@article {43941, title = {Multilocus sequence typing of Ochrobactrum spp. isolated from gastric niche}, journal = {Journal of Infection and Public Health }, volume = {10}, year = {2017}, month = {MAR-APR}, pages = {201-210}, type = {Journal Article}, abstract = {The human stomach is colonized by diverse bacterial species. The presence of non-Helicobacter pylori bacteria in urease-positive biopsies of individuals has been reported. Bacteria belonging to the Ochrobactrum genus have been documented in the human gastric niche. The co-occurrence of Ochrobactrum spp. with H. pylori was previously reported in an antral biopsy of a non-ulcer dyspeptic (NUD) subject from Northern India. There is no information on the genetic diversity of Ochrobactrum spp. isolated from the gastric niche in the stomach. We aimed to study the species distribution and diversity of Ochrobactrum spp. with and without H. pylori in urease-positive biopsies across three different geographical regions in India. Sixty-two Ochrobactrum isolates recovered from patients with an upper gastric disorder (n=218) were subjected to molecular identification and multilocus sequence typing. H. pylori DNA was found in the majority of biopsies, which had a variable degree of Ochrobactrum spp present. Interestingly, some of the urease-positive biopsies only had Ochrobactrum without any H. pylori DNA. Based on phylogenetic analysis, the Ochrobactrum isolates were distributed into the O. intermedium, O. anthropi and O. oryzae groups. This indicates there are multiple species in the gastric niche irrespective of the presence or absence of H. pylori. Antibiotyping based on colistin and polymyxin B could differentiate between O. intermedium and O. anthropi without revealing the resistance-driven diversity. Considering the prevalence of multiple Ochrobactrum spp. in the human gastric niche, it is important to evaluate the commensal and/or pathogenic nature of non-H. pylori bacteria with respect to their geographical distribution, lifestyle and nutrition needs.}, keywords = {Helicobater Pyroli, MLST, Non-Ulcer Dyspepsia, Ochrobactrum}, doi = {10.1016/j.jiph.2016.04.013}, author = {Kulkarni, Girish}, editor = {Gohil, Kushal} } @article {44448, title = {Dephytinizing and probiotic potentials of saccharomyces cerevisiae (NCIM 3662) strain for amelioration of nutritional quality of functional foods}, journal = {Probiotics and Antimicrobial Proteins}, volume = {11}, year = {2018}, month = {MAR}, pages = {604-617}, type = {Article}, abstract = {Increase of undigested complexes of phytic acid in food is gaining serious attention to overcome nutritional challenges due to chelation effects. We investigated soil-borne yeast phytase from Saccharomyces cerevisiae (NCIM 3662) for dephytinization of foods, probiotic properties, and process development. The strain produced 45 IU/DCG by cell-bound phytase in an unoptimized medium was increased fourfold (164 IU/DCG) in 12 h using statistical media optimization. The process was scaled-up up to 10-L fermenter scale with increased phytase productivity of 6.4 IU/DCG/h as compared to the lab scale. The strain displayed probiotic characteristics like tolerance to artificial gastric acid conditions, hydrophobicity, autoaggregation, coaggregation, and bile salt hydrolase (BSH) activity. Further, it could dephytinize (removal of phytic acid; an anti-nutritional factor) functional foods like ragi (finger millet) flour, soya flour, chickpea flour, and poultry animal feed. A combination of cell-bound dephytinizing phytase and nutrition-ameliorating probiotic traits of S. cerevisiae (NCIM 3662) presents profound applications in food technology sector.}, doi = {10.1007/s12602-018-9394-y}, author = {Kumar Raja Puppala and Kumar , V. Ravi and Khire, Jayant and Dharne, Mahesh} } @article {44471, title = {Evaluation of Candida tropicalis (NCIM 3321) extracellular phytase having plant growth promoting potential and process development}, journal = {Biocatalysis and Agricultural Biotechnology}, volume = {13}, year = {2018}, month = {JAN}, abstract = {

Phytase is known to provide a solution for depletion of phosphorus (P). It helps it by hydrolyzing the insoluble P source in soil which is phytate. In this study, provides insight on yeast Candida tropicalis (NCIM 3321) which produces cell bound and extracellular thermostable phytase. The media components were optimized to enhance the enzyme production and checked for plant growth promoting activity. On optimization the isolate exhibited enhanced cell bound and extracellular phytase activity by four folds (from 236 to 1024 IU DCG$^{-}${\textonesuperior}) and by five folds (from 0.46 to 1.95 IU ml$^{-}${\textonesuperior}) respectively in 36 h. The production time decreased to 24 h compare to shake flask on Up-scaling the production process upto 10 L scale, thus increasing the productivity of cell bound (1810 IU DCG$^{-}${\textonesuperior}day$^{-}${\textonesuperior}) and extracellular phytase (6.08 IU ml$^{-}${\textonesuperior} day$^{-}${\textonesuperior}). The crude phytase (12 IU) from NCIM 3321 strain was studied for plant growth promotion activity in lab scale and field level experiments with maize crop. Findings of the study revealed that the extracellular phytase derived from non pathogenic C. tropicalis (NCIM 3321) was found to be plant growth stimulating by increasing the available P in soil. Our findings of phytase isolated from non-pathogenic yeast C. tropicalis NCIM 3321 exhibited dephytinization potential. Therefore, current study may have profound application in sustainable agriculture.

}, doi = {10.1016/j.bcab.2017.12.013}, author = {Puppala, Kumar Raja and Naik, Tejali and Shaik, Alfina and Dastager, Syed and Kumar, V. Ravi and Khire, Jayant and Dharne, Mahesh} } @article {44528, title = {Mixed bacterial culture mediated direct conversion of bio-glycerol to diols}, journal = {Bioresource Technology}, volume = {250}, year = {2018}, month = {FEB}, pages = {86-93}, abstract = {

Direct and economic transformation of biodiesel derived crude glycerol is gaining more significance. During screening of bacterial cultures Klebsiella pneumoniae and Enterobacter aerogenes were able to convert crude bio-glycerol to 2,3-butanediol (2,3-BDO) and 1,3-propanediol (1,3-PDO), as major compounds, ethanol and acetoin as minor compounds, with a conversion of 69\% and 79\% respectively. Process optimization could achieve maximum conversion at pH 7.0, 37 degrees C, 30-40 g/L glycerol and 1.5 g of inoculum until 120 h. Mixed cultures led to complete glycerol conversion with optimal yield and productivity. An innovative approach of using crude glycerol for sustained growth and tolerance of bacteria as source of carbon and energy makes this study more significant. In addition to this, a mixed culture concept introduced here is expected to make impact in process economics for industrial scale synthesis for direct transformation of glycerol into C3 and specifically, C4 diols.

}, keywords = {1, 2, 3-Butanediol, 3-Propanediol, Bioconversion, Bioglycerol, Mixed culture}, issn = {0960-8524}, doi = {10.1016/j.biortech.2017.11.019}, author = {Parate, Roopa and Mane, Rasika and Dharne, Mahesh and Rode, Chandrashekhar} } @article {47167, title = {Draft genome sequence of freshwater-derived streptomyces sp. strain BPSDS2, isolated from damte stream, northeast India}, journal = {American Society for Microbiology}, year = {2019}, month = {OCT}, type = {Article}, abstract = {

We report the draft genome sequence of Streptomyces sp. strain BPSDS2, isolated from freshwater sediments in Northeast India. The draft genome has a size of 8.27 Mb and 7,559 protein-coding sequences.

}, doi = {10.1128/MRA.00874-19}, author = {Zothanpuia and Passari, Ajit Kumar and Deka, Vinay and Rajput, Lakshmi P. M. and Priya, Purbajyoti and Dharne, Mahesh and Dastager, Syed and Mathew, Oommen K. and Hashem, Abeer and Abd_ Allah, Elsayed Fathi and Singh, Bhim Pratap} } @article {46698, title = {Comprehensive metagenomic insights into a unique mass gathering and bathing event reveals transient influence on a riverine ecosystem}, journal = {Ecotoxicology and Environmental Safety}, volume = {202}, year = {2020}, month = {OCT }, pages = {110938}, type = {Article}, abstract = {

The religious mass gathering and bathing can pose a multitude of significant public health challenges and lead to severe alterations in the river microbial ecology. The Pandharpur Wari is an annual pilgrimage of Maharashtra, India, where millions of devotees carry the footprints of the saint-poets and pay their obeisance to Lord Vitthal on the 11th day of moon{\textquoteright}s waxing phase (Ashadi Ekadashi). As a part of the ritual, the engrossed devotees, walk over 250 km, take a first holy dip in a sacred river Indrayani at Alandi and secondly in Bhima River at Pandharpur. The MinION-based shotgun metagenomic approach was employed to examine the impact of spiritual mass bathing on environmental changes (concerning the river microbial community structure and functions); and public health aspects (in terms of changes in the pathogenic potential and antibiotic resistance). The analysis of bathing and post-bathing samples of both the rivers revealed alterations in the alpha and beta diversity, indicating significant spatiotemporal variations in the overall microbial structure and function. Furthermore, the analysis revealed up to 80\% of differences in the abundance of virulence genes between the bathing and post bathing samples. We observed parallel increase of priority skin and enteric pathogens (ranging from 11\% to 80\%) such as Acinetobacter baumannii, Staphylococcus aureus, Streptococcus pyogenes, Mycobacterium tuberculosis, and Pseudomonas aeruginosa during the bathing event. Moreover, we observed a significant increase in the antibiotic resistance in the bathing samples of Bhima and Indrayani rivers respectively. Altogether, this is the first comprehensive metagenomic study unravelling the influence of religious mass-bathing on the riverine ecosystem.

}, keywords = {Antibiotic resistance, Mass bathing, MinION sequencing, Priority pathogens, Virulence genes}, issn = {0147-6513}, doi = {10.1016/j.ecoenv.2020.110938}, author = {Yadav, Rakeshkumar and Rajput, Vinay and Gohil, Kushal and Khairnar, Krishna and Dharne, Mahesh} } @article {47315, title = {Metagenome sequencing to unveil microbial community composition and prevalence of antibiotic and metal resistance genes in hypersaline and hyperalkaline Lonar Lake, India}, journal = {Ecological Indicators}, volume = {110}, year = {2020}, month = {MAR}, pages = {105827}, type = {Article}, abstract = {

Lonar Lake (India) is a hyperalkaline and hypersaline soda lake encompassing unique microbial composition and functions. This ecosystem has not been explored for taxonomic diversity and functional aspects (with emphasis on antibiotic and metal resistance genes) using whole metagenome sequencing for multiple years. Bacterial diversity analysis during year 2013, 2016, and 2018 depicted differences in the dominance of Proteobacteria, Firmicutes and Bacteroidetes. For archaeal diversity, a similar pattern persisted with higher abundance of Euryarchaeota. Functional metagenome analyses, indicated presence of antibiotic resistance gene (ARG) and metal resistance gene (MRG) profiles in the lake. A wider continuum of resistance genes with dominant ARG types as multidrug resistance efflux pumps and beta-lactams were also observed. The lake resistome demonstrated fluoroquinolone and acriflavine resistance genes indicating sewage water contamination in the lake. The MRGs linked with resistance to toxic metals (arsenic, cobalt, cadmium, copper, and zinc) and cation efflux protein CusA and cobalt-zinc-cadmium resistance protein revealed metal contamination. This study could be a baseline for understanding prevalence of antibiotic and metal resistance mechanisms resulting from various anthropogenic activities nearby lake, and find integrated approaches for conservation of the precious Lonar Lake ecosystem.

}, keywords = {Archaeal diversity, ARGs, Bacterial diversity, Illumina sequencing, Lonar lake, MRGs}, issn = {1470-160X}, doi = {10.1016/j.ecolind.2019.105827}, author = {Chakraborty, Jaya and Sapkale, Vibhavari and Shah, Manan and Rajput, Vinay and Mehetre, Gajanan and Agawane, Sachin and Kamble, Sanjay and Dharne, Mahesh} } @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 = {

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.

}, 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 {46882, title = {Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India}, journal = {Ecotoxicology and Environmental Safety}, volume = {194}, year = {2020}, month = {MAY}, pages = {110443}, type = {Article}, abstract = {

Anthropogenic activities mediated antibiotic resistance genes (ARGs) in the pristine aquatic bodies (lakes) is raising concern worldwide. Long read shotgun sequencing was used to assess taxonomic diversity, distribution of ARGs and metal resistance genes (MRGs) and mobile genetic elements (MGEs) in six sites within hypersaline Lonar soda lake (India) prone to various anthropogenic activities. Proteobacteria and Euryarchaeota were dominant phyla under domain Bacteria and Archaea respectively. Higher abundance of Bacteroidetes was pragmatic at sites 18LN5 and 18LN6. Functional analysis indicated 26 broad-spectrum ARGs types, not reported earlier in this ecosystem. Abundant ARG types identified were multidrug efflux, glycopepetide, bacitracin, tetracycline and aminogylcoside resistance. Sites 18LN1 and 18LN5 depicted 167 and 160 different ARGs subtypes respectively and rpoB2, bcrA, tetA(48), mupA, ompR, patA, vanR and multidrug ABC transporter genes were present in all samples. The rpoB2 gene was dominant in 18LN1, whereas bcrA gene in 18LN2-18LN6 sites. Around 24 MRGs types were detected with higher abundance of arsenic in 18LN1 and copper in 18LN2-18LN6, signifying metal contamination linked to MRGs. The bacterial taxa Pseudomonas, Thioalkalivibrio, Burkholderia, Clostridium, Paenibacillus, Bacillus and Streptomyces were significantly associated with ARGs. This study highlights the resistomic hotspots in the lake for deploying policies for conservation efforts.

}, keywords = {ARGs, diversity, Lonar lake, MGEs, MRGs, Nanopore sequencing}, issn = {0147-6513}, doi = {10.1016/j.ecoenv.2020.110443}, author = {Chakraborty, Jaya and Sapkale, Vibhavari and Rajput, Vinay and Shah, Manan and Kamble, Sanjay and Dharne, Mahesh} } @article {47114, title = {Bioglycerol (C3) upgrading to 2,3-butanediol (C4) by cell-free extracts of Enterobacter aerogenes NCIM 2695}, journal = {Journal of Chemical Technology and Biotechnology}, volume = {96}, year = {2021}, month = {MAY}, pages = {1316-1325}, type = {Article}, abstract = {

BACKGROUND Production of biobased chemicals from renewable resources is a green starring approach that serves as a substitute to petroleum derivatives. Bioglycerol, with its growing production as a co-product of biodiesel, is an attractive low-cost feedstock for the synthesis of platform chemicals by microbial fermentation. 2,3-butanediol (2,3-BDO) is amongst the top biorefinery platform chemicals that can be produced by glycerol fermentation. RESULTS The {\textquoteleft}Circular Economy{\textquoteright} concept is demonstrated by converting the by-product bioglycerol using a cell-free extract of Enterobacter aerogenes NCIM 2695 (National Collection of Industrial Microorganisms, NCIM), yielding 22 g L-1 2,3-BDO, in 96 h, 98\% atom economy and 0.4 g/g E factor. The cell-free bioglycerol conversion to 2,3-BDO was proved using a modified procedure for determining glycerol dehydrogenase enzyme assay by protein analysis and it was also shown to be cell-bounded. CONCLUSION Our study offers an effective utilization of the leftover material (i.e. cell-free extract) that biocatalysed C3 to C4 diol, which adds value to the overall economics of the process using only crude glycerol (C3) itself as a fermentative medium.

}, keywords = {2, 3-Butanediol, atom economy, circular economy, E factor, Glycerol, glycerol dehydrogenase}, issn = {0268-2575}, doi = {10.1002/jctb.6650, Early Access Date = JAN 2021}, author = {Parate, Roopa and Borgave, Mrunal and Dharne, Mahesh and Rode, Chandrashekhar} } @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 = {

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.

}, 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 {47451, title = {Metagenomic analysis of a mega-city river network reveals microbial compositional heterogeneity among urban and peri-urban river stretch}, journal = {Science of the Total Environment}, volume = {783}, year = {2021}, month = {AUG }, pages = {146960}, type = {Article}, abstract = {

The rivers in the megacities face a constant inflow of extremely polluted wastewaters from various sources, and their influence on the connected peri-urban river is still poorly understood. The riverine system in Pune consists of Rivers Mula, Ramnadi, Pawana, Mutha, and Mula-Mutha, traversing through the urban settlements of Pune before joining River Bhima in the peri-urban region. We used MinION-based metagenomic sequencing to generate a comprehensive understanding of the microbial diversity differ-ences between the urban and peri-urban zones, which has not been explored at the meta scale until date. The taxonomic analysis revealed significant enrichment of pollution indicators microbial taxa (Welsch{\textquoteright}s t-test, p \< 0.05, Benjamini-Hochberg FDR test) such as Bacteriodetes, Firmicutes, Spirochaetes, Synergistetes, Euryarcheota in the urban waters as compared to peri-urban waters. Further, the peri-urban waters showed a significantly higher prevalence of ammonium oxidising archaeal groups such as Nitrososphaeraceae (Student{\textquoteright}s t-test p-value \<0.05 with FDR correction), thereby probably suggesting the influence of agricultural runoffs. Besides, the microbial community diversity assessment also indicated the significant dissimilarity in the microbial community of urban and peri-urban waters. Overall, the analysis predicted 295 virulence genes mapping to 38 different path-ogenic bacteria in the riverine system. Moreover, the higher genome coverage (at least 60\%) for priority patho-gens such as Pseudomonas, Klebsiella, Acinetobacter, Escherichia, Aeromonas in the sediment metagenome consolidates their dominance in this riverine system. To conclude, our investigation showed that the unre-strained anthropogenic and related activities could potentially contribute to the overall dismal conditions and in-fluence the connected riverine stretches on the outskirts of the city . (c) 2021 Elsevier B.V. All rights reserved.

}, keywords = {Industrialisation, Peri-urban, Riverine system, Urbanisation, Virulence factors}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2021.146960}, author = {Yadav, Rakeshkumar and Rajput, Vinay and Dharne, Mahesh} } @article {47134, title = {Probiotics in the prophylaxis of COVID-19: something is better than nothing}, journal = {3 Biotech}, volume = {11}, year = {2021}, month = {JAN}, type = {Review}, abstract = {

The new viral pandemic of COVID-19 is caused by a novel coronavirus (SARS-CoV-2) that has brought the world at another unprecedented crisis in terms of health and economy. The lack of specific therapeutics necessitates other strategies to prevent the spread of infection caused by this previously unknown viral etiological agent. Recent pieces of evidence have shown an association between COVID-19 disease and intestinal dysbiosis. Probiotics comprise living microbes that upon oral administration benefit human health by reshaping the composition of gut microbiota. The close kinship of the gastrointestinal and respiratory tract suggests why the dysfunction of one may incite illness in others. The emerging studies suggest the capability of probiotics to regulate immune responses in the respiratory system. The efficacy of probiotics has been studied previously on several respiratory tract viral infections. Therefore, the purpose of this review is to comprehend existing information on the gut mediated-pulmonary immunity conferred by probiotic bacteria, in the course of respiratory virus infections and administration as a prophylactic measure in COVID-19 pandemic in managing intestinal dysbiosis as well.

}, keywords = {Anti-viral, COVID-19, Gut-lung axis, Probiotics, Respiratory tract infection}, issn = {2190-572X}, doi = {10.1007/s13205-020-02554-1}, author = {Gohil, Kushal and Samson, Rachel and Dastager, Syed and Dharne, Mahesh} } @article {47442, title = {Spatio-temporal resolution of taxonomic and functional microbiome of Lonar soda lake of India reveals metabolic potential for bioremediation}, journal = {Chemosphere}, volume = {264}, year = {2021}, month = {FEB}, pages = {128574}, type = {Article}, abstract = {

Lonar Lake, India; a hypersaline and hyperalkaline extremophilic ecosystem having a unique microbial population has been rarely explored for bioremediation aspects. MinION-based shotgun sequencing was used to comprehensively compare the microbial diversity and functional potential of xenobiotic degradation pathways with seasonal changes. Proteobacteria and Firmicutes were prevalent bacterial phyla in the pre-monsoon and post-monsoon samples. Functional analysis from SEED-subsystem and KEGG database revealed 28 subsystems and 18 metabolic pathways for the metabolism of aromatic compounds and xenobiotic biodegradation respectively. Occurrence of N-phenyl alkanoic, benzoate, biphenyl, chloroaromatic, naphthalene, and phenol degradation genes depicted varied abundance in the pre-monsoon and post-monsoon samples. Further, KEGG analysis indicated nitrotoluene degradation pathway (ko00633) abundant in post-monsoon samples, and the benzoate degradation pathway (ko00362) predominant in 19LN4S (pre-monsoon) than 18LN7S (post-monsoon) samples. The abundant genes for benzoate degradation were pcaI: 3-oxoadipate CoA-transferase, alpha subunit, pcaH: protocatechuate 3,4-dioxygenase, beta subunit, and pcaB: 3-carboxy-cis, cis-muconate cycloisomerase, and 4-oxalocrotonate tautomerase. This metagenomic study provides a unique blueprint of hitherto unexplored xenobiotic biodegradation genes/pathways in terms of seasonal variations in the Lonar Lake, and warrants active exploitation of microbes for bioremediation purposes.

}, doi = {10.1016/j.chemosphere.2020.128574}, author = {Chakraborty, Jaya and Rajput, Vinay and Sapkale, Vibhavari and Kamble, Sanjay and Dharne, Mahesh} } @article {47613, title = {Translating SARS-CoV-2 wastewater-based epidemiology for prioritizing mass vaccination: a strategic overview}, journal = {Environmental Science and Pollution Research}, volume = {28}, year = {2021}, month = {AUG}, pages = {42975-42980}, type = {Article}, abstract = {The inception of the novel coronavirus has forced the world into despair. Rapid progress has been made in addressing the situation, and various clinical diagnostic methods were developed for early detection of transmission. However, with a rapidly increasing number of infected populations worldwide, the testing of each individual was impractical. The wastewater-based epidemiology (WBE) has been implemented to evaluate disease outbreaks as an early warning system for pandemic preparedness. Numerous studies reported the presence of SARS-CoV-2 in the open drains and STPs across the globe via recovery efficiency of surrogate virus from existing virus concentration protocols. However, the such reported studies did not justify the use of WBE to identify or pinpoint the specific hotspots of transmission which could be prioritized for rapid efforts to contain or accelerate active vaccination efforts. Identifying precise locations of hotspots could be an essential aspect in controlling the outbreak and surge of wave by prioritizing the region for primary outbreak response. This article focuses on the issues relating to the primary focus for WBE that can be adapted, and its suitability for utilization in the mass vaccination program is discussed. Effective use of WBE information in terms of source tracking might be crucial as we move towards mass vaccination to control outbreaks of COVID-19 pandemic.}, keywords = {Epidemiology, Policy making, SARS-CoV-2, Vaccination, wastewater}, issn = {0944-1344}, doi = {10.1007/s11356-021-15169-7}, author = {Dharmadhikari, Tanmay and Yadav, Rakeshkumar and Dastager, Syed and Dharne, Mahesh} } @article {47624, title = {COVID-19 associated mucormycosis: evolving technologies for early and rapid diagnosis}, journal = {3 Biotech}, volume = {12}, year = {2022}, month = {JAN}, pages = {6}, type = {Review}, abstract = {The post-coronavirus disease (COVID-19) mucormycosis is a deadly addition to the pandemic spectrum. Although it{\textquoteright}s a rare, aggressive, and opportunistic disease, the associated morbidity and mortality are significant. The complex interplay of factors aggravating CAM is uncontrolled diabetes, irrational and excessive use of antibiotics, steroids, and an impaired immune system. Recently, India has been witnessing a rapid surge in the cases of coronavirus disease-associated mucormycosis (CAM), since the second wave of COVID-19. The devastating and lethal implications of CAM had now become a matter of global attention. A delayed diagnosis is often associated with a poor prognosis. Therefore, the rapid and early diagnosis of infection would be life-saving. Prevention and effective management of mucormycosis depend upon its early and accurate diagnosis followed by a multimodal therapeutic approach. The current review summarizes an array of detection methods and highlights certain evolving technologies for early and rapid diagnosis of CAM. Furthermore, several potential management strategies have also been discussed, which would aid in tackling the neglected yet fatal crisis of mucormycosis associated with COVID-19.}, keywords = {Biosensors, COVID-19, Diagnostics, Mucormycosis, Probiotics}, issn = {2190-572X}, doi = {10.1007/s13205-021-03080-4}, author = {Samson, Rachel and Dharne, Mahesh} } @article {48236, title = {Machine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys}, journal = {Computers in Biology and Medicine}, volume = {146}, year = {2022}, month = {JUL}, pages = {105419}, type = {Article}, abstract = {

Data science has been an invaluable part of the COVID-19 pandemic response with multiple applications, ranging from tracking viral evolution to understanding the vaccine effectiveness. Asymptomatic breakthrough infections have been a major problem in assessing vaccine effectiveness in populations globally. Serological discrimination of vaccine response from infection has so far been limited to Spike protein vaccines since whole virion vaccines generate antibodies against all the viral proteins. Here, we show how a statistical and machine learning (ML) based approach can be used to discriminate between SARS-CoV-2 infection and immune response to an inactivated whole virion vaccine (BBV152, Covaxin). For this, we assessed serial data on antibodies against Spike and Nucleocapsid antigens, along with age, sex, number of doses taken, and days since last dose, for 1823 Covaxin recipients. An ensemble ML model, incorporating a consensus clustering approach alongside the support vector machine model, was built on 1063 samples where reliable qualifying data existed, and then applied to the entire dataset. Of 1448 self-reported negative subjects, our ensemble ML model classified 724 to be infected. For method validation, we determined the relative ability of a random subset of samples to neutralize Delta versus wild-type strain using a surrogate neutralization assay. We worked on the premise that antibodies generated by a whole virion vaccine would neutralize wild type more efficiently than delta strain. In 100 of 156 samples, where ML prediction differed from self-reported uninfected status, neutralization against Delta strain was more effective, indicating infection. We found 71.8\% subjects predicted to be infected during the surge, which is concordant with the percentage of sequences classified as Delta (75.6\%-80.2\%) over the same period. Our approach will help in real-world vaccine effectiveness assessments where whole virion vaccines are commonly used.

}, keywords = {BBV152, Covaxin, COVID-19, Ensemble methods, Infection, machine learning, SARS-CoV-2}, issn = {0010-4825}, doi = {10.1016/j.compbiomed.2022.105419}, author = {Singh, Prateek and Ujjainiya, Rajat and Prakash, Satyartha and Naushin, Salwa and Sardana, Viren and Bhatheja, Nitin and Singh, Ajay Pratap and Barman, Joydeb and Kumar, Kartik and Gayali, Saurabh and Khan, Raju and Rawat, Birendra Singh and Tallapaka, Karthik Bharadwaj and Anumalla, Mahesh and Lahiri, Amit and Kar, Susanta and Bhosale, Vivek and Srivastava, Mrigank and Mugale, Madhav Nilakanth and Pandey, C. P. and Khan, Shaziya and Katiyar, Shivani and Raj, Desh and Ishteyaque, Sharmeen and Khanka, Sonu and Rani, Ankita and Promila and Sharma, Jyotsna and Seth, Anuradha and Dutta, Mukul and Saurabh, Nishant and Veerapandian, Murugan and Venkatachalam, Ganesh and Bansal, Deepak and Gupta, Dinesh and Halami, Prakash M. and Peddha, Muthukumar Serva and Veeranna, Ravindra P. and Pal, Anirban and Singh, Ranvijay Kumar and Anandasadagopan, Suresh Kumar and Karuppanan, Parimala and Rahman, Syed Nasar and Selvakumar, Gopika and Venkatesan, Subramanian and Karmakar, Malay Kumar and Sardana, Harish Kumar and Kothari, Anamika and Parihar, Devendra Singh and Thakur, Anupma and Saifi, Anas and Gupta, Naman and Singh, Yogita and Reddu, Ritu and Gautam, Rizul and Mishra, Anuj and Mishra, Avinash and Gogeri, Iranna and Rayasam, Geethavani and Padwad, Yogendra and Patial, Vikram and Hallan, Vipin and Singh, Damanpreet and Tirpude, Narendra and Chakrabarti, Partha and Maity, Sujay Krishna and Ganguly, Dipyaman and Sistla, Ramakrishna and Balthu, Narender Kumar and Kumar, Kiran A. and Ranjith, Siva and Kumar, B. Vijay and Jamwal, Piyush Singh and Wali, Anshu and Ahmed, Sajad and Chouhan, Rekha and Gandhi, Sumit G. and Sharma, Nancy and Rai, Garima and Irshad, Faisal and Jamwal, Vijay Lakshmi and Paddar, Masroor Ahmad and Khan, Sameer Ullah and Malik, Fayaz and Ghosh, Debashish and Thakkar, Ghanshyam and Barik, S. K. and Tripathi, Prabhanshu and Satija, Yatendra Kumar and Mohanty, Sneha and Khan, Md Tauseef and Subudhi, Umakanta and Sen, Pradip and Kumar, Rashmi and Bhardwaj, Anshu and Gupta, Pawan and Sharma, Deepak and Tuli, Amit and Chaudhuri, Saumya Ray and Krishnamurthi, Srinivasan and Prakash, L. and Rao, V. Ch and Singh, B. N. and Chaurasiya, Arvindkumar and Chaurasiya, Meera and Bhadange, Mayuri and Likhitkar, Bhagyashree and Mohite, Sharada and Patil, Yogita and Kulkarni, Mahesh and Joshi, Rakesh and Pandya, Vaibhav and Mahajan, Sachin and Patil, Amita and Samson, Rachel and Vare, Tejas and Dharne, Mahesh and Giri, Ashok and Mahajan, Sachin and Paranjape, Shilpa and Sastry, G. Narahari and Kalita, Jatin and Phukan, Tridip and Manna, Prasenjit and Romi, Wahengbam and Bharali, Pankaj and Ozah, Dibyajyoti and Sahu, RaviKumar and Dutta, Prachurjya and Singh, Moirangthem Goutam and Gogoi, Gayatri and Tapadar, Yasmin Begam and Babu, Elapavalooru V. S. S. K. and Sukumaran, Rajeev K. and Nair, Aishwarya R. and Puthiyamadam, Anoop and Valappil, Prajeesh Kooloth and Prasannakumari, Adrash Velayudhan Pillai and Chodankar, Kalpana and Damare, Samir and Agrawal, Ved Varun and Chaudhary, Kumardeep and Agrawal, Anurag and Sengupta, Shantanu and Dash, Debasis} } @article {48127, title = {Metagenomic mining of Indian river confluence reveal functional microbial community with lignocelluloytic potential}, journal = {3 Biotech}, volume = {12}, year = {2022}, month = {JUN}, pages = {132}, type = {Article}, abstract = {

Microbial carbohydrate-active enzymes (CAZyme) can be harnessed for valorization of Lignocellulosic biomass (LCB) to value-added chemicals/products. The two Indian Rivers Ganges and the Yamuna having different origins and flow, face accumulation of carbon-rich substrates due to the discharge of wastewater from adjoining paper and pulp industries, which could potentially contribute to the natural enrichment of LCB utilizing genes, especially at their confluence. We analyzed CAZyme diversity in metagenomic datasets across the sacred confluence of the Rivers Ganges and Yamuna. Functional annotation using CAZyme database identified a total of 77,815 putative genes with functional domains involved in the catalysis of carbohydrate degradation or synthesis of glycosidic bonds. The metagenomic analysis detected similar to 41\% CAZymes catalyzing the hydrolysis of lignocellulosic biomass polymers- cellulose, hemicellulose, lignin, and pectin. The Beta diversity analysis suggested higher CAZyme diversity at downstream region of the river confluence, which could be useful niche for culture-based studies. Taxonomic origin for CAZymes revealed the predominance of bacteria (97\%), followed by archaea (1.67\%), Eukaryota (0.63\%), and viruses (0.7\%). Metagenome guided CAZyme diversity of the microflora spanning across the confluence of Ganges-Yamuna River, could be harnessed for biomass and bioenergy applications.

}, keywords = {CAZymes, Confluence (Sangam), Lignocellulosic, River Ganges, River Yamuna}, issn = {2190-572X}, doi = {10.1007/s13205-022-03190-7}, author = {Rajput, Vinay and Samson, Rachel and Yadav, Rakeshkumar and Dastager, Syed and Khairnar, Krishna and Dharne, Mahesh} } @article {48489, title = {Comparative evaluation of advanced oxidation processes (AOPs) for reducing SARS-CoV-2 viral load from campus sewage water}, journal = {Journal of Environmental Chemical Engineering}, volume = {11}, year = {2023}, month = {JUN}, pages = {109673}, type = {Article}, abstract = {

Presence of SARS-CoV-2 in wastewater is a major concern as the wastewater meets rivers and other water bodies and is used by the population for various purposes. Hence it is very important to treat sewage water in an efficient manner in order to reduce the public health risk. In the present work, various advanced oxidation processes (AOPs) have been evaluated for disinfection of SARS-CoV-2 from sewage water collected from STP inlet of academic institutional residential. The sewage water was subjected to ten AOPs, which include Ozone (O3), Hydrodynamic cavitation (HC), Ultraviolet radiation (UV), and their hybrid combinations like HC/O3, HC/O3/ H2O2, HC/H2O2, O3/UV, UV/H2O2, UV/H2O2/O3, and O3/H2O2 to reduce SARS-CoV-2 viral load. Further, AOP treated sewage water was subjected to total nucleic acid isolation followed by RT-qPCR for viral load estimation. The sewage water treatment techniques were evaluated based on their viral concentration-reducing efficiency. It was found that ozone and ozone-coupled hybrid AOPs showed the most promising result with more than 98 \% SARS-CoV-2 viral load reducing efficiency from sewage water. Interestingly, the best six AOPs used in this study significantly reduced both the SARS-CoV-2 and PMMoV (faecal indicator) viral load and improved water quality in terms of increasing DO and decreasing TOC.

}, keywords = {AOPs and hybrid AOPs, Hydrodynamic cavitation, Ozonation, PMMoV, SARS-CoV-2, Sewage water treatment}, issn = {2213-2929}, doi = {10.1016/j.jece.2023.109673}, author = {Pramanik, Rinka and Bodawar, Narendra and Brahme, Aashay and Kamble, Sanjay and Dharne, Mahesh} } @article {48995, title = {Genomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India}, journal = {Environmental Science and Pollution Research }, volume = {30}, year = {2023}, month = {DEC}, pages = {118976-118988}, type = {Article}, abstract = {

The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods to detect and monitor the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool for proactive analysis and quantification of infectious pathogens within a population before clinical cases emerge. In the present study, we aimed to assess the trend and dynamics of SARS-CoV-2 variants using a longitudinal approach. Our objective included early detection and monitoring of these variants to enhance our understanding of their prevalence and potential impact. To achieve our goals, we conducted real-time quantitative polymerase chain reaction (RT-qPCR) and Illumina sequencing on 442 wastewater (WW) samples collected from 10 sewage treatment plants (STPs) in Pune city, India, spanning from November 2021 to April 2022. Our comprehensive analysis identified 426 distinct lineages representing 17 highly transmissible variants of SARS-CoV-2. Notably, fragments of Omicron variant were detected in WW samples prior to its first clinical detection in Botswana. Furthermore, we observed highly contagious sub-lineages of the Omicron variant, including BA.1 (similar to 28\%), BA.1.X (1.0-72\%), BA.2 (1.0-18\%), BA.2.X (1.0-97.4\%) BA.2.12 (0.8-0.25\%), BA.2.38 (0.8-1.0\%), BA.2.75 (0.01-0.02\%), BA.3 (0.09-6.3\%), BA.4 (0.24-0.29\%), and XBB (0.01-21.83\%), with varying prevalence rates. Overall, the present study demonstrated the practicality of WBE in the early detection of SARS-CoV-2 variants, which could help track future outbreaks of SARS-CoV-2. Such approaches could be implicated in monitoring infectious agents before they appear in clinical cases.

}, keywords = {Bioinformatics pipeline, COVID-19, Early warning, India, Next-generation sequencing, Omicron, Public health, SARS-CoV-2, wastewater, Wastewater-based epidemiology}, issn = {0944-1344}, doi = {10.1007/s11356-023-30709-z}, author = {Rajput, Vinay and Pramanik, Rinka and Malik, Vinita and Yadav, Rakeshkumar and Samson, Rachel and Kadam, Pradnya and Bhalerao, Unnati and Tupekar, Manisha and Deshpande, Dipti and Shah, Priyanki and Shashidhara, L. S. and Boargaonkar, Radhika and Patil, Dhawal and Kale, Saurabh and Bhalerao, Asim and Jain, Nidhi and Kamble, Sanjay and Dastager, Syed and Karmodiya, Krishanpal and Dharne, Mahesh} } @article {48322, title = {Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India}, journal = {Science of the Total Environment}, volume = {872}, year = {2023}, month = {MAY}, pages = {162125}, type = {Article}, abstract = {

Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequenc-ing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p \< 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic as-sessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.

}, keywords = {Antibiotics (ARGs), Bacteriophages, Heavy metals (MRGs), Metagenomics, Microbiome, River Ganges}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2023.162125}, author = {Samson, Rachel and Rajput, Vinay and Yadav, Rakeshkumar and Shah, Manan and Dastager, Syed and Khairnar, Krishna and Dharne, Mahesh} } @article {48961, title = {Bacteriophages: status quo and emerging trends toward one health approach}, journal = {Science of The Total Environment}, volume = {908}, year = {2024}, month = {JAN}, type = {Review}, abstract = {

The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the {\textquoteleft}{\textquoteleft}One Health{\textquoteright}{\textquoteright} framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft

}, keywords = {Antimicrobial resistance (AMR), Bacteriophages, One-health, Therapeutics commercialization}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2023.168461}, author = {Samson, Rachel and Dharne, Mahesh and Khairnar, Krishna} } @article {49455, title = {Early detection of KP.2 SARS-CoV-2 variant using wastewater-based genomic surveillance in Pune, Maharashtra, India}, journal = {Journal of Travel Medicine}, year = {2024}, month = {JUL}, type = {Article}, doi = {https://doi.org/10.1093/jtm/taae097}, author = {Rajput, Vinay and Das, Rashmita and Pramanik, Rinka and Nannaware, Kiran and Sushma, Y. and Taji, Nyabom and Rajput, Vishal and Rajkhowa, Riyakshi and Pacharne, Poonam and Shah, Priyanki and Gogate, Niharika and Sangwar, Poornima and Bhalerao, Asim and Jain, Nidhi and Kamble, Sanjay and Dastager, Syed and Shashidhara, L. S. and Karyakarte, Rajesh and Dharne, Mahesh} } @article {49049, title = {Utility of metagenomics for bioremediation: a comprehensive review on bioremediation mechanisms and microbial dynamics of river ecosystem}, journal = {Environmental Science and Pollution Research}, volume = {31}, year = {2024}, month = {MAR}, pages = {18422-18434}, type = {Review}, abstract = {

Global industrialization has contributed substantial amounts of chemical pollutants in rivers, resulting in an uninhabitable state and impacting different life forms. Moreover, water macrophytes, such as water hyacinths, are abundantly present in polluted rivers, significantly affecting the overall water biogeochemistry. Bioremediation involves utilizing microbial metabolic machinery and is one of the most viable approaches for removing toxic pollutants. Conventional techniques generate limited information on the indigenous microbial population and their xenobiotic metabolism, failing the bioremediation process. Metagenomics can overcome these limitations by providing in-depth details of microbial taxa and functionality-related information required for successful biostimulation and augmentation. An in-depth summary of the findings related to pollutant metabolizing genes and enzymes in rivers still needs to be collated. The present study details bioremediation genes and enzymes functionally mined from polluted river ecosystems worldwide using a metagenomic approach. Several studies reported a wide variety of pollutant-degrading enzymes involved in the metabolism of dyes, plastics, persistent organic pollutants, and aromatic hydrocarbons. Additionally, few studies also noted a shift in the microbiome of the rivers upon exposure to contaminants, crucially affecting the ecological determinant processes. Furthermore, minimal studies have focused on the role of water-hyacinth-associated microbes in the bioremediation potentials, suggesting the need for the bioprospecting of these lesser-studied microbes. Overall, our study summarizes the prospects and utilities of the metagenomic approach and proposes the need to employ it for efficient bioremediation.

}, keywords = {Bioremediation, Metagenomics, Rivers, Water hyacinth, Xenobiotic}, issn = {0944-1344}, doi = {10.1007/s11356-024-32373-3}, author = {Yadav, Rakeshkumar and Dharne, Mahesh} } @article {49548, title = {Characterization of novel phages KPAФ1, KP149Ф1, and KP149Ф2 for lytic efficiency against clinical MDR Klebsiella pneumoniae infections}, journal = {Microbial Pathogenesis}, volume = {202}, year = {2025}, month = {MAY}, pages = {107440}, type = {Article}, abstract = {

Phage therapy offers a promising approach to the increasing antimicrobial resistance of Klebsiella pneumoniae. This study highlights three novel lytic bacteriophages-KPAc1, KP149c1, and KP149c2-targeting multidrugresistant (MDR) K. pneumoniae. These phages belong to the Myoviridae and Podoviridae family and demonstrate their efficacy and stability across a wide range of temperatures (up to 60 degrees C) and pH levels (pH 4 to 11). Genomic analysis reveals that they are free from virulence, toxicity, and antimicrobial resistance genes, making them promising candidates for therapeutic use. Among these phages, KPAc1 showed the highest lytic activity with a 26.15\% lysis against MDR K. pneumoniae isolates. Additionally, a phage cocktail comprising all three phages improved lytic efficacy to 32.30\%. This study also examined the antimicrobial resistance profiles of K. pneumoniae isolates, emphasizing the critical need for alternative treatments. By effectively targeting resistant strains, these phages offer a potential candidacy to be used as a viable alternative or a complementary antimicrobial agent to traditional antibiotics, opening up the possibility for advanced phage-based therapies. The promising results from this study pave the way for developing new treatments that could significantly improve patient care and outcomes from the growing issue of resistant bacterial infections.

}, keywords = {Antimicrobial resistance, Bacteriophage, MDR-Klebsiella pneumoniae, Phage cocktail, Phage therapy}, issn = {0882-4010}, doi = {10.1016/j.micpath.2025.107440}, author = {Dandekar, Shraddha S. and Thanikkal, Sinta and Londhe, Arti and Bhutada, Pankhudi and Saha, Ujjayni and Pawar, Shubhankar and Samson, Rachel and Dharne, Mahesh and Saroj, Sunil D. and Koratkar, Santosh} } @article {49521, title = {Genome mining, probiotic characteristics, and in-silico safety assessment of Limosilactobacillus fermentum AV7 isolated from Avocado fruit pulp}, journal = {LWT-Food Science and Technology}, volume = {216}, year = {2025}, month = {JAN}, pages = {117231}, type = {Article}, abstract = {

Limosilactobacillus fermentum holds substantial promise for probiotic applications in human health and various industries. Herein, we present the first report of L. fermentum AV7 isolated from the avocado pulp and assessed for its probiotic potentials and safety through probiogenomic analyses and In-vitro probiotic assays. The genomic insights revealed genes associated with acid and bile tolerance and antimicrobial peptide production, highlighting the probiotic potential of the strain AV7. Notably, the in-silico safety analysis showed that the genome of L.fermentum AV7 is devoid of plasmid and lacks any putative antibiotic resistance or pathogenic traits, ensuring its safety for human consumption. Beyond the genomic and in-silico analysis, we also aimed to evaluate the probiotic potentials of AV7 strain using in- vitro tests for acid, gastric juice, intestinal fluid and bile tolerance, resilience to osmotic stress, followed by auto-aggregation and co-aggregation assays with Escherichia coli ATCC 8739. The data obtained through in-vitro studies confirmed the efficacy of L.fermentum AV7 as a probiotic strain, and positions it as a potent probiotic candidate, expanding the scope of probiotic research. Our study investigates avocados, a nutrient-dense fruit, as a novel source of beneficial lactic acid bacteria, thereby attracting innovative dietary and therapeutic applications. By introducing L .fermentum AV7 into the probiotic landscape, we pave the way for new health benefits from this beloved fruit. The research not only adds a new dimension to avocado utilization but also contributes to the relatively unexplored field of isolating beneficial bacteria from avocados, promising exciting advancements in human health.

}, issn = {0023-6438}, doi = {10.1016/j.lwt.2024.117231}, author = {Mahajan, Vaishnavi and Samson, Rachel and Dharne, Mahesh} } @article {49583, title = {Monitoring influenza A (H1N1, H3N2), RSV, and SARS-CoV-2 using wastewater-based epidemiology: A 2-year longitudinal study in an Indian megacity covering omicron and post-omicron phases}, journal = {Food and Environmental Virology}, volume = {17}, year = {2025}, month = {MAR}, pages = {3}, type = {Article}, abstract = {

{The bourgeoning field of wastewater-based epidemiology (WBE) for the surveillance of several respiratory viruses which includes Influenza A, H1N1pdm09, H3N2, respiratory syncytial viruses (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of interest for public health concerns. However, there are few long-term monitoring studies globally. In this study, respiratory viruses were detected and quantified from 11 sewer sheds by utilizing reverse transcription-quantitative polymerase chain reaction analysis in Pune city, India, from Jan 2022 to Dec 2023. The RNA fragments of respiratory viruses were detected in sewage samples before clinical cases were reported, underscoring the potential of WBE for early detection and monitoring within the population. The Spearman correlation of wastewater viral copies was positively and significantly correlated with the clinically positive case of H1N1pdm09 (rho = 0.55

}, keywords = {Influenza A, Quantitative reverse transcription-PCR, Respiratory viruses, SARS-CoV-2, Wastewater-based epidemiology}, issn = {1867-0334}, doi = {10.1007/s12560-024-09618-y}, author = {Pramanik, Rinka and Nannaware, Kiran and Malik, Vinita and Shah, Priyanki and Sangewar, Poornima and Gogate, Niharika and Shashidhara, L. S. and Boargaonkar, Radhika and Patil, Dhawal and Kale, Saurabh and Bhalerao, Asim and Jain, Nidhi and Kamble, Sanjay and Dastager, Syed and Dharne, Mahesh} }