02605nas a2200265   4500008004100000245008000041210006900121260001200190300001200202490000700214520178100221653002302002653000902025653002402034653001702058100002102075700001802096700001902114700002302133700001902156700001902175700002002194700001902214856010602233       2017                        eng d00aMultilocus sequence typing of Ochrobactrum spp. isolated from gastric niche0 aMultilocus sequence typing of Ochrobactrum spp isolated from gas  cMAR-APR  a201-2100 v103 aThe 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.10aHelicobater Pyroli10aMLST10aNon-Ulcer Dyspepsia10aOchrobactrum1 aKulkarni, Girish1 aGohil, Kushal1 aMisra, Vatsala1 aKakrani, Arjun, L.1 aMisra, Sri, P.1 aPatole, Milind1 aShouche, Yogesh1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/multilocus-sequence-typing-ochrobactrum-spp-isolated-gastric-niche01815nas a2200169   4500008004100000245015000041210006900191260000800260300001200268490000700280520116000287100002501447700001601472700001801488700001901506856012001525       2018                        eng d00aDephytinizing and probiotic potentials of saccharomyces cerevisiae (NCIM 3662) strain for amelioration of nutritional quality of functional foods0 aDephytinizing and probiotic potentials of saccharomyces cerevisi  cMAR  a604-6170 v113 aIncrease 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.1 aPuppala, Kumar, Raja1 aKumar, Ravi1 aKhire, Jayant1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/dephytinizing-and-probiotic-potentials-saccharomyces-cerevisiae-ncim-3662-strain02137nas a2200193   4500008004100000245013500041210006900176260000800245490000700253520142000260100002501680700001701705700001801722700001901740700001601759700001801775700001901793856013101812       2018                        eng d00aEvaluation of Candida tropicalis (NCIM 3321) extracellular phytase having plant growth promoting potential and process development0 aEvaluation of Candida tropicalis NCIM 3321 extracellular phytase  cJAN0 v133 a<p>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⁻¹) and by five folds (from 0.46 to 1.95 IU ml⁻¹) 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⁻¹day⁻¹) and extracellular phytase (6.08 IU ml⁻¹ day⁻¹). 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.</p>1 aPuppala, Kumar, Raja1 aNaik, Tejali1 aShaik, Alfina1 aDastager, Syed1 aKumar, Ravi1 aKhire, Jayant1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/evaluation-candida-tropicalis-ncim-3321-extracellular-phytase-having-plant-growth-promoting01784nas a2200265   4500008004100000022001400041245008000055210006900135260000800204300001000212490000800222520100100230653000601231653000601237653001701243653001801260653001801278653001601296653001801312100001801330700001701348700001901365700002501384856010901409       2018                        eng d  a0960-852400aMixed bacterial culture mediated direct conversion of bio-glycerol to diols0 aMixed bacterial culture mediated direct conversion of bioglycero  cFEB  a86-930 v2503 a<p>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.</p>10a110a210a3-Butanediol10a3-Propanediol10aBioconversion10aBioglycerol10aMixed culture1 aParate, Roopa1 aMane, Rasika1 aDharne, Mahesh1 aRode, Chandrashekhar  uhttps://library.ncl.res.in/content/mixed-bacterial-culture-mediated-direct-conversion-bio-glycerol-diols01129nas a2200229   4500008004100000245012400041210006900165260000800234520028600242100001500528700002500543700001600568700002700584700002200611700001900633700001900652700002300671700001800694700003100712700002400743856013200767       2019                        eng d00aDraft genome sequence of freshwater-derived streptomyces sp. strain BPSDS2, isolated from damte stream, northeast India0 aDraft genome sequence of freshwaterderived streptomyces sp strai  cOCT3 a<p>We report the draft genome sequence of <span class="named-content genus-species" id="named-content-2">Streptomyces</span> 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.</p>
1 aZothanpuia1 aPassari, Ajit, Kumar1 aDeka, Vinay1 aRajput, Lakshmi, P. M.1 aPriya, Purbajyoti1 aDharne, Mahesh1 aDastager, Syed1 aMathew, Oommen, K.1 aHashem, Abeer1 aAllah, Elsayed, Fathi Abd_1 aSingh, Bhim, Pratap  uhttps://library.ncl.res.in/content/draft-genome-sequence-freshwater-derived-streptomyces-sp-strain-bpsds2-isolated-damte-stream02667nas a2200253   4500008004100000022001400041245013800055210006900193260000900262300001100271490000800282520178300290653002602073653001702099653002202116653002302138653002002161100002302181700001802204700001802222700002202240700001902262856013202281       2020                        eng d  a0147-651300aComprehensive metagenomic insights into a unique mass gathering and bathing event reveals transient influence on a riverine ecosystem0 aComprehensive metagenomic insights into a unique mass gathering   cOCT   a1109380 v2023 a<p>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'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.</p>
10aAntibiotic resistance10aMass bathing10aMinION sequencing10aPriority pathogens10aVirulence genes1 aYadav, Rakeshkumar1 aRajput, Vinay1 aGohil, Kushal1 aKhairnar, Krishna1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/comprehensive-metagenomic-insights-unique-mass-gathering-and-bathing-event-reveals-transient02447nas a2200301   4500008004100000022001400041245017500055210006900230260000800299300001100307490000800318520142700326653002301753653000901776653002401785653002401809653001501833653000901848100002201857700002301879700001601902700001801918700002101936700002001957700001901977700001901996856013002015       2020                        eng d  a1470-160X00aMetagenome sequencing to unveil microbial community composition and prevalence of antibiotic and metal resistance genes in hypersaline and hyperalkaline Lonar Lake, India0 aMetagenome sequencing to unveil microbial community composition   cMAR  a1058270 v1103 a<p>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.</p>10aArchaeal diversity10aARGs10aBacterial diversity10aIllumina sequencing10aLonar lake10aMRGs1 aChakraborty, Jaya1 aSapkale, Vibhavari1 aShah, Manan1 aRajput, Vinay1 aMehetre, Gajanan1 aAgawane, Sachin1 aKamble, Sanjay1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/metagenome-sequencing-unveil-microbial-community-composition-and-prevalence-antibiotic-and02632nas a2200241   4500008004100000022001400041245012900055210006900184260000800253300001400261490000800275520178200283653002602065653003202091653003902123653001502162653001102177653002202188100001802210700001802228700001902246856012502265       2020                        eng d  a0888-754300aPan-genomics of Ochrobactrum species from clinical and environmental origins reveals distinct populations and possible links0 aPangenomics of Ochrobactrum species from clinical and environmen  cSEP  a3003-30120 v1123 a<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>
10aAntibiotic resistance10aAverage nucleotide identity10aClinical and environmental strains10aCore genes10aMinION10aVirulence factors1 aGohil, Kushal1 aRajput, Vinay1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/pan-genomics-ochrobactrum-species-clinical-and-environmental-origins-reveals-distinct02375nas a2200277   4500008004100000022001400041245012200055210006900177260000800246300001100254490000800265520149800273653000901771653001401780653001501794653000901809653000901818653002401827100002201851700002301873700001801896700001601914700001901930700001901949856012901968       2020                        eng d  a0147-651300aShotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India0 aShotgun metagenome guided exploration of anthropogenically drive  cMAY  a1104430 v1943 a<p>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.</p>
10aARGs10adiversity10aLonar lake10aMGEs10aMRGs10aNanopore sequencing1 aChakraborty, Jaya1 aSapkale, Vibhavari1 aRajput, Vinay1 aShah, Manan1 aKamble, Sanjay1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/shotgun-metagenome-guided-exploration-anthropogenically-driven-resistomic-hotspots-within02064nas a2200265   4500008004100000022001400041245011200055210006900167260000800236300001400244490000700258520120900265653000601474653001701480653001701497653002101514653001301535653001301548653002701561100001801588700002001606700001901626700002501645856012801670       2021                        eng d  a0268-257500aBioglycerol (C3) upgrading to 2,3-butanediol (C4) by cell-free extracts of Enterobacter aerogenes NCIM 26950 aBioglycerol C3 upgrading to 23butanediol C4 by cellfree extracts  cMAY  a1316-13250 v963 a<p>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 `Circular Economy' 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.</p>
10a210a3-Butanediol10aatom economy10acircular economy10aE factor10aGlycerol10aglycerol dehydrogenase1 aParate, Roopa1 aBorgave, Mrunal1 aDharne, Mahesh1 aRode, Chandrashekhar  uhttps://library.ncl.res.in/content/bioglycerol-c3-upgrading-23-butanediol-c4-cell-free-extracts-enterobacter-aerogenes-ncim02623nas a2200229   4500008004100000022001400041245012800055210006900183260000800252300001100260490000800271520184300279653001302122653001902135653001102154653002002165653001602185100002302201700001802224700001902242856013202261       2021                        eng d  a0013-935100aFunctional metagenomic landscape of polluted river reveals potential genes involved in degradation of xenobiotic pollutants0 aFunctional metagenomic landscape of polluted river reveals poten  cJAN  a1103320 v1923 a<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>
10aBenzoate10aBioremediation10aMinION10aRiverine system10aXenobiotics1 aYadav, Rakeshkumar1 aRajput, Vinay1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/functional-metagenomic-landscape-polluted-river-reveals-potential-genes-involved-degradation02765nas a2200229   4500008004100000022001400041245014100055210006900196260000900265300001100274490000800285520195600293653002202249653001502271653002002286653001702306653002202323100002302345700001802368700001902386856013002405       2021                        eng d  a0048-969700aMetagenomic analysis of a mega-city river network reveals microbial compositional heterogeneity among urban and peri-urban river stretch0 aMetagenomic analysis of a megacity river network reveals microbi  cAUG   a1469600 v7833 a<p>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's t-test, p &lt; 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's t-test p-value &lt;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.</p>10aIndustrialisation10aPeri-urban10aRiverine system10aUrbanisation10aVirulence factors1 aYadav, Rakeshkumar1 aRajput, Vinay1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/metagenomic-analysis-mega-city-river-network-reveals-microbial-compositional-heterogeneity01942nas a2200229   4500008004100000022001400041245008000055210006900135260000800204490000700212520122900219653001501448653001301463653001801476653001501494653003201509100001801541700001901559700001901578700001901597856009601616       2021                        eng d  a2190-572X00aProbiotics in the prophylaxis of COVID-19: something is better than nothing0 aProbiotics in the prophylaxis of COVID19 something is better tha  cJAN0 v113 a<p>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.</p>
10aAnti-viral10aCOVID-1910aGut-lung axis10aProbiotics10aRespiratory tract infection1 aGohil, Kushal1 aSamson, Rachel1 aDastager, Syed1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/probiotics-prophylaxis-covid-19-something-better-nothing02589nas a2200181   4500008004100000245014500041210006900186260000800255300001100263490000800274520189200282100002202174700001802196700002302214700001902237700001902256856013202275       2021                        eng d00aSpatio-temporal resolution of taxonomic and functional microbiome of Lonar soda lake of India reveals metabolic potential for bioremediation0 aSpatiotemporal resolution of taxonomic and functional microbiome  cFEB  a1285740 v2643 a<p><span style="color: rgb(33, 33, 33); font-family: BlinkMacSystemFont, -apple-system, &quot;Segoe UI&quot;, Roboto, Oxygen, Ubuntu, Cantarell, &quot;Fira Sans&quot;, &quot;Droid Sans&quot;, &quot;Helvetica Neue&quot;, sans-serif; font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400;">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.</span></p>1 aChakraborty, Jaya1 aRajput, Vinay1 aSapkale, Vibhavari1 aKamble, Sanjay1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/spatio-temporal-resolution-taxonomic-and-functional-microbiome-lonar-soda-lake-india-reveals02228nas a2200241   4500008004100000022001400041245011300055210006900168260000800237300001600245490000700261520141800268653001701686653001801703653001501721653001601736653001501752100002601767700002301793700001901816700001901835856013201854       2021                        eng d  a0944-134400aTranslating SARS-CoV-2 wastewater-based epidemiology for prioritizing mass vaccination: a strategic overview0 aTranslating SARSCoV2 wastewaterbased epidemiology for prioritizi  cAUG  a42975-429800 v283 aThe 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.10aEpidemiology10aPolicy making10aSARS-CoV-210aVaccination10awastewater1 aDharmadhikari, Tanmay1 aYadav, Rakeshkumar1 aDastager, Syed1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/translating-sars-cov-2-wastewater-based-epidemiology-prioritizing-mass-vaccination-strategic01919nas a2200217   4500008004100000022001400041245009000055210006900145260000800214300000600222490000700228520123200235653001501467653001301482653001601495653001701511653001501528100001901543700001901562856012001581       2022                        eng d  a2190-572X00aCOVID-19 associated mucormycosis: evolving technologies for early and rapid diagnosis0 aCOVID19 associated mucormycosis evolving technologies for early   cJAN  a60 v123 aThe post-coronavirus disease (COVID-19) mucormycosis is a deadly addition to the pandemic spectrum. Although it'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-19.10aBiosensors10aCOVID-1910aDiagnostics10aMucormycosis10aProbiotics1 aSamson, Rachel1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/covid-19-associated-mucormycosis-evolving-technologies-early-and-rapid-diagnosis07622nas a2201957   4500008004100000022001400041245016800055210006900223260000800292300001100300490000800311520199500319653001102314653001202325653001302337653002102350653001402371653002102385653001502406100001902421700002102440700002302461700001902484700001902503700002002522700002402542700001902566700001802585700002002603700001502623700002702638700003402665700002102699700001702720700001702737700001902754700002402773700003002797700001902827700001802846700002102864700001402885700002502899700001702924700001702941700001202958700002002970700001902990700001703009700002103026700002603047700002603073700001903099700001803118700002403136700003003160700002703190700001703217700002703234700003503261700002503296700002403321700002303345700002803368700002703396700002703423700002103450700002903471700001903500700001603519700001703535700001803552700001603570700001803586700001703604700002003621700001903641700002403660700002103684700001903705700001803724700002203742700002203764700002403786700002603810700002203836700002403858700002803882700002103910700001803931700001703949700002603966700001603992700001704008700001904025700002204044700001804066700001604084700001904100700002704119700002704146700002404173700001704197700002104214700002304235700001804258700002504276700002804301700001904329700002204348700002204370700001604392700001804408700002004426700001704446700001904463700001504482700002704497700003004524700001604554700001204570700001804582700002804600700002204628700002104650700002704671700002004698700001804718700002104736700001804757700002004775700002004795700001704815700001904832700001604851700001904867700001604886700002004902700002204922700002104944700001804965700001904983700002105002700002005023700002005043700002105063700002005084700002205104700003105126700001905157700002705176700003505203700002605238700002405264700002405288700003205312700003905344700002305383700001805406700002405424700002505448700002005473700002305493700001805516856013005534       2022                        eng d  a0010-482500aMachine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys0 aMachine learningbased approach to determine infection status in   cJUL  a1054190 v1463 a<p>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.</p>
10aBBV15210aCovaxin10aCOVID-1910aEnsemble methods10aInfection10amachine learning10aSARS-CoV-21 aSingh, Prateek1 aUjjainiya, Rajat1 aPrakash, Satyartha1 aNaushin, Salwa1 aSardana, Viren1 aBhatheja, Nitin1 aSingh, Ajay, Pratap1 aBarman, Joydeb1 aKumar, Kartik1 aGayali, Saurabh1 aKhan, Raju1 aRawat, Birendra, Singh1 aTallapaka, Karthik, Bharadwaj1 aAnumalla, Mahesh1 aLahiri, Amit1 aKar, Susanta1 aBhosale, Vivek1 aSrivastava, Mrigank1 aMugale, Madhav, Nilakanth1 aPandey, C., P.1 aKhan, Shaziya1 aKatiyar, Shivani1 aRaj, Desh1 aIshteyaque, Sharmeen1 aKhanka, Sonu1 aRani, Ankita1 aPromila1 aSharma, Jyotsna1 aSeth, Anuradha1 aDutta, Mukul1 aSaurabh, Nishant1 aVeerapandian, Murugan1 aVenkatachalam, Ganesh1 aBansal, Deepak1 aGupta, Dinesh1 aHalami, Prakash, M.1 aPeddha, Muthukumar, Serva1 aVeeranna, Ravindra, P.1 aPal, Anirban1 aSingh, Ranvijay, Kumar1 aAnandasadagopan, Suresh, Kumar1 aKaruppanan, Parimala1 aRahman, Syed, Nasar1 aSelvakumar, Gopika1 aVenkatesan, Subramanian1 aKarmakar, Malay, Kumar1 aSardana, Harish, Kumar1 aKothari, Anamika1 aParihar, Devendra, Singh1 aThakur, Anupma1 aSaifi, Anas1 aGupta, Naman1 aSingh, Yogita1 aReddu, Ritu1 aGautam, Rizul1 aMishra, Anuj1 aMishra, Avinash1 aGogeri, Iranna1 aRayasam, Geethavani1 aPadwad, Yogendra1 aPatial, Vikram1 aHallan, Vipin1 aSingh, Damanpreet1 aTirpude, Narendra1 aChakrabarti, Partha1 aMaity, Sujay, Krishna1 aGanguly, Dipyaman1 aSistla, Ramakrishna1 aBalthu, Narender, Kumar1 aKumar, Kiran, A.1 aRanjith, Siva1 aKumar, Vijay1 aJamwal, Piyush, Singh1 aWali, Anshu1 aAhmed, Sajad1 aChouhan, Rekha1 aGandhi, Sumit, G.1 aSharma, Nancy1 aRai, Garima1 aIrshad, Faisal1 aJamwal, Vijay, Lakshmi1 aPaddar, Masroor, Ahmad1 aKhan, Sameer, Ullah1 aMalik, Fayaz1 aGhosh, Debashish1 aThakkar, Ghanshyam1 aBarik, S., K.1 aTripathi, Prabhanshu1 aSatija, Yatendra, Kumar1 aMohanty, Sneha1 aKhan, Md, Tauseef1 aSubudhi, Umakanta1 aSen, Pradip1 aKumar, Rashmi1 aBhardwaj, Anshu1 aGupta, Pawan1 aSharma, Deepak1 aTuli, Amit1 aChaudhuri, Saumya, Ray1 aKrishnamurthi, Srinivasan1 aPrakash, L.1 aRao, Ch1 aSingh, B., N.1 aChaurasiya, Arvindkumar1 aChaurasiya, Meera1 aBhadange, Mayuri1 aLikhitkar, Bhagyashree1 aMohite, Sharada1 aPatil, Yogita1 aKulkarni, Mahesh1 aJoshi, Rakesh1 aPandya, Vaibhav1 aMahajan, Sachin1 aPatil, Amita1 aSamson, Rachel1 aVare, Tejas1 aDharne, Mahesh1 aGiri, Ashok1 aMahajan, Sachin1 aParanjape, Shilpa1 aSastry, Narahari1 aKalita, Jatin1 aPhukan, Tridip1 aManna, Prasenjit1 aRomi, Wahengbam1 aBharali, Pankaj1 aOzah, Dibyajyoti1 aSahu, RaviKumar1 aDutta, Prachurjya1 aSingh, Moirangthem, Goutam1 aGogoi, Gayatri1 aTapadar, Yasmin, Begam1 aBabu, Elapavalooru, V. S. S. K1 aSukumaran, Rajeev, K.1 aNair, Aishwarya, R.1 aPuthiyamadam, Anoop1 aValappil, Prajeesh, Kooloth1 aPrasannakumari, Adrash, Velayudhan1 aChodankar, Kalpana1 aDamare, Samir1 aAgrawal, Ved, Varun1 aChaudhary, Kumardeep1 aAgrawal, Anurag1 aSengupta, Shantanu1 aDash, Debasis  uhttps://library.ncl.res.in/content/machine-learning-based-approach-determine-infection-status-recipients-bbv152-covaxin-whole02298nas a2200265   4500008004100000022001400041245012000055210006900175260000800244300000800252490000700260520143500267653001201702653002401714653002001738653001701758653001701775100001801792700001901810700002301829700001901852700002201871700001901893856012001912       2022                        eng d  a2190-572X00aMetagenomic mining of Indian river confluence reveal functional microbial community with lignocelluloytic potential0 aMetagenomic mining of Indian river confluence reveal functional   cJUN  a1320 v123 a<p>
	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.</p>
10aCAZymes10aConfluence (Sangam)10aLignocellulosic10aRiver Ganges10aRiver Yamuna1 aRajput, Vinay1 aSamson, Rachel1 aYadav, Rakeshkumar1 aDastager, Syed1 aKhairnar, Krishna1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/metagenomic-mining-indian-river-confluence-reveal-functional-microbial-community02254nas a2200265   4500008004100000022001400041245012600055210006900181260000800250300001100258490000700269520136700276653002501643653002801668653001401696653001001710653001501720653002701735100002001762700002201782700001901804700001901823700001901842856012701861       2023                        eng d  a2213-292900aComparative evaluation of advanced oxidation processes (AOPs) for reducing SARS-CoV-2 viral load from campus sewage water0 aComparative evaluation of advanced oxidation processes AOPs for   cJUN  a1096730 v113 a<p>
	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.</p>
10aAOPs and hybrid AOPs10aHydrodynamic cavitation10aOzonation10aPMMoV10aSARS-CoV-210aSewage water treatment1 aPramanik, Rinka1 aBodawar, Narendra1 aBrahme, Aashay1 aKamble, Sanjay1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/comparative-evaluation-advanced-oxidation-processes-aops-reducing-sars-cov-2-viral-load03254nas a2200493   4500008004100000022001400041245016200055210006900217260000800286300001800294490000700312520171400319653002802033653001302061653001802074653001002092653003102102653001202133653001802145653001502163653001502178653003402193100001802227700002002245700001802265700002302283700001902306700001902325700002102344700002102365700002102386700001902407700002402426700002502450700001802475700001802493700001902511700001602530700001902546700001902565700002602584700001902610856013102629       2023                        eng d  a0944-134400aGenomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India0 aGenomic surveillance reveals early detection and transition of d  cDEC  a118976-1189880 v303 a<p>
	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.</p>
10aBioinformatics pipeline10aCOVID-1910aEarly warning10aIndia10aNext-generation sequencing10aOmicron10aPublic health10aSARS-CoV-210awastewater10aWastewater-based epidemiology1 aRajput, Vinay1 aPramanik, Rinka1 aMalik, Vinita1 aYadav, Rakeshkumar1 aSamson, Rachel1 aKadam, Pradnya1 aBhalerao, Unnati1 aTupekar, Manisha1 aDeshpande, Dipti1 aShah, Priyanki1 aShashidhara, L., S.1 aBoargaonkar, Radhika1 aPatil, Dhawal1 aKale, Saurabh1 aBhalerao, Asim1 aJain, Nidhi1 aKamble, Sanjay1 aDastager, Syed1 aKarmodiya, Krishanpal1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/genomic-surveillance-reveals-early-detection-and-transition-delta-omicron-lineages-sars-cov02808nas a2200289   4500008004100000022001400041245014300055210006900198260000800267300001100275490000800286520184800294653002302142653001902165653002402184653001702208653001502225653001702240100001902257700001802276700002302294700001602317700001902333700002202352700001902374856012502393       2023                        eng d  a0048-969700aSpatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India0 aSpatiotemporal variation of the microbiome and resistome reperto  cMAY  a1621250 v8723 a<p>
	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 &lt; 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.</p>
10aAntibiotics (ARGs)10aBacteriophages10aHeavy metals (MRGs)10aMetagenomics10aMicrobiome10aRiver Ganges1 aSamson, Rachel1 aRajput, Vinay1 aYadav, Rakeshkumar1 aShah, Manan1 aDastager, Syed1 aKhairnar, Krishna1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/spatio-temporal-variation-microbiome-and-resistome-repertoire-along-anthropogenically01816nas a2200205   4500008004100000022001400041245007800055210006900133260000800202490000800210520111600218653003501334653001901369653001501388653003501403100001901438700001901457700002201476856011201498       2024                        eng d  a0048-969700aBacteriophages: status quo and emerging trends toward one health approach0 aBacteriophages status quo and emerging trends toward one health   cJAN0 v9083 a<p>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 ``One Health'' 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</p>
10aAntimicrobial resistance (AMR)10aBacteriophages10aOne-health10aTherapeutics commercialization1 aSamson, Rachel1 aDharne, Mahesh1 aKhairnar, Krishna  uhttps://library.ncl.res.in/content/bacteriophages-status-quo-and-emerging-trends-toward-one-health-approach03345nas a2200253   4500008004100000022001400041245013800055210006900193260000800262520238100270653003102651653002102682653003102703653002302734653001902757653003702776100002702813700002302840700002102863700001902884700002802903700003002931856013002961       2024                        eng d  a1867-130600aDietary supplementation of lactococcus lactis subsp. lactis BIONCL17752 on growth performance, and gut microbiota of broiler chickens0 aDietary supplementation of lactococcus lactis subsp lactis BIONC  cJUN3 a<p>
	The rapid rise of antimicrobial resistance (AMR) is a global concern, being triggered by the overuse or misuse of antibiotics in poultry farming sector. We evaluated Lactococcus lactis subsp. lactis BIONCL17752 strain, and characterized its probiotic potential to endure hostile gastrointestinal conditions. Genome sequencing analysis revealed probiotics traits, and gene clusters involved in bacteriocins, lactococcin A, and sactipeptides production. The absence of genes for antibiotic resistance, virulence, and biogenic amine production indicates the potential of probiotic strain. The BIONCL17752 strain was explored for antibiotic-free feed supplement for growth promotor in broiler chicken. The feed supplemented with 4 x 109 CFU/kg of probiotic strain, in combination with various concentrations of fructooligosaccharides (FOS) 1.0, 2.5, and 5.0 kg/tonne in starter, grower, and finisher diets, respectively. A significant improvement of body weight 152 to 171 g/bird (p &lt; 0.05), and a low feed conversion ratio (FCR) of 1.62, was achieved without using synthetic antibiotics for growth promotion. The results of biochemical, hematological, and histological examinations showed normal features, indicating that the treatment had no harmful effects on the bird's health. Reduced levels of cholesterol, triglycerides, high-density lipoprotein (HDL), and low-density lipoprotein (LDL) in serum are an indication of the health benefits for the treated birds. Microbial community analysis of fecal samples of poultry birds exhibited a higher abundance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, and Fusobacteria. Probiotic treatment resulted in reduced Firmicutes and increased Bacteroidetes (F/B ratio) in the broiler's gut which highlights the benefits of probiotic dietary supplements. Importantly, the probiotic-fed group exhibited a high abundance of carbohydrate-active enzymes (CAZyme) such as glycoside hydrolases (GH), glycoside transferases (GT), and carbohydrate-binding module (CBM) hydrolases which are essential for the degradation of complex sugar molecules. The probiotic potential of the BIONCL17752 strain contributes to broilers' health by positively affecting intestinal microbiota, achieving optimal growth, and lowering mortality, demonstrating the economic benefits of probiotic treatment in organic poultry farming.</p>
10aAntibiotic growth promotor10aBroiler chickens10aFunctional genome analysis10aGrowth performance10aGut microbiota10aLactococcus lactis subsp. lactis1 aNavale, Vishwambar, D.1 aYadav, Rakeshkumar1 aKhilari, Ajinkya1 aDharne, Mahesh1 aShanmugam, Dhanasekaran1 aVamkudoth, Koteswara, Rao  uhttps://library.ncl.res.in/content/dietary-supplementation-lactococcus-lactis-subsp-lactis-bioncl17752-growth-performance-and01051nas a2200313   4500008004100000245011900041210006900160260000800229100001800237700001800255700002000273700002100293700001500314700001700329700001900346700002300365700002100388700001900409700002100428700002200449700001900471700001600490700001900506700001900525700002400544700002300568700001900591856012700610       2024                        eng d00aEarly detection of KP.2 SARS-CoV-2 variant using wastewater-based genomic surveillance in Pune, Maharashtra, India0 aEarly detection of KP2 SARSCoV2 variant using wastewaterbased ge  cJUL1 aRajput, Vinay1 aDas, Rashmita1 aPramanik, Rinka1 aNannaware, Kiran1 aSushma, Y.1 aTaji, Nyabom1 aRajput, Vishal1 aRajkhowa, Riyakshi1 aPacharne, Poonam1 aShah, Priyanki1 aGogate, Niharika1 aSangwar, Poornima1 aBhalerao, Asim1 aJain, Nidhi1 aKamble, Sanjay1 aDastager, Syed1 aShashidhara, L., S.1 aKaryakarte, Rajesh1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/early-detection-kp2-sars-cov-2-variant-using-wastewater-based-genomic-surveillance-pune02128nas a2200241   4500008004100000022001400041245014400055210006900199260000800268300001100276490000800287520128400295653002501579653002201604653002301626653001501649653001701664100001901681700001901700700001901719700001701738856013101755       2024                        eng d  a0304-389400aHarnessing the potential of Achromobacter sp. M1 to remediate heavy metals from wastewater: genomic insights and environmental applications0 aHarnessing the potential of Achromobacter sp M1 to remediate hea  cDEC  a1361250 v4803 a<p>
	Lead, mercury, and cadmium are classified as toxic under the toxic Substances' Priority List by CDC-ATSDR (Center for Disease Control-Agency for Toxic Substances and Disease Registry). This toxic trio is capable of disrupting the one-health harmony due to its human, animal, and environmental hazards. The present study aimed in removing the toxic trio within 24 h using a novel Achromobacter sp. M1. Atomic absorption spectroscopic evaluation for removal efficiency of Pb, Hg, and Cd by M1 was 68.8 +/- 0.9%, 82.7 +/- 1.9%, and 94.9 +/- 1.2 %, respectively, within 24 h. Lab-scale evaluation of strain M1 with wastewater showed the removal of the toxic trio together with the reduction in TSS from 140 to 118 ppm, BOD from 100 to 58 ppm, and COD from 381 to 222 ppm. Furthermore, strain M1 was capable of mitigating heavy metal stress and promoting plant growth, evidenced through chlorophyll, malondialdehyde, and proline estimation, together with the production of indole acetic acid (23.84 mu g/mL), siderophore (85 %), and solubilization of silica (39.66 mu g/mL). Whole genome sequencing revealed an ANI of 89 %, indicating a novel species of Achromobacter genus. A total of 23 putative genes for Cd, Hg, and Pb resistance were identified through genome mining.</p>
10aAchromobacter sp. M110aMetal biosorption10aMetal transporters10aToxic trio10aWhole genome1 aMahale, Mithil1 aSamson, Rachel1 aDharne, Mahesh1 aKodam, Kisan  uhttps://library.ncl.res.in/content/harnessing-potential-achromobacter-sp-m1-remediate-heavy-metals-wastewater-genomic-insights02557nas a2200217   4500008004100000022001400041245014200055210006900197260000800266300001600274490000700290520179300297653001902090653001702109653001102126653001902137653001502156100002302171700001902194856012602213       2024                        eng d  a0944-134400aUtility of metagenomics for bioremediation: a comprehensive review on bioremediation mechanisms and microbial dynamics of river ecosystem0 aUtility of metagenomics for bioremediation a comprehensive revie  cMAR  a18422-184340 v313 a<p>
	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.</p>
10aBioremediation10aMetagenomics10aRivers10aWater hyacinth10aXenobiotic1 aYadav, Rakeshkumar1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/utility-metagenomics-bioremediation-comprehensive-review-bioremediation-mechanisms-and02244nas a2200265   4500008004100000022001400041245014700055210006900202260000800271300001100279490000700290520137700297653001901674653001201693653001301705653001101718653001901729653001101748653001501759100001901774700001701793700002201810700001901832856012701851       2025                        eng d  a2213-292900aCharacterization of a novel Tequatrovirus phage from pristine stretch of the Ganges River, India, in reducing bacterial load from sewage water0 aCharacterization of a novel Tequatrovirus phage from pristine st  cJUN  a1163150 v133 a<p>
	Effective treatment of wastewater (WW) and its reuse is necessary to meet certain sustainable development goals and a circular economy. Escherichia coli is one of the primary contaminants in the WW, and its extra-intestinal occurrence poses a considerable threat under one health. This study is the first report of a novel broadspectrum phage (&amp; fcy;ERS-1) isolated from a pristine stretch of the Ganges River in the biocontrol of E. coli, resistant to 3rd-and 4th generation cephalosporins and aztreonam. This is the first report of a phage from the Tequatrovirus genus to infect P. aeruginosa. The &amp; fcy;ERS-1 could reduce the abundance of E. coli cells by 8.22 log10 CFU/mL &lt;= 24 hrs. Additionally, phi ERS-1 disrupted the biofilm of E. coli with a reduction of 3.88 log10 CFU/mL. Further, phi ERS-1 could inhibit biofilm by multiple strains of E. coli (ATCC 8739, 25922, 43888) and multiple generaincluding E. coli ATCC 8739, Shigella boydii ATCC 9207, P. aeruginosa (ATCC 9027). The phage phi ERS-1 reduced bacterial counts in raw WW by 2 log10 CFU/mL and 4 log10 CFU/mL reduction in coliform-enriched WW in &lt;= 24 hours. Overall, this study suggests that phi ERS-1 could be used as an effective alternative to be combined with other treatments for improving the quality of WW disposal and environmental health by reducing the bacterial load.</p>
10aAntibiofouling10aBiofilm10aColiform10aGanges10aGreen approach10aPhages10awastewater1 aSamson, Rachel1 aPawar, Ameya1 aKhairnar, Krishna1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/characterization-novel-tequatrovirus-phage-pristine-stretch-ganges-river-india-reducing02494nas a2200313   4500008004100000022001400041245014300055210007200198260000800270300001100278490000800289520141700297653002901714653001801743653003001761653001901791653001801810100002701828700002101855700001701876700002201893700001801915700002201933700001901955700001901974700002101993700002202014856014402036       2025                        eng d  a0882-401000aCharacterization of novel phages KPAФ1, KP149Ф1, and KP149Ф2 for lytic efficiency against clinical MDR Klebsiella pneumoniae infections0 aCharacterization of novel phages KPAФ1 KP149Ф1 and KP149Ф2 for l  cMAY  a1074400 v2023 a<p>
	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.</p>
10aAntimicrobial resistance10aBacteriophage10aMDR-Klebsiella pneumoniae10aPhage cocktail10aPhage therapy1 aDandekar, Shraddha, S.1 aThanikkal, Sinta1 aLondhe, Arti1 aBhutada, Pankhudi1 aSaha, Ujjayni1 aPawar, Shubhankar1 aSamson, Rachel1 aDharne, Mahesh1 aSaroj, Sunil, D.1 aKoratkar, Santosh  uhttps://library.ncl.res.in/content/characterization-novel-phages-kpa%D1%841-kp149%D1%841-and-kp149%D1%842-lytic-efficiency-against-clinical02874nas a2200229   4500008004100000245011900041210006900160260000800229490000700237520206500244653001902309653002302328653001502351653002602366653002302392100001902415700001902434700001902453700002202472700001902494856013102513       2025                        eng d00aDeciphering the comprehensive microbiome of glacier-fed Ganges and functional aspects: implications for one health0 aDeciphering the comprehensive microbiome of glacierfed Ganges an  cAUG0 v133 a<p>
	Glacier-fed rivers are significant ecological components of the river catchments, yet their microbial diversity and the associated antimicrobial potential remain underexplored. The Ganges is a glacier-fed river of immense cultural, religious, and ecological significance that supports over 400 million people downstream, providing essential water for agriculture, industry, and daily use. Despite its importance, the microbial community composition and antimicrobial potential, across its relatively pristine origin, remain largely underexplored. One possible explanation for this could be the lower microbial load in the upstream glacier-fed region, which likely results in a reduced DNA yield, insufficient for whole-metagenome sequencing, in contrast to the more biologically diverse and nutrient-rich lower reaches. In this study, we developed an efficient DNA extraction and amplification method using low-input DNA to sequence the microbiome from sediments of the glacier-fed Ganges River in pre-monsoon and post-monsoon over 2 years. Taxonomic and functional diversity of bacterial and viral (phage) communities were analyzed, together with the seasonal variations in their composition. Significant differences in microbial communities were observed in response to seasonal shifts (P &lt; 0.05). During the dry season, Proteobacteria and Actinobacteria were predominant, while Bacteroidetes and Firmicutes were abundant post-monsoon (P &lt; 0.05). The microbiome harbors potential for the biosynthesis of streptomycin, phenylpropanoid, penicillin, and cephalosporins. Bacteriophages from Podoviridae, Myoviridae, and Siphoviridae showed lytic potential against putrefying and pathogenic bacteria. This first comprehensive study on the glacier-fed Ganges River highlights significant seasonal shifts in microbial diversity. The initial insights into the functional profile of the bacterial and phage diversity offer opportunities to explore various natural compounds and enzymes to tackle antimicrobial resistance under the one-health canopy.</p>
10aBacteriophages10aglacier-fed-Ganges10aMicrobiome10aSecondary metabolites10aspecial properties1 aSamson, Rachel1 aKumar, Shubham1 aDastager, Syed1 aKhairnar, Krishna1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/deciphering-comprehensive-microbiome-glacier-fed-ganges-and-functional-aspects-implications03415nas a2200193   4500008004100000245018700041210007000228260000800298300001100306490000700317520263500324100002302959700002102982700002003003700002303023700001703046700001903063856013903082       2025                        eng d00aGenome mining of carbohydrate-active enzymes (CAZyme) and poly-γ-glutamic acid (γ-PGA) synthesis by Bacillus velezensis (WA11) directly from lignocellulosic biomass-based substrate0 aGenome mining of carbohydrateactive enzymes CAZyme and polyγglut  cNOV  a1037470 v693 a<p>
	<span style="color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, &quot;Times New Roman&quot;, Times, STIXGeneral, &quot;Cambria Math&quot;, &quot;Lucida Sans Unicode&quot;, &quot;Microsoft Sans Serif&quot;, &quot;Segoe UI Symbol&quot;, &quot;Arial Unicode MS&quot;, serif, sans-serif; font-size: 16px;">Poly-γ-glutamic acid (γ-PGA/PGA), a non-toxic and biodegradable polymer with additional diverse properties such as higher heat resistance and water retention, is widely implicated in myriad applications, including agricultural and food processing, medical treatments, and cosmetics. The industrial bio-based production of γ-PGA is primarily hindered by the potential of microbial strains and substrate costs, which are attributed primarily to the carbon sources. The present study is a proof-of-concept study, wherein a bacterial isolate,&nbsp;</span><em style="box-sizing: border-box; margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, &quot;Times New Roman&quot;, Times, STIXGeneral, &quot;Cambria Math&quot;, &quot;Lucida Sans Unicode&quot;, &quot;Microsoft Sans Serif&quot;, &quot;Segoe UI Symbol&quot;, &quot;Arial Unicode MS&quot;, serif, sans-serif; font-size: 16px;">Bacillus velezensis</em><span style="color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, &quot;Times New Roman&quot;, Times, STIXGeneral, &quot;Cambria Math&quot;, &quot;Lucida Sans Unicode&quot;, &quot;Microsoft Sans Serif&quot;, &quot;Segoe UI Symbol&quot;, &quot;Arial Unicode MS&quot;, serif, sans-serif; font-size: 16px;">&nbsp;WA11 strain, was employed for the production of γ-PGA from sugarcane bagasse (lignocellulosic biomass) without any pretreatment or pre-processing. The CAZyme annotation identified several enzyme families involved in metabolizing complex polysaccharides, including cellulose, xylan, and lignin. We obtained 104.3&nbsp;g/L γ-PGA production with a productivity of 1.09&nbsp;g/L/h in the optimized synthetic medium containing maltose as a carbon source, 2.9-fold higher than the earlier study using maltose as a carbon source. Further, substituting maltose with untreated sugarcane bagasse resulted in 12&nbsp;g/L of γ-PGA, higher than most of the reported studies utilizing pretreated lignocellulosic biomass (LCB) lysates for producing γ-PGA. The present study demonstrates the production of γ-PGA using lignocellulosic biomass without pretreatment, providing a chemical-free, sustainable avenue for directly utilizing untreated lignocellulosic biomass (LCB) to produce expensive polymers by employing potential bacterial strains.</span></p>
1 aYadav, Rakeshkumar1 aAwathare, Pranay1 aShitut, Pushkar1 aMahajan, Vaishnavi1 aNair, Pranav1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/genome-mining-carbohydrate-active-enzymes-cazyme-and-poly-%CE%B3-glutamic-acid-%CE%B3-pga-synthesis02417nas a2200169   4500008004100000022001400041245014800055210006900203260000800272300001100280490000800291520175900299100002302058700001902081700001902100856012802119       2025                        eng d  a0023-643800aGenome mining, probiotic characteristics, and in-silico safety assessment of Limosilactobacillus fermentum AV7 isolated from Avocado fruit pulp0 aGenome mining probiotic characteristics and insilico safety asse  cJAN  a1172310 v2163 a<p>
	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.</p>
1 aMahajan, Vaishnavi1 aSamson, Rachel1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/genome-mining-probiotic-characteristics-and-silico-safety-assessment-limosilactobacillus02600nas a2200289   4500008004100000245015500041210006900196260000800265300001400273490000600287520161600293100002001909700001801929700001801947700002101965700001701986700001502003700001902018700001902037700002502056700001902081700002002100700001902120700002602139700001902165856012602184       2025                        eng d00aLong-term genomic surveillance of SARS-CoV-2 in campus wastewater depicts lineage trends and public health implications during and after omicron waves0 aLongterm genomic surveillance of SARSCoV2 in campus wastewater d  cJUN  a908–9190 v33 a<p>
	<span style="color: rgb(21, 21, 21); font-family: Roboto, arial, sans-serif; font-size: 16px;">SARS-CoV-2 transmission and detection on academic campuses in low- to middle-income countries has not been explored. The present study explored wastewater surveillance of SARS-CoV-2 in a campus setting in Pune, Maharashtra, India, offering insights into variant-specific trends and their correlation with clinical cases over a 2.5 year period from November 2021 to April 2024. We collected 242 wastewater samples from the campus sewershed and processed them to extract RNA and perform RT-qPCR and sequencing, followed by lineage assignment using the LCS tool. Early signals of different SARS-CoV-2 variants, such as BA.2.X, JN.1.X, and KP.2.X, were detected in wastewater prior to its first clinical report in Maharashtra, India. Wastewater viral load strongly correlated with clinical cases during the Omicron phase (ρ = 0.73–0.81) compared to the post-Omicron phase (ρ = −0.06 to 0.31). This study also highlights that alerts and warnings issued on the basis of wastewater viral hikes have proven instrumental in preventing outbreaks of SARS-CoV-2 variants on campus. However, downgrading COVID-19 from pandemic status by the WHO resulted in a subsequent decrease in public vigilance, changing the viral dynamic in the last phase of the study. This study showcases the utility of wastewater surveillance in a campus setting as an early warning system and understands the interplay of public health policy effects in viral dynamics within controlled ecosystems, such as campuses or offices.</span></p>
1 aPramanik, Rinka1 aRajput, Vinay1 aMalik, Vinita1 aNannaware, Kiran1 aMatra, Sejal1 aJoshi, Sai1 aKumar, Shubham1 aSamson, Rachel1 aYadav, Rakesh, Kumar1 aShah, Priyanki1 aShashidhara, LS1 aDastager, Syed1 aKarmodiya, Krishanpal1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/long-term-genomic-surveillance-sars-cov-2-campus-wastewater-depicts-lineage-trends-and02225nas a2200373   4500008004100000022001400041245018900055210006900244260000800313300000600321490000700327520095400334653001601288653004301304653002401347653001501371653003401386100002001420700002101440700001801461700001901479700002301498700002101521700002401542700002501566700001801591700001801609700001901627700001601646700001901662700001901681700001901700856013201719       2025                        eng d  a1867-033400aMonitoring 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 phases0 aMonitoring influenza A H1N1 H3N2 RSV and SARSCoV2 using wastewat  cMAR  a30 v173 a<p>
	{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</p>
10aInfluenza A10aQuantitative reverse transcription-PCR10aRespiratory viruses10aSARS-CoV-210aWastewater-based epidemiology1 aPramanik, Rinka1 aNannaware, Kiran1 aMalik, Vinita1 aShah, Priyanki1 aSangewar, Poornima1 aGogate, Niharika1 aShashidhara, L., S.1 aBoargaonkar, Radhika1 aPatil, Dhawal1 aKale, Saurabh1 aBhalerao, Asim1 aJain, Nidhi1 aKamble, Sanjay1 aDastager, Syed1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/monitoring-influenza-h1n1-h3n2-rsv-and-sars-cov-2-using-wastewater-based-epidemiology-2-year03253nas a2200313   4500008004100000022001400041245018600055210006900241260000800310300001200318490000700330520212500337653002002462653001302482653001802495653002202513653003202535100002502567700002902592700002202621700001802643700002102661700002702682700002102709700001902730700003302749700002602782856013102808       2026                        eng d  a2044-605500aExploring the mechanisms of yoga-based cardiac rehabilitation in heart failure via assessment of endothelial function, genomics and arterial health (Yoga-EndOmics): a study protocol0 aExploring the mechanisms of yogabased cardiac rehabilitation in   cJAN  ae1102390 v163 a<p>
	Introduction Heart failure (HF) remains a major global health challenge, particularly in low-resource settings where access to comprehensive cardiac rehabilitation (CR) is limited. Yoga, a culturally contextualised mind-body intervention, holds promise as an adjunctive therapy in CR. The Yoga-EndOmics study aims to evaluate the effects of Yoga-based cardiac rehabilitation (Yoga-CaRe) on gene expression, endothelial function, vascular biomarkers and clinical outcomes in systolic HF, providing mechanistic insights into its potential integration into conventional cardiac rehabilitation.Methods and analysis This is a prospective, randomised, open-label, blinded-endpoint (PROBE) mechanistic trial enrolling 78 patients with HF with reduced ejection fraction (HFrEF). Participants will be randomised in a 1:1 ratio to receive either a structured Yoga-CaRe intervention or enhanced standard care for 3 months. The Yoga-CaRe group will attend 20 supervised sessions with guided home practice involving tailored asanas, pranayama and meditation. Primary outcomes are changes in endothelial-dependent flow-mediated dilation (FMD) and functional exercise capacity at 3 months. Secondary outcomes include changes in arterial compliance and stiffness, circulating biomarkers of endothelial dysfunction, oxidative stress and inflammation, and immediate changes in global gene expression profiles in peripheral blood mononuclear cells following the Yoga-CaRe intervention. Data will be analysed using analysis of covariance (ANCOVA) for between-group comparisons and significant analysis of microarray (SAM) for global gene expression profiles.Ethics and dissemination The study has received ethical clearance from the Institutional Ethics Committee of the SDM College of Medical Sciences and Hospital, India (SDMIEC/2025/1072) and is registered with the Clinical Trials Registry of India. Findings will be disseminated through peer-reviewed journals, scientific conferences and stakeholder engagement platforms to inform future integrative strategies in HF management.Trial registration number CTRI/2023/12/060758</p>
10aDNA Methylation10aGenetics10aHeart failure10aMolecular Biology10aRandomized Controlled Trial1 aShetty, Vindya, Vasu1 aPatil, Laxmi, Ramchandra1 aPatil, Satish, G.1 aAithal, Kiran1 aOli, Ajay, Kumar1 aYenagi, Vijay, Aravind1 aKaulgud, Ram, S.1 aDharne, Mahesh1 aSekaran, Ambalam, M. Chandra1 aPrabhakaran, Dorairaj  uhttps://library.ncl.res.in/content/exploring-mechanisms-yoga-based-cardiac-rehabilitation-heart-failure-assessment-endothelial01316nas a2200157   4500008004100000245006900041210006800110260000800178300000700186490000700193520079500200100001900995700002101014700001901035856010401054       2026                        eng d00aGut virome-microbiome interactions across hosts and environments0 aGut viromemicrobiome interactions across hosts and environments  cAPR  a870 v123 a<p>
	<span style="font-family: -apple-system, BlinkMacSystemFont, &quot;Segoe UI&quot;, Roboto, Oxygen-Sans, Ubuntu, Cantarell, &quot;Helvetica Neue&quot;, sans-serif; font-size: 18px; font-weight: 700;">The Gut microbiome-virome dynamics and interactions Collection highlights gut viruses, mainly bacteriophages, as determinants of microbial community structure and host-relevant functions across human, animal, and environmental systems. The Collection welcomes studies that quantify virus-microbe interactions, evidence-based linking viruses to microbial hosts, characterise infection dynamics, and connect them to ecological or clinical outcomes. It prioritises methodological rigour and translational relevance in diagnostics, surveillance, and phage-based interventions.</span></p>
1 aSamson, Rachel1 aHassard, Francis1 aDharne, Mahesh  uhttps://library.ncl.res.in/content/gut-virome-microbiome-interactions-across-hosts-and-environments03252nas a2200757   4500008004100000022001400041245013700055210006900192260000800261300001600269490000800285520091900293653003101212653002301243653001201266653002401278653001301302100003201315700002101347700003701368700001901405700002101424700002301445700002301468700001701491700002201508700002101530700002001551700002301571700003401594700002201628700001801650700002801668700001701696700002401713700001701737700002701754700002701781700001701808700001801825700002001843700001901863700003301882700002701915700002801942700002601970700001701996700001902013700002602032700001602058700002802074700003202102700002202134700002002156700001902176700001902195700002402214700001802238700002002256700001802276700001802294700001902312700001702331700002202348856012402370       2026                        eng d  a0022-189900aTracking plasmodium knowlesi through fecal DNA for monitoring zoonotic transmission in wild macaques across southeast and south asia0 aTracking plasmodium knowlesi through fecal DNA for monitoring zo  cMAY  ae1238-e12430 v2333 a<p>
	We conducted the noninvasive surveillance of Plasmodium knowlesi in wild macaques using 4752 fecal samples collected across 9 endemic countries. Parasite DNA was detected in 390 samples (8.2%), with positivity rates ranging from 1.4% to 18.4%. This provides the first field-based evidence that P. knowlesi DNA in feces shed by macaques and present under natural conditions can be detected. These findings validate fecal sampling as a practical and scalable tool for tracking zoonotic-malaria. The results support integration into forest-runoff and rural wastewater surveillance systems, offering new opportunities for early detection of pathogens and environmental monitoring at the human-wildlife interface. This study validates noninvasive fecal sampling for tracking Plasmodium knowlesi in wild macaques, providing a scalable tool for early pathogen detection and environmental malaria surveillance.</p>
10aenvironmental surveillance10afecal surveillance10amacaque10aPlasmodium knowlesi10azoonosis1 aWannigama, Dhammika, Leshan1 aAmarasiri, Mohan1 aPhattharapornjaroen, Phatthranit1 aHurst, Cameron1 aModchang, Charin1 aCynthia, Bernadina1 aMiyanaga, Kazuhiko1 aCui, Longzhu1 aFernandez, Stefan1 aMelhem, Nada, M.1 aLuk-in, Sirirat1 aSinger, Andrew, C.1 aRagupathi, Naveen, Kumar Deva1 aHtun, Thin, Sandi1 aSei, Kazunari1 aNgamwongsatit, Natharin1 aHui, Ng, Sin1 aShimotai, Yoshitaka1 aOunjai, Puey1 aKanthawee, Phitsanuruk1 aTacharoenmuang, Ratana1 aKauba, Alice1 aEang, Chorney1 aRomone, Lavinia1 aDharne, Mahesh1 aDe Araujo, Juliana, Calabria1 aNdatuwong, Lazarus, G.1 aWerawatte, W., K. C. P.1 aChanthasiri, Traychit1 aZhao, Jinxin1 aMori, Hirotake1 aBesa, John, Jefferson1 aKurt, Ozgur1 aKanjanabuch, Talerngsak1 aZahraei-Ramazani, Ali, Reza1 aHiggins, Paul, G.1 aAoyagi, Tetsuji1 aKicic, Anthony1 aTrowsdale, Sam1 aHongsing, Parichart1 aYang, Xiaonan1 aWang, Yangzhong1 aKhatib, Aisha1 aSano, Daisuke1 aShibuya, Kenji1 aAbe, Shuichi1 aHamamoto, Hiroshi  uhttps://library.ncl.res.in/content/tracking-plasmodium-knowlesi-through-fecal-dna-monitoring-zoonotic-transmission-wild