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-functional02195nas a2200217 4500008004100000022001400041245005700055210005500112260000800167300000800175490000700183520157300190653001501763653001301778653002001791653001501811100001901826700002401845700002301869856008501892 2020 eng d a2190-572X00aBiosensors: frontiers in rapid detection of COVID-190 aBiosensors frontiers in rapid detection of COVID19 cAUG a3850 v103 a

The rapid community-spread of novel human coronavirus 2019 (nCOVID19 or SARS-Cov2) and morbidity statistics has put forth an unprecedented urge for rapid diagnostics for quick and sensitive detection followed by contact tracing and containment strategies, especially when no vaccine or therapeutics are known. Currently, quantitative real-time polymerase chain reaction (qRT-PCR) is being used widely to detect COVID-19 from various types of biological specimens, which is time-consuming, labor-intensive and may not be rapidly deployable in remote or resource-limited settings. This might lead to hindrance in acquiring realistic data of infectivity and community spread of SARS-CoV-2 in the population. This review summarizes the existing status of current diagnostic methods, their possible limitations, and the advantages of biosensor-based diagnostics over the conventional ones for the detection of SARS-Cov-2. Novel biosensors used to detect RNA-viruses include CRISPR-Cas9 based paper strip, nucleic-acid based, aptamer-based, antigen-Au/Ag nanoparticles-based electrochemical biosensor, optical biosensor, and Surface Plasmon Resonance. These could be effective tools for rapid, authentic, portable, and more promising diagnosis in the current pandemic that has affected the world economies and humanity. Present challenges and future perspectives of developing robust biosensors devices for rapid, scalable, and sensitive detection and management of COVID-19 are presented in light of the test-test-test theme of the World Health Organization (WHO).

10aBiosensors10aCOVID-1910aRapid detection10aSARS-CoV-21 aSamson, Rachel1 aNavale, Govinda, R.1 aDharne, Mahesh, S. uhttps://library.ncl.res.in/content/biosensors-frontiers-rapid-detection-covid-1905367nas 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-within01942nas 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

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.

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-nothing01919nas 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

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.

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

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-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

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

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-approach02128nas 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

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.

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-insights02244nas 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

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 (& 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 & fcy;ERS-1 could reduce the abundance of E. coli cells by 8.22 log10 CFU/mL <= 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 <= 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.

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

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.

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

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 < 0.05). During the dry season, Proteobacteria and Actinobacteria were predominant, while Bacteroidetes and Firmicutes were abundant post-monsoon (P < 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.

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-implications02417nas 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

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.

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

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.

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-and