Complete Genome Analysis of Undecylprodigiosin Pigment Biosynthesizing Marine Streptomyces Species Displaying Potential Bioactive Applications.

Marine Streptomyces species are underexplored for their pigment molecules and genes. In this study, we report the genome of the undecylprodigiosin biosynthesizing gene cluster carrying Streptomyces sp. strain BSE6.1, displaying antioxidant, antimicrobial, and staining properties. This Gram-positive obligate aerobic bacterium was isolated from the coastal sediment of the Andaman and Nicobar Islands, India. Pink to reddish pigmented colonies with whitish powdery spores on both agar and broth media are the important morphological characteristics of this bacterium. Growth tolerance to NaCl concentrations was 2 to 7%. The assembled genome of Streptomyces sp. BSE6.1 contains one linear chromosome 8.02 Mb in length with 7157 protein-coding genes, 82 tRNAs, 3 rRNAs and at least 11 gene clusters related to the synthesis of various secondary metabolites, including undecylprodigiosin. This strain carries type I, type II, and type III polyketide synthases (PKS) genes. Type I PKS gene cluster is involved in the biosynthesis of red pigment undecylprodigiosin of BSE6.1, similar to the one found in the S. coelicolor A3(2). This red pigment was reported to have various applications in the food and pharmaceutical industries. The genome of Streptomyces sp. BSE6.1 was submitted to NCBI with a BioProject ID of PRJNA514840 (Sequence Read Archive ID: SRR10849367 and Genome accession ID: CP085300).

Draft genome sequence of marine sediment-derived red pigmented bacteria Zooshikella sp. strain S2.1 with potential biomedical applications.

The present study is aimed to determine the draft genome of novel species of Zooshikella strain S2.1, a potential red pigmented strain isolated recently from the coastal sediment of Andaman and Nicobar Islands, India. This Gram negative, rod shaped aerobic bacterium produces pink, yellowish-red and dark red with metallic green sheen pigmentation on agar plates. It is able to grow under NaCl concentrations of 1 to 9%. This species has antimicrobial, antioxidant, dye and food colorant applications. Whole genome sequence analysis revealed that strain S2.1 represents a novel species of the genus Zooshikella. Draft genome and 16 s rRNA sequences of this species were deposited in GenBank under the Sequence Read Archive accession number PRJNA514840 and GenBank number MK680108, respectively. Here we report the draft genome of Zooshikella sp. strain S2.1 with ~5.9 Mb of chromosomal content and ~0.34 Mb of extra-chromosomal content.

Elucidating the richness of bacterial groups in the gut of Nicobarese tribal community - Perspective on their lifestyle transition.

Lifestyle and dietary habits are crucial features that can alter the gut microbiome of humans. Humans, along with their gut microbes, have coevolved in order to sustain themselves in different environments. They were able to adapt themselves to the dietary sources available in their environment. The relation between humans and their gut microbiota and the link with coevolution forms an interesting aspect of research. To understand this association, the participation of ancient communities with less exposure to urbanization is a prerequisite. The current study quantifies the richness of bacterial groups in the gut of Nicobarese. This group of population is an ethnic community of Nicobar group of islands, who have migrated from the remote to rural and urban areas. Alterations in the dominant bacterial groups in relation to their lifestyle transition were emphasized, by comparing the participants from remote, rural and urban settings. The remote cohort remains diverse and stable than the other two cohorts and had higher numbers of Bacteroidetes. Prevotella forms the dominant genus in the Bacteroidetes phylum, indicating the carbohydrate-rich diet of remote Nicobarese. Whereas, the urban cohort is dominated by Bifidobacterium group rather than the Bacteroidetes. Implications of dietary patterns, the transition to different lifestyles and their impact on the microbiota among these cohorts are discussed.

Natural transmission of dengue virus serotype 3 by Aedes albopictus (Skuse) during an outbreak in Havelock Island: Entomological characteristics.

From May to June 2014, an outbreak of dengue virus (DENV) illness occurred in the Havelock Island, South Andaman. Entomological investigations were undertaken during the peak of the outbreak, from 26th May-4th June, to identify the primary vector(s) involved in the transmission so that appropriate public health measures could be implemented. Adult mosquitoes were collected by BG-Sentinel traps in houses and neighborhoods of clinically ill patients. Water holding containers were inspected for the presence of mosquito larvae and pupae. Adult mosquitoes were analyzed by RT-PCR for the presence of nucleic acids of DENV and CHIKV. A total of 498 mosquitoes were collected and processed in 27 pools. The species composition comprised of 58.3% Aedes albopictus, 7.5% Aedes aegypti and 4.2% Aedes edwardsi and 3.1% constituted others. Two A. albopictus pools were found to be positive for DENV RNA. Sequencing of the RT PCR 511 base pair amplicon positive samples showed homology with DENV-3, suggesting that serotype-3 was responsible for the outbreak and A. albopictus was the primary vector responsible. This was supported by high container (10.1%), premise (25.4%) and Breteau (27.9) indices, with miscellaneous receptacles (2.4%), tree holes (1.2%) and discarded tires (1.2%) registering relatively higher container indices. This is the first report of detection of DENV in A. albopictus from Andaman and Nicobar Islands.

Association of Oligoadenylate Synthetase Gene Cluster and DC-SIGN (CD209) Gene Polymorphisms with Clinical Symptoms in Chikungunya Virus Infection.

Biology and pathogenesis of chikungunya virus (CHIKV) are not clearly established. Host factors play an important role in determining the progression and severity of the disease. Polymorphisms in the promoter region of CD209 gene (rs735239, rs4804803, rs2287886) and OAS1 (rs1131454 and rs10774671), OAS2 (rs15895 and rs1732778), and OAS3 (rs2285932 and rs2072136) genes were investigated in 100 patients with CHIKV infection and 101 healthy controls to find out the association of these polymorphisms with CHIKV infection. To evaluate the association of OAS and CD209 gene polymorphisms with the presence or absence of disease symptoms in CHIKV-infected patients. DNA was extracted and typed using polymerase chain reaction followed by restriction fragment length polymorphism methods. Results revealed that the allele and genotype frequencies of OAS1, OAS3, and OAS2 gene polymorphisms were not different between healthy controls and CHIKV patients. The frequency of CD209 gene G/G genotype of rs4804803 was significantly higher in CHIKV patients compared to healthy controls (p = 0.046). The present study suggests that rs4804803 GG genotype of CD209 gene is associated with susceptibility to CHIKV infection. To conclude, the present preliminary study suggests that OAS gene cluster and CD209 gene polymorphisms influence the risk of developing clinical symptoms in CHIKV-infected patients. Further follow-up studies with a large number of samples are needed to assess the role of these genes in association with post-sequela symptoms observed in CHIKV patients. A detailed research is required in these directions to understand the biology behind CHIKV infection and disease severity.

HLA class II allele polymorphism in an outbreak of chikungunya fever in Middle Andaman, India.

A sudden upsurge of fever cases with joint pain was observed in the outpatient department, Community Health Centre, Rangat during July-August 2010 in Rangat Middle Andaman, India. The aetiological agent responsible for the outbreak was identified as chikungunya virus (CHIKV), by using RT-PCR and IgM ELISA. The study investigated the association of polymorphisms in the human leucocyte antigen class II genes with susceptibility or protection against CHIKV. One hundred and one patients with clinical features suggestive of CHIKV infection and 104 healthy subjects were included in the study. DNA was extracted and typed for HLA-DRB1 and DQB1 alleles. Based on the amino acid sequences of HLA-DQB1 retrieved from the IMGT/HLA database, critical amino acid differences in the specific peptide-binding pockets of HLA-DQB1 molecules were investigated. The frequencies of HLA-DRB1 alleles were not significantly different, whereas lower frequency of HLA-DQB1*03:03 was observed in CHIKV patients compared with the control population [P = 0·001, corrected P = 0·024; odds ratio (OR)  = 0, 95% confidence interval (95% CI) 0·0-0·331; Peto's OR = 0·1317, 95% CI 0·0428-0·405). Significantly lower frequency of glutamic acid at position 86 of peptide-binding pocket 1 coding HLA-DQB1 genotypes was observed in CHIKV patients compared with healthy controls (P = 0·004, OR = 0·307, 95% CI 0·125-0·707). Computational binding predictions of CD4 epitopes of CHIKV by NetMHCII revealed that HLA-DQ molecules are known to bind more CHIKV peptides than HLA-DRB1 molecules. The results suggest that HLA-DQB1 alleles and critical amino acid differences in the peptide-binding pockets of HLA-DQB1 alleles might have role in influencing infection and pathogenesis of CHIKV.