03154nas a2200289 4500008004100000022001400041245016500055210006900220260000800289300001200297490000800309520217000317653002002487653001102507653001702518653002402535653001102559100001902570700001602589700002302605700002102628700001802649700002302667700002302690700002202713856012902735 2019 eng d a0048-969700aMetagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges0 aMetagenomic insights to understand transient influence of Yamuna cJUL a288-2990 v6743 a

River confluences are interesting ecosystems to investigate for their microbial community structure and functional potentials. River Ganges is one of the most important and holy river of India with great mythological history and religious significance. The Yamuna River meets Ganges at the Prayagraj (formerly known as Allahabad), India to form a unique confluence. The influence of Yamuna River on taxonomic and functional aspects of microbiome at this confluence and its downstream, remains unexplored. To unveil this dearth, whole metagenome sequencing of the microbial (bacterial and archaeal) community from the sediment samples of December 2017 sampling expedition was executed using high throughput MinION technology. Results revealed differences in the relative abundance of bacterial and archaeal communities across the confluence. Grouped by the confluence, a higher abundance of Proteobacteria and lower abundance of Bacteroidetes and Firnacutes was observed for Yamuna River (G15Y) and at immediate downstream of confluence of Ganges (G15DS), as compared to the upstream, confluence, and farther downstream of confluence. A similar trend was observed for archaeal communities with a higher abundance of Euryarchaeoto in G15Y and G15DS, indicating Yamuna River's influence. Functional gene(s) analysis revealed the influence of Yamuna River on xenobiotic degradation, resistance to toxic compounds, and antibiotic resistance interceded by the autochthonous microbes at the confluence and succeeding downstream locations. Overall, similar taxonomic and functional profiles of microbial communities before confluence (upstream of Ganges) and farther downstream of confluence, suggested a transient influence of Yamuna River. Our study is significant since it may be foundational basis to understand impact of Yamuna River and also rare event of mass bathing on the microbiome of River Ganges. Further investigation would be required to understand, the underlying cause behind the restoration of microbial profiles post-confluence farther zone, to unravel the rejuvenation aspects of this unique ecosystem. (C) 2019 Elsevier B.A. All rights reserved.

10aConfluence zone10aGanges10aMetagenomics10aTransient influence10aYamuna1 aSamson, Rachel1 aShah, Manan1 aYadav, Rakeshkumar1 aSarode, Priyanka1 aRajput, Vinay1 aDastager, Syed, G.1 aDharne, Mahesh, S.1 aKhairnar, Krishna uhttps://library.ncl.res.in/content/metagenomic-insights-understand-transient-influence-yamuna-river-taxonomic-and-functional02667nas 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

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.

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-transient05367nas a2200205 4500008004100000245017900041210006900220260000800289490000800297520456800305100001904873700001804892700001604910700002304926700002104949700002304970700002304993700002205016856012305038 2020 eng d00aDeciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities0 aDeciphering taxonomic and functional diversity of fungi as poten cAUG0 v2523 a

River confluences are interesting ecological niche with limited information in respect of the structure and the functions of diverse microbial communities. Fungi are gaining global attention as promising biological spectacles for defining the trophic status of riverine systems. We condense existing knowledge in confluence diversity in two Indian rivers (i.e. Ganges and Yamuna), by combining sediment metagenomics using long read aided MinION nanopore sequencing. A total of 63 OTU’s were observed, of which top 20 OTU’s were considered based on relative abundance of each OTU at a particular location. Fungal genera such as Aspergillus, PenicilliumKluveromyces, Lodderomyces, and Nakaseomyces were deciphered as potential bio indicators of river pollution and eutrophication in the confluent zone. In silico functional gene analysis uncovered hits for neurodegenerative diseases and xenobiotic degradation potential, supporting bioindication of river pollution in wake of anthropogenic intervention.

1 aSamson, Rachel1 aRajput, Vinay1 aShah, Manan1 aYadav, Rakeshkumar1 aSarode, Priyanka1 aDastager, Syed, G.1 aDharne, Mahesh, S.1 aKhairnar, Krishna uhttps://library.ncl.res.in/content/deciphering-taxonomic-and-functional-diversity-fungi-potential-bioindicators-within02623nas 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

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.

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

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 < 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 <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.

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-heterogeneity03383nas a2200181 4500008004100000245014500041210006900186260000800255300001100263490000800274520267700282100002602959700002302985700001803008700002303026700002103049856013103070 2021 eng d00aMetagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome0 aMetagenomic analysis reveals genetic insights on biogeochemical  cAUG a1127380 v2923 a

Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.

1 aMohapatra, Madhusmita1 aYadav, Rakeshkumar1 aRajput, Vinay1 aDharne, Mahesh, S.1 aRastogi, Gurdeep uhttps://library.ncl.res.in/content/metagenomic-analysis-reveals-genetic-insights-biogeochemical-cycling-xenobiotic-degradation01978nas a2200217 4500008004100000022001400041245014800055210006900203260000800272300001600280490000700296520118800303653002601491653001101517653002201528653001701550100001801567700002301585700002301608856012901631 2021 eng d a0944-134400aMetagenomic exploration reveals a differential patterning of antibiotic resistance genes in urban and peri-urban stretches of a riverine system0 aMetagenomic exploration reveals a differential patterning of ant cDEC a66477-664840 v283 a{Antimicrobial resistance in the riverine ecosystem of urban areas is an alarming concern worldwide, indicating the importance of molecular monitoring to understand their patterning in urban and peri-urban areas. In the present study, we evaluated the influence of urban rivers on the connected peri-urban rivers of a riverine system of India in the context of antibiotic resistance genes. The rivers traversing through urban (Mula, Mutha, Pawana, and Ramnadi) and peri-urban stretches (Bhima and Indrayani) form the riverine system of Pune district in Maharashtra, India. The MinION-based shotgun metagenomic analysis revealed the resistome against 26 classes of antibiotics, including the last line of antibiotics. In total, we observed 278 ARG subtypes conferring resistance against multiple drugs (40%), bacitracin (10%), aminoglycoside (7.5%), tetracycline (7%), and glycopeptide (5%). Further, the alpha diversity analysis suggested relatively higher ARG diversity in the urban stretches than peri-urban stretches of the riverine system. The NMDS (non-metric multidimensional scaling) analysis revealed significant differences with overlapping similarities (stress value = 0.1410aAntibiotic resistance10aMinION10aPeri-urban rivers10aUrbanization1 aRajput, Vinay1 aYadav, Rakeshkumar1 aDharne, Mahesh, S. uhttps://library.ncl.res.in/content/metagenomic-exploration-reveals-differential-patterning-antibiotic-resistance-genes-urban02228nas 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-strategic00781nas a2200205 4500008004100000022001400041245012100055210006900176260001200245300000900257490000700266100002300273700001800296700002300314700001800337700002300355700004200378700002700420856012800447 2022 eng d a0972-232700aGut microbiota dysbiosis in patients with intracranial sino-venous thrombosis and acute ischemic stroke in the young0 aGut microbiota dysbiosis in patients with intracranial sinovenou cSEP-OCT a980+0 v251 aPrabhu, Varsha, A.1 aRajput, Vinay1 aYadav, Rakeshkumar1 aGohil, Kushal1 aDharne, Mahesh, S.1 aUnnikrishnan, Mazhuvancherry, Kesavan1 aGorthi, Sankar, Prasad uhttps://library.ncl.res.in/content/gut-microbiota-dysbiosis-patients-intracranial-sino-venous-thrombosis-and-acute-ischemic02709nas a2200313 4500008004100000022001400041245011200055210006900167260000900236300001100245490000800256520169600264653001901960653001701979653001701996653002402013653001502037653001502052100002602067700001802093700002302111700002502134700001802159700001802177700002302195700002302218700002302241856013102264 2022 eng d a0048-969700aHigh throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India0 aHigh throughput sequencing based direct detection of SARSCoV2 fr cFEB  a1510380 v8073 aGiven a large number of SARS-CoV-2 infected individuals, clinical detection has proved challenging. The wastewater-based epidemiological paradigm would cover the clinically escaped asymptomatic individuals owing to the faecal shedding of the virus. We hypothesised using wastewater as a valuable resource for analysing SARS-CoV-2 mutations circulating in the wastewater of Pune region (Maharashtra; India), one of the most affected during the covid-19 pandemic. We conducted study in open wastewater drains from December 2020- March 2021 to assess the presence of SARS-CoV-2 nucleic acid and further detect mutations using ARTIC protocol of MinION sequencing. The analysis revealed 108 mutations across six samples categorised into 39 types of mutations. We report the occurrence of mutations associated with Delta variant lineage in March-2021 samples, simultaneously also reported as a Variant of Concern (VoC) responsible for the rapid increase in infections. The study also revealed four mutations; S:N801, S:C480R, NSP14:C279F and NSP3:L550del not currently reported from wastewater or clinical data in India but reported worldwide. Further, a novel mutation NSP13:G206F mapping to NSP13 region was observed from wastewater. Notably, S:P1140del mutation was detected in December 2020 samples while it was reported in February 2021 from clinical data, indicating the instrumentality of wastewater data in early detection. This is the first study in India to demonstrate utility of sequencing in wastewater based epidemiology to identify mutations associated with SARS-CoV-2 virus fragments from wastewater as an early warning indicator system. (c) 2021 Elsevier B.V. All rights reserved.10aARTIC protocol10aEpidemiology10aMetagenomics10aNanopore sequencing10aSARS-CoV-210awastewater1 aDharmadhikari, Tanmay1 aRajput, Vinay1 aYadav, Rakeshkumar1 aBoargaonkar, Radhika1 aPatil, Dhawal1 aKale, Saurabh1 aKamble, Sanjay, P.1 aDastager, Syed, G.1 aDharne, Mahesh, S. uhttps://library.ncl.res.in/content/high-throughput-sequencing-based-direct-detection-sars-cov-2-fragments-wastewater-pune-west02298nas 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

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.

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-community03254nas 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

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.

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

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.

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-anthropogenically03345nas 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

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 < 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.

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-and02557nas 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

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.

10aBioremediation10aMetagenomics10aRivers10aWater hyacinth10aXenobiotic1 aYadav, Rakeshkumar1 aDharne, Mahesh uhttps://library.ncl.res.in/content/utility-metagenomics-bioremediation-comprehensive-review-bioremediation-mechanisms-and03415nas 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

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, Bacillus velezensis 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 g/L γ-PGA production with a productivity of 1.09 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 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.

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-synthesis