Comparative Genomics and Characterization of Shigella flexneri Isolated from Urban Wastewater.

Shigella species are a group of highly transmissible Gram-negative pathogens. Increasing reports of infection with extensively drug-resistant varieties of this stomach bug has convinced the World Health Organization to prioritize Shigella for novel therapeutic interventions. We herein coupled the whole-genome sequencing of a natural isolate of Shigella flexneri with a pangenome ana-lysis to characterize pathogen genomics within this species, which will provide us with an insight into its existing genomic diversity and highlight the root causes behind the emergence of quick vaccine escape variants. The isolated novel strain of S. flexneri contained ~4,500 protein-coding genes, 57 of which imparted resistance to antibiotics. A comparative pan-genomic ana-lysis revealed genomic variability of ~64%, the shared conservation of core genes in central metabolic processes, and the enrichment of unique/accessory genes in virulence and defense mechanisms that contributed to much of the observed antimicrobial resistance (AMR). A pathway ana-lysis of the core genome mapped 22 genes to 2 antimicrobial resistance pathways, with the bulk coding for multidrug efflux pumps and two component regulatory systems that are considered to work synergistically towards the development of resistance phenotypes. The prospective evolvability of Shigella species as witnessed by the marked difference in genomic content, the strain-specific essentiality of unique/accessory genes, and the inclusion of a potent resistance mechanism within the core genome, strengthens the possibility of novel serotypes emerging in the near future and emphasizes the importance of tracking down genomic diversity in drug/vaccine design and AMR governance.

First report of gut bacterial dataset of a tribal Bhutia family from West Bengal, India.

The tribes of West Bengal are distributed in geographically distinct regions with distinctive features of their habitats and many of these tribes still practice a traditional livelihood avoiding the western diet. Hence, it is expected that their gut should remain pristine. In this study, we report the gut bacterial abundance of a Drukpa Bhutia tribal family of Lepchakha, inhabiting the hilly terrain of the Buxa region of Alipurduar district. First fecal matter was collected followed by Illumina Hiseq sequencing. Following standard protocols for metagenomic analysis, quality control (FASTQC), taxonomic profiling (QIIME, KRONA) and pathogenic load analysis were performed. This study revealed a set of core gut bacteria among which Bacteroides was identified to be the most abundant followed by Bifidobacterium, Streptococcus etc. Genera exhibiting lowest abundance were Eggerthella, Ruminococcus, Enterococcus etc. among the male, kid and female respectively. This data provides important insights into the distribution of bacterial members under study.

Bioaugmentation of Enterobacter cloacae AKS7 causes an enhanced degradation of low-density polyethylene (LDPE) in soil: a promising approach for the sustainable management of LDPE waste.

Enterobacter cloacae AKS7 was previously reported to degrade UV-treated low-density polyethylene (LDPE) more efficiently than UV-untreated LDPE. However, the degradation of LDPE by Enterobacter cloacae AKS7 at the LDPE-contaminated soil remained unaddressed. To address this issue, soil microcosms were prepared in which an equal amount of either UV-treated or UV-untreated LDPE was added. Then, the microcosms were either augmented with AKS7 or left non-augmented. We observed that the bioaugmented microcosms exhibited approximately twofold greater polymer degradation than non-bioaugmented microcosms. To investigate the underlying cause, we found that the abundance of LDPE-degrading organisms got increased by approximately fivefold in bioaugmented microcosms than non-bioaugmented microcosms. The microbial biomass carbon and nitrogen content got enhanced by approximately twofold in bioaugmented microcosms as contrasted to non-bioaugmented microcosms. Furthermore, the bioaugmented microcosms showed almost twofold increase in the level of dehydrogenase and fluorescein diacetate (FDA) hydrolyzing activity than the non-bioaugmented microcosms. To add on, Shannon-diversity index and Gini coefficient were determined in each microcosm to measure the microbial richness and evenness, respectively, using the results of carbon source utilization pattern of BiOLOG ECO plate. The bioaugmented microcosms exhibited ~ 30% higher functional richness and ~ 30% enhanced functional evenness than the non-bioaugmented microcosms indicating the formation of an enriched ecosystem that could offer various functions including polymer degradation. Taken together, the results suggested that Enterobacter cloacae AKS7 could be used as a promising bioaugmenting agent for the sustainable degradation of LDPE waste at a contaminated site.

Comparative metagenomic dataset of hospital effluent microbiome from rural and urban hospitals in West Bengal.

The unsafe disposal of hospital effluents contributes to gross contamination of water bodies with antibiotic residues, antibiotic resistance genes and antibiotic resistance bacteria. This study reports the microbial community profile of hospital wastes collected from various regions of West Bengal, India, using 16S rRNA gene amplicon sequencing. The data set Liquid Sludge (LS) contains 15,372,973 reads with an average length of 301 bps with average 52 ± 5% GC content. The data set Solid Sludge (SS) contains 16,071,594 reads with an average length of 301 bps with average 53 ± 4% GC content. Data of this study are available at NCBI BioProject (PRJNA360379). In sample LS, an abundance of 19.3% for the members of Bacteroidetes was observed. In sample SS, an abundance of 19.7% for the members of Euryarchaeota was observed.