Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes.

The discharge of solid and liquid waste from domestic, municipal, and hospital premises pollutes the soil and river ecosystems. However, the diversity and functions of the microbial communities present in these polluted environments are not well understood and may contain harmful microbial communities with specialized metabolic potential. In this present study, we adapted the Illumina sequencing technology to analyze microbial communities and their metabolic capabilities in polluted environments. A total of 1113884 sequences of v3-v4 hypervariable region of the 16S rRNA were obtained using Illumina sequencing and assigned to the corresponding taxonomical ranks using Greengenes databases. Proteobacteria and Bacteroidetes were dominantly present in all the four studied sites (solid waste dumping site (SWD); Chite river site (CHR), Turial river site (TUR), and Tuikual river site (TUKR)). It was found that the SWD was dominated by Firmicutes, Actinobacteria; CHR by Acidobacteria, Verrucomicrobia, Planctomycetes; TUR by Verrucomicrobia, Acidobacteria; and TUKR by Verrucomicrobia and Firmicutes, respectively. The dominant bacterial genus present in all samples was Acinetobacter, Flavobacterium, Prevotella, Corynebacterium, Comamonas, Bacteroides, Wautersiella, Cloacibacterium, Stenotrophomonas, Sphingobacterium, and Pseudomonas. Twenty-seven putative bacterial pathogens were identified from the contaminated sites belonging to Salmonella enterica, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. Functional analysis showed a high representation of genes in the KEGG pathway involved in the metabolism of amino acids and carbohydrates and identified several genes associated with antibiotic resistance and xenobiotic degradation in these environments, which can be a serious problem for human health and environment. The results from this research will provide a new understanding of the possible management practices to minimize the spread of pathogenic microorganisms in the environment.

Antimicrobial, antioxidant and probiotics characterization of dominant bacterial isolates from traditional fermented fish of Manipur, North-East India.

Utonga-kupsu, Hentak and Ngari are traditional fermented fish products produced by the Manipuri people living in the North-Eastern part of India. The present study was designed with the aim to isolate, identify and characterize the microorganisms present in these fermented foods. Bacterial pure cultures were isolated using serially diluted samples and were further identified by conventional biochemical tests and Sanger sequencing of 16s rRNA gene. Results show that the number of bacterial count in Nutrient agar and Starch casein agar was 14-20 and 10-16 CFU/g, respectively. A total of 46 morphologically different bacterial strains were identified and assigned under the phylum Firmicutes. Identified bacterial strains belonged to the genus Bacillus and Staphylococcus and majority of the isolates were Bacillus subtilis and Staphylococcus nepalensis. Bacterial isolate HNS60 isolated from Hentak and identified as Bacillus subtilis was shown to possess high antimicrobial activity against Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. Most of the identified bacteria were shown to possess DPPH radical scavenging as well as phosphatase, amylase, protease and cellulose activities. The isolate HNS60 contain high antimicrobial, enzymatic and probiotics activity which might responsible for the possible health benefits of the fermented foods. Utonga-kupsu, Hentak and Ngari thus can be further exploited as a potential source of probiotics and natural antioxidants.

The complete mitochondrial genome of the Indian honey bee, Apis cerena cerana (Hymenoptera: Apidae: Apinae).

The complete mitogenome of Apis cerana cerana (Hymenoptera: Apidae: Apinae) was sequenced using Illumina NextSeq500 platform and found to be 15 831 bp long. The mitogenome contains 37 genes (13 PCGs, 22 tRNAs, and 2 rRNAs) and a control region. The base composition is biased towards A-T (83.9%). The control region is 498 bp long with polyT stretch and poly [TA (A)]n-like stretch. The phylogenetic tree constructed using concatenated PCGs showed that A. cerana cerana clustered with other cavity nesting Apis species.

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.