Dhiraj Paul

National Centre for Cell Science

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Yogesh S. Shouche

National Centre for Cell Science

Pinaki Sar

Indian Institute of Technology Kharagpur

Dhiraj Dhotre

National Centre for Cell Science

Natarajan Amaresan

Uka Tarsadia University

Sufia K. Kazy

National Institute of Technology Durgapur

Angana Sarkar

National Institute of Technology Rourkela

Sonal Manik Chavan

National Centre for Cell Science

Yogesh S. Shouche

National Centre for Cell Science

Kisan M. Kodam

Savitribai Phule Pune University

Kumar Siddharth Singh

Academy of Scientific and Innovative Research

Cooperative Institutions

National Centre for Cell Science

Savitribai Phule Pune University

University of Eastern Finland

National Chemical Laboratory

Academy of Scientific and Innovative Research

Indian Institute of Technology Kharagpur

All India Institute of Medical Sciences

Unilever (India)

Finland University

Uka Tarsadia University

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Functional antagonistic interactions and genomic insights into the biosynthetic potential of human gut-derived microbiota

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Aehtesham Hussain Umera Patwekar Dattatray Mongad Yogesh Nimonkar Swapnil Ashok Mundhe

ABSTRACT Concerning the biological interactions within the gut microbiome, the specialized small molecules encoded by commensal microbes mediate distinct functional aspects. However, the landscape of antagonistic interactions mediated by specialized strains and their small molecules broadly remains. Here, we sought to evaluate antimicrobial interactions as a defensive contributor to gain new insights into structure-related functions or to bring the therapeutic potential of derived molecules. We elucidated the antagonistic landscape within a collection of 330 human-gut-derived commensal microbial strains cultivated from healthy human subjects. We characterized potential antagonistic strains and found a strain-specific selective inhibition contrary to common antimicrobial drugs that wipe out a broad range of species usually found in environmental microbes. Using functional and genomic approaches for accessing biologically active natural product molecules, we identified significant biosynthetic gene clusters (BGCs) encoding the important compound families in representative gut strains which contribute to antagonistic activities and are important in host defense or maintaining homeostasis in the gut. The subsets of the BGCs were represented in metagenomics sequencing data from healthy individuals. The cell culture secretome of strains revealed potential biomarkers linked to hallmark pathways. Together, these microorganisms encode biosynthetic novelty and represent a source of biologically significant natural products important in developing new treatments for infectious diseases to cut the usage of broad-spectrum antibiotics and represent a way to combat antimicrobial resistance. Consortia of such strains can be utilized as an option for precise editing of the microbiomes or fine-tuning the microbiota-modulating therapies.

Natural product

10.1101/2023.02.20.529173

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High Antibiotic Resistance in Indian Sewage Shows Distinct Trends and might be Disjoint from in-situ Antibiotic Levels

Water Air & Soil Pollution (2023)

Kumar Siddharth Singh Abhishek Keer Aakib Zed Rahila Jasmeen Kamini Mishra

10.1007/s11270-023-06479-2

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Molecular analysis of microbial community in arsenic-rich groundwater of Kolsor, West Bengal

Journal of Environmental Science and Health Part A (2015)

Angana Sarkar Dhiraj Paul Sufia K. Kazy Pinaki Sar

Bacterial community composition within the highly arsenic (As) contaminated groundwater from Kolsur, West Bengal was analyzed over a period of 3 years using 16S rRNA gene clone library and Denaturing Gradient Gel Electrophoresis (DGGE). Molecular phylogenetic study revealed abundance of α-Proteobacteria (56%) and Firmicutes (29%) along with members of β-Proteobacteria, Verrucomicrobia and Sphingobacteria as relatively minor groups. Along with consistent physicochemical environment, a stable microbial community structure comprising of bacterial genera Agrobacterium-Rhizobium, Ochrobactrum, Pseudomonas, Anoxybacillus and Penibacillus was recorded over the three years study period. Presence of cytosolic arsenate reductase (arsC) gene was observed within the microbial community. Phylogenetic analyses revealed that all the arsC sequences were closely related to the same gene from γ-proteobacterial members while the community was consisted of mainly α-proteobacterial groups. Such phylogenetic incongruence between 16S rRNA and arsC genes possibly indicated horizontal gene transfer (HGT) of the ars genes within the groundwater community. Overall, the study reported a nearly stable geomicrobial environment and genetic determinant related to As homeostasis gene, and provided a better insight on biogeochemistry of As contaminated aquifer of West Bengal.

Verrucomicrobia

10.1080/10934529.2015.1094339

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Bacterial Diversity in the Metal-Rich Terrestrial Deep Subsurface Sediments of Krishna Godavari Basin, India

Figshare (2019)

Preeti Nema Dhiraj Paul Nitin R. Karmalkar Yogesh S. Shouche

Krishna Godavari (KG) basin, located in the eastern continental margin of India, is a geological region well known for the abundance of economically important minerals. However, less is known about the microbial ecology of its subsurface sediments. The present study is the first report on the comprehensive culture-independent census of bacterial communities of deep subsurface of KG basin and their relationship with the geochemical environment. Elemental and mineralogical characterization of the sediments highlighted the presence of carbon and nitrogen deprived conditions along with the abundance of metalliferous minerals, especially rich in valuable elements like zirconium, vanadium, cesium, and rare earth elements. Diversity analysis based on Illumina MiSeq high-throughput sequencing platform revealed the predominance of Firmicutes (44.24%), Proteobacteria (34.17%), Bacteroidetes (15.18%), and Actinobacteria (3.81%) in the deep subsurface of this basin. ‘Abundant’ and ‘rare’ sub-communities analysis indicated that a large number of phyla like Acidobacteria, Armatimonadetes, Chloroflexi, and Deinococcus-Thermus were exclusively present as a rare community. Statistical analyses demonstrated that geochemical parameters, especially depth, pH, and metal content, showed significant influence on the microbial community structure. The present study should help future investigations for microbial mediated sustainable utilization of mineral-rich sediments of the region.

10.6084/m9.figshare.9736022

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Exploring the core microbiota in scented rice (Oryza sativa L.) rhizosphere through metagenomics approach

Microbiological Research (2022)

Harshal V. Dhondge Vitthal T. Barvkar Dhiraj Paul Syed G. Dastager Anupama A. Pable

10.1016/j.micres.2022.127157

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Deep sequencing analysis of bacterial community structure of Soldhar hot spring, India

Microbiology (2017)

Avinash Sharma Dhiraj Paul Dhiraj Dhotre Kunal Jani Anita Pandey

Hot spring

10.1134/s0026261717010118

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Arsenic-gut microbiome interaction: effects on exposed popopulations of Bihar, India

ISEE Conference Abstracts (2020)

Debapriya Mondal Dhiraj Paul Yogesh S. Shouche S. Suman Ranjit Kumar

Background: Arsenic exposure from drinking water and food continues to pose an important environmental public health challenge especially in south-east Asia where millions are affected. Though numerous mechanisms have been proposed for arsenic induced diseases, no scientific consensus has been reached. Ability of arsenic to affect gut microbes has been proposed as a possible mode of action. The aim of this study is to determine the effects of arsenic exposure on the gut microbiome in exposed populations of Bihar, India. Methods: Samples were collected from participants residing in arsenic contaminated areas of Bihar, India, as a part of on-going Nutri-SAM project. After taking informed consent, data on dietary intake using FFQ and 24-hour recall methods, data on demographic, socio-economic and health status were collected using questionnaires. Food and drinking water samples were collected from every household and analysed for arsenic. Fecal samples were collected from both male and female and bacterial community structure was investigated by high-throughput V4 region specific 16S rRNA gene sequencing using Illumina MiSeq platform.Results: We estimated the overall inorganic arsenic exposure from drinking water, cooked rice, potato and wheat intake and obtained a mean exposure of 1.99 μg/kgbw/day (n=153, 0.03-11.17μg/kgbw/day) in the surveyed population. Among 38 participants with gut microbial data till date, 14 had overall inorganic arsenic exposure <0.3μg/kgbw/day (mean±SD: 0.19±0.06) considered as low exposed group and 24 had exposure ≥0.3μg/kgbw/day (mean±SD: 1.85±1.52) considered as the high exposed group. Among the four most prevalent phyla in the studied population, we found an increased relative abundance of Firmicutes and Bacteriodates and decreased abundances of Proteobacteria and Actinobacteria in the high exposed group after adjusting for confounders. Conclusion: Arsenic exposure might influence the gut microbial diversity in the studied population. Even at the observed environmentally relevant concentrations of arsenic exposure the gut microbiota might get altered.

Arsenic toxicity

10.1289/isee.2020.virtual.o-os-515

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Metagenomic exploration of microbial community in mine tailings of Malanjkhand copper project, India

Genomics Data (2017)

Abhishek Gupta Avishek Dutta Jayeeta Sarkar Dhiraj Paul Mruganka K. Panigrahi

Mine tailings from copper mines are considered as one of the sources of highly hazardous acid mine drainage (AMD) due to bio-oxidation of its sulfidic constituents. This study was designed to understand microbial community composition and potential for acid generation using samples from mine tailings of Malanjkhand copper project (MCP), India through 16S rRNA gene based amplicon sequencing approach (targeting V4 region). Three tailings samples (T1, T2 and T3) with varied physiochemical properties selected for the study revealed distinct microbial assemblages. Sample (T3) with most extreme nature (pH < 2.0) harbored

Acid Mine Drainage

Chloroflexi (class)

Copper mine

10.1016/j.gdata.2017.02.004

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Upper circumpolar deep water influences microbial functional gene composition and diversity along the southern Central Indian Ridge and eastern Southwest Indian Ridge

Microbiology Spectrum (2024)

Sheryl Oliveira Fernandes Dhiraj Paul Surya Prakash Lankalapalli Srinivas Rao Arvapalli.Vidya PJ

ABSTRACT Deep sea microbial communities play a significant role in global biogeochemical processes. However, the depth-wise metabolic potential of microbial communities in hydrothermally influenced Central Indian Ridge (CIR) and Southwest Indian Ridge (SWIR) remains elusive. In this study, a comprehensive functional microarray-based approach was used to understand factors influencing the metabolic potential of microbial communities and depth-driven differences in microbial functional gene composition in CIR and SWIR. Stratified water column sampling at surface, mid, turbid/plume layer, and near bottom was done along with pertinent environmental variables at various locations along the ridges. The majority of genes (~38%–41%) throughout the water column in both regions encoded for C-cycling, particularly starch degradation indicating the predominance of heterotrophy. Genes encoding for nitrate reduction and arsenic and mercury resistance were enriched in the turbid and/or near-bottom waters, suggesting a localized influence of hydrothermally derived substrates on the metabolic potential of microbial communities. Indices for microbial functional gene diversity ( H = 9.18) and evenness ( J = 0.90) were highest for samples from turbid waters at SWIR. Potential temperature-salinity profiles showed the presence of nutrient-rich upper circumpolar deep water (UCDW) at >2,000 m in the study areas. Principal component analysis revealed that inorganic nutrient availability largely influenced functional gene diversity in deeper waters. The study signifies that rather than hydrothermal input, nutrients brought into the region through the UCDW could have a larger impact on metabolic processes mediated by autochthonous microbial communities and consequently have implications on deep-sea productivity. IMPORTANCE Little is known about depth-wise metabolic potential of microbial communities in hydrothermally influenced Central Indian Ridge (CIR) and Southwest Indian Ridge (SWIR) waters. In the present study, a comprehensive functional gene microarray approach was used to reveal the metabolic potential and depth-wise variation in microbial functional genes along the ridges. Up to 41% of microbial functional genes at both locations encoded for C-cycling. Availability of hydrothermally derived substrates in plumes detected along the ridges triggered an increase in the abundance of genes encoding for remediation of polycyclic aromatics, nitrate reduction, and arsenic and mercury resistance. Rather than hydrothermal input, the functional gene diversity at >2,000 m was largely influenced by inorganic nutrients transported by the nutrient-rich upper circumpolar deep water. Findings of this study are expanding the existing knowledge on new sites of hydrothermal activity along CIR and SWIR and gaining insights into ecosystem functioning in the deep sea.

Biogeochemical Cycle

10.1128/spectrum.03306-23

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Concurrent removal of reactive blue HERD dye and Cr(VI) by aerobic bacterial granules

Journal of Cleaner Production (2022)

Ashvini U. Chaudhari Dhiraj Paul Viresh Thamke Aditi Bagade Vishwas A. Bapat

Biotransformation

10.1016/j.jclepro.2022.133075

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Citations (13)