@article {46726,
	title = {Pan-genomics of Ochrobactrum species from clinical and environmental origins reveals distinct populations and possible links},
	journal = {Genomics},
	volume = {112},
	year = {2020},
	month = {SEP},
	pages = {3003-3012},
	type = {Article},
	abstract = {<p>Ochrobactrum genus is comprised of soil-dwelling Gram-negative bacteria mainly reported for bioremediation of toxic compounds. Since last few years, mainly two species of this genus, O. intermedium and O. anthropi were documented for causing infections mostly in the immunocompromised patients. Despite such ubiquitous presence, study of adaptation in various niches is still lacking. Thus, to gain insights into the niche adaptation strategies, pan-genome analysis was carried out by comparing 67 genome sequences belonging to Ochrobactrum species. Pan-genome analysis revealed it is an open pan-genome indicative of the continuously evolving nature of the genus. The presence/absence of gene clusters also illustrated the unique presence of antibiotic efflux transporter genes and type IV secretion system genes in the clinical strains while the genes of solvent resistance and exporter pumps in the environmental strains. A phylogenomic investigation based on 75 core genes depicted better and robust phylogenetic resolution and topology than the 16S rRNA gene. To support the pan-genome analysis, individual genomes were also investigated for the mobile genetic elements (MGE), antibiotic resistance genes (ARG), metal resistance genes (MRG) and virulence factors (VF). The analysis revealed the presence of MGE, ARG, and MRG in all the strains which play an important role in the species evolution which is in agreement with the pan-genome analysis. The average nucleotide identity (ANI) based on the genetic relatedness between the Ochrobactrum species indicated a distinction between individual species. Interestingly, the ANI tool was able to classify the Ochrobactrum genomes to the species level which were assigned till the genus level on the NCBI database.</p>
},
	keywords = {Antibiotic resistance, Average nucleotide identity, Clinical and environmental strains, Core genes, MinION, Virulence factors},
	issn = {0888-7543},
	doi = {10.1016/j.ygeno.2020.04.030},
	author = {Gohil, Kushal and Rajput, Vinay and Dharne, Mahesh}
}
@article {47132,
	title = {Functional metagenomic landscape of polluted river reveals potential genes involved in degradation of xenobiotic pollutants},
	journal = {Environmental Research},
	volume = {192},
	year = {2021},
	month = {JAN},
	pages = {110332},
	type = {Article},
	abstract = {<p>Rapid industrialization contributes substantially to xenobiotic pollutants in rivers. As a result, most of the rivers traversing urban settlements are in significantly deteriorated conditions. These pollutants are recalcitrant, requiring robust catabolic machinery for their complete transformation into bioavailable and non-toxic byproducts. Microbes are versatile dwellers that could adapt to such contaminants by using them as a source of nutrients during growth. However, efficient bioremediation requires an in-depth knowledge of microbial diversity and their metabolism related genes in the polluted niches. We employed MinION shotgun sequencing, to comprehend the biodegradation related genes and their function potential operating in the polluted urban riverine system of Western India. A vast number of catabolic genes were detected for the xenobiotic pollutants such as Benzoate, Nitrotoluene, Aminobenzoate, Drug metabolism, and Polycyclic Aromatic Hydrocarbons. Aerobic, and anaerobic catabolism genes, were mapped for their ability of degradation of xenobiotics. Interestingly, catabolism profiles of multiple aromatic compounds culminated into the Benzoate degradation pathway, suggesting it as a plausible central pathway for the autochthonous bacterial communities. Further mapping with RemeDB database, predicted plastic and dye degrading enzymes. Moreover, the diversity indices for the pollutant degrading enzymes suggested little variations (R-2 value of 18\%) between the city and non-city (outskirts of city limits) riverine stretch indicating the impact of industrialization in the outskirts of the city stretch as well. Altogether, this study would serve as a preliminary baseline for future explorations concerning river cleaning programs and also exploiting such microbes for bioremediation applications.</p>
},
	keywords = {Benzoate, Bioremediation, MinION, Riverine system, Xenobiotics},
	issn = {0013-9351},
	doi = {10.1016/j.envres.2020.110332},
	author = {Yadav, Rakeshkumar and Rajput, Vinay and Dharne, Mahesh}
}
@article {47636,
	title = {Metagenomic exploration reveals a differential patterning of antibiotic resistance genes in urban and peri-urban stretches of a riverine system},
	journal = {Environmental Science and Pollution Research},
	volume = {28},
	year = {2021},
	month = {DEC},
	pages = {66477-66484},
	type = {Article},
	abstract = {{Antimicrobial resistance in the riverine ecosystem of urban areas is an alarming concern worldwide, indicating the importance of molecular monitoring to understand their patterning in urban and peri-urban areas. In the present study, we evaluated the influence of urban rivers on the connected peri-urban rivers of a riverine system of India in the context of antibiotic resistance genes. The rivers traversing through urban (Mula, Mutha, Pawana, and Ramnadi) and peri-urban stretches (Bhima and Indrayani) form the riverine system of Pune district in Maharashtra, India. The MinION-based shotgun metagenomic analysis revealed the resistome against 26 classes of antibiotics, including the last line of antibiotics. In total, we observed 278 ARG subtypes conferring resistance against multiple drugs (40\%), bacitracin (10\%), aminoglycoside (7.5\%), tetracycline (7\%), and glycopeptide (5\%). Further, the alpha diversity analysis suggested relatively higher ARG diversity in the urban stretches than peri-urban stretches of the riverine system. The NMDS (non-metric multidimensional scaling) analysis revealed significant differences with overlapping similarities (stress value = 0.14},
	keywords = {Antibiotic resistance, MinION, Peri-urban rivers, Urbanization},
	issn = {0944-1344},
	doi = {10.1007/s11356-021-16910-y},
	author = {Rajput, Vinay and Yadav, Rakeshkumar and Dharne, Mahesh S.}
}
