagenome comprised of 533,120 raw reads with an average base quality (Phred score) 36.75 and G + C content is 57.61%. A total of 18 bacterial phyla were detected with following abundant genus — Mycobacterium (21.72%), Rhodococcus (7.09%), Alteromonas (1.42%), Holomonas (0.7%) and Salinisphaera (0.20%). Majority portion of the sequences (68%) is unclassified at the genus level indicating the possibilities for the presence of novel species in this cave. This study reports the cave bacterial diversity from the biodiversity hotspot region of Eastern Himalayas. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. SRP056890.