@article {46178, title = {Re-purposing is needed for beneficial bugs, not for the drugs}, journal = {International Microbiology}, volume = {22}, year = {2019}, month = {MAR}, pages = {1-6}, type = {Review}, abstract = {

Between 150 and 200 species of plants, insects, birds or mammals go extinct every day. We do not have any idea what the global extinction rate for microorganisms is. What is clear is that we have already lost a maximum number of the microbes that used to live in and on our skins. Many of our microbial partners are facing extinction as we apply selection pressures that are unprecedented in our long-standing relationships. Recent estimates are that we have lost at least one third of the diversity of our skin microbiome. Every day, most of us bath or shower in water that contains chlorine or fluorine; these additives do a great job of killing pathogenic microbes, but they are probably not helping our skin microbiome. Most of the people apply cosmetic products every day, as these products contain preservatives that prevent microbial growth on the shelf. These same chemicals may well kill microbes on the skin. The daily use of high-pH soaps probably will not help microbial life that is adapted to living on the skin{\textquoteright}s natural pH of 5. The rise in the rate of C-section births from around 5\% in 1970 to more than 30\% today is likely to be a contributing factor. Vaginal microbes seed our skins at birth and C-sections disrupt this process. The overuse of broad-spectrum antibiotics has contributed to the loss of our microbial partners in all body sites and the skin is no exception. It is now clear that skin is an ecosystem that is dependent on commensal microbes for optimal health. In general, a diverse ecosystem is a healthy ecosystem that is robust in the face of change. Low-diversity ecosystems are more fragile and susceptible to dysbiosis. Eczema and acne rates have increased rapidly over the last 50 years. These diseases are almost unknown in hunter-gatherer communities. Now, we face two exciting challenges: finding out which species matter and how to get them back.

}, keywords = {Drugs, Dysbiosis, Microbiome, Probiotics}, issn = {1139-6709}, doi = {10.1007/s10123-018-00049-x}, author = {Ram, Hari and Dastager, Syed G.} } @article {46188, title = {Web-gLV: a web based platform for lotka-volterra based modeling and simulation of microbial populations}, journal = {Frontiers in Microbiology}, volume = {10}, year = {2019}, month = {FEB }, pages = {288}, type = {Article}, abstract = {

The affordability of high throughput DNA sequencing has allowed us to explore the dynamics of microbial populations in various ecosystems. Mathematical modeling and simulation of such microbiome time series data can help in getting better understanding of bacterial communities. In this paper; we present Web-gLV- a GUI based interactive platform for generalized Lotka-Volterra (gLV) based modeling and simulation of microbial populations. The tool can be used to generate the mathematical models with automatic estimation of parameters and use them to predict future trajectories using numerical simulations. We also demonstrate the utility of our tool on few publicly available datasets. The case studies demonstrate the ease with which the current tool can be used by biologists to model bacterial populations and simulate their dynamics to get biological insights. We expect Web-gLV to be a valuable contribution in the field of ecological modeling and metagenomic systems biology.

}, keywords = {lotka-volterra, microbial population, Microbiome, Modeling, numerical-simulation, time-series, visualization, web-server}, issn = {1664-302X}, doi = {10.3389/fmicb.2019.00288}, author = {Kuntal, Bhusan K. and Gadgil, Chetan and Mande, Sharmila S.} } @article {46654, title = {EviMass: a literature evidence-based miner for human microbial associations (vol 10, 849, 2019)}, journal = {Frontiers in Genetics}, volume = {11}, year = {2020}, month = {NOV }, pages = {614051}, type = {Correction}, keywords = {Human Disease, literature mining, microbial association, Microbiome, Web server}, doi = {10.3389/fgene.2020.614051}, author = {Srivastava, Divyanshu and Baksi, Krishanu D. and Kuntal, Bhusan K. and Mande, Sharmila S.} } @article {47336, title = {Time: a web application for obtaining insights into microbial ecology using longitudinal microbiome data (vol 9, 36, 2018)}, journal = {Frontiers in Microbiology}, volume = {11}, year = {2020}, month = {NOV}, pages = {605295}, type = {Correction}, keywords = {clustering, community state, Granger causality algorithm, Microbiome, time series, visualization, Web server}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.605295}, author = {Baksi, Krishanu D. and Kuntal, Bhusan K. and Mande, Sharmila S.} } @article {47112, title = {Web-gLV: a web based platform for lotka-volterra based modeling and simulation of microbial populations (vol 10, 288, 2019)}, journal = {Frontiers in Microbiology}, volume = {11}, year = {2021}, month = {JAN }, pages = {605308}, type = {Correction}, keywords = {lotka-volterra, microbial population, Microbiome, Modeling, numerical-simulation, time-series, visualization, web-server}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.605308}, author = {Kuntal, Bhusan K. and Gadgil, Chetan and Mande, Sharmila S.} } @article {48177, title = {Exploring the core microbiota in scented rice (Oryza sativa L.) rhizosphere through metagenomics approach}, journal = {Microbiological Research}, volume = {263}, year = {2022}, month = {OCT}, pages = {127157}, type = {Article}, abstract = {

Rice is a major food crop cultivated around the globe. Specially scented rice varieties are of commercial importance but they are low-yielding. The rhizospheric microflora plays a significant role in improving yield and aroma. However, the core microbiome of the scented rice rhizosphere is comparatively less explored. Here, we analyzed the core microbiome associated with the rhizosphere of the scented (Ambemohar-157 and Dehradun basmati) in comparison with non-scented rice (Kolam and Arize 6444 Gold) cultivated at two different geoclimatic zones of India (Maharashtra and Uttarakhand) using the metagenomics approach. The alpha and beta diversity analysis showed that the microbial communities associated with scented and non-scented varieties significantly changes with respect to richness, diversity, and evenness. The taxonomic profiling revealed the variation in composition, diversity, and abundance of the microbiome in terms of phyla and genera associated with scented rice varieties over non-scented. The cluster analysis distinguishes the microbial communities based on their geographical positions. The core microbiome analysis revealed that scented rice rhizosphere shelters distinct and unique microbiota. 28.6 \% of genera were exclusively present only in the scented rice rhizosphere. The putative functional gene annotation revealed the high abundance of genes related to the biosynthesis of 2-acetyl-1-pyrroline (2AP) precursors in scented rice. The precursor feeding analysis revealed proline as a preferred substrate by 2AP synthesizing bacteria. The 2AP precursor proline and proline metabolism genes showed a positive correlation. The scented rice-specific rhizobacteria pointed out in this study can be used as bioinoculants for enhancing aroma, yield, and sustainable rice cultivation.

}, keywords = {Metagenome, Microbial community, Microbiome, Oryza sativa, Rhizosphere, rice}, issn = {0944-5013}, doi = {10.1016/j.micres.2022.127157}, author = {Dhondge, V. Harshal and Barvkar, Vitthal T. and Paul, Dhiraj and Dastager, Syed G. and Pable, Anupama A. and Nadaf, Altafhusain B.} } @article {48322, title = {Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India}, journal = {Science of the Total Environment}, volume = {872}, year = {2023}, month = {MAY}, pages = {162125}, type = {Article}, abstract = {

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

}, keywords = {Antibiotics (ARGs), Bacteriophages, Heavy metals (MRGs), Metagenomics, Microbiome, River Ganges}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2023.162125}, author = {Samson, Rachel and Rajput, Vinay and Yadav, Rakeshkumar and Shah, Manan and Dastager, Syed and Khairnar, Krishna and Dharne, Mahesh} }