Bhabatosh Das

Introduction: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection profoundly affects the upper respiratory tract, yet the dynamics of the resident virome across different stages of Coronavirus Disease 2019 (COVID-19) and recovery remain poorly understood. Methods: This study profiled alterations in the virome and microbiome in 143 SARS-CoV-2–positive adults, stratified by disease severity (Non-Severe, Severe, Critical), compared with 96 RT-PCR–negative controls. Nasal and oral swabs underwent targeted viral enrichment and next-generation sequencing, followed by virome profiling. Results: The respiratory virome of SARS-CoV-2-positive individuals was dominated by SARS-CoV-2, with co-detected viruses such as Human Mastadenovirus C, which increased with disease severity and persisting post-recovery. Alpha diversity was highest in Non-Severe cases and declined in Severe and Critical groups, suggesting increasing disruption of the virome with disease severity. Beta diversity showed clear separation between controls and cases, and across severity levels. LEfSe identified distinct viral signatures differentiating infection status, and logistic regression of key viral taxa accurately classified Critical versus post-recovery samples (AUC = 0.91). Although the study focused on viruses, bacterial taxa including Rothia mucilaginosa and Haemophilus parahaemolyticus were also detected with severity-linked variation, highlighting viral–bacterial interactions. Longitudinal paired analysis revealed consistent post-recovery enrichment of Streptococcus-specific bacteriophages across all severity groups, suggesting restoration of Streptococcus-associated phage dynamics during convalescence. Discussion: Overall, this study reveals SARS-CoV-2–associated alterations in the respiratory virome and microbiome and highlights specific microbial taxa with potential as biomarkers for disease severity and post-infection recovery.

The global emergence of multidrug-resistant (MDR) ESKAPE pathogens has significantly reduced the effectiveness of existing antibiotics, highlighting the urgent need for new strategies to restore antimicrobial susceptibility. Here, we report the discovery and mechanism of BMM_1567, a peptide potentiator that enhances aminoglycoside efficacy against MDR pathogens. A genetically defined reporter-based screen identified BMM_1567 as a potent inhibitor of aminoglycoside resistance, potentiating spectinomycin activity against MDR Gram-negative ESKAPE isolates at low micromolar concentrations. Structural modeling and molecular dynamics simulations indicated that BMM_1567 interacts with residues lining the antibiotic-binding groove of aminoglycoside-modifying enzymes (ANT, APH, AAC), with highest affinity for ANT (ΔG_bind = –62.25 kcal/mol), suggesting competitive inhibition of substrate binding. Site-directed mutagenesis of key ANT residues identified critical amino acids involved in BMM_1567 binding, confirming their role in mediating spectinomycin potentiation. In murine abscess model using XDR E. coli , BMM_1567 in combination with spectinomycin significantly reduced bacterial burden and pro-inflammatory cytokine levels, comparable to colistin. Collectively, these findings establish BMM_1567 as a promising aminoglycoside potentiator that restores antibiotic activity against MDR pathogens through direct inhibition of resistance enzymes, while exhibiting in vivo efficacy and a remarkably low propensity for resistance development.

Lead contamination in soil represents a serious threat to soil-dwelling invertebrates. Despite the ecological importance of Collembola, their responses to heavy metal stress in tropical environments remain insufficiently explored. This study investigated the physiological stress response and lead accumulation in the soil microarthropod Cyphoderus javanus under chronic exposure to sublethal concentrations of lead-contaminated garden soil under tropical conditions. Individuals were maintained in an environmental chamber at 28 ± 0.5 °C, with soil moisture regulated using distilled water.Lead toxicity was evaluated by assessing moulting frequency, reproductive output, survival, and the bioconcentration factor (BCF). The results demonstrated concentration-dependent physiological stress, evidenced by reduced moulting frequency, decreased reproductive output, and lowersurvival at increased lead concentrations. BCF analysis indicated a time- and concentration-dependent increase in lead accumulation, although the relationship was not strictly linear, particularly at lower exposure levels. Nevertheless, lead bioaccumulation was significantly elevated with prolonged exposure and higher concentrations. These findings highlight the sensitivity of soil Collembola to lead contamination and underscore the ecological risks posed by heavy metal pollution. The study emphasizes the need to protect soil fauna to maintain ecosystem stability and soil health, which are essential for sustainable terrestrial ecosystem functioning.

Environmental pressures and repeated exposure to antimicrobials drive microbial evolution, often through genomic changes or acquisition of mobile genetic elements that enhance fitness and resistance. This has critically influenced the control of cholera, particularly with the emergence of multidrug-resistant Vibrio cholerae strains, such as those recently reported in Yemen. To explore the long-term dynamics of antimicrobial resistance (AMR), we analyzed 149 clinical Vibrio isolates collected in India over 16 years (2008–2023), including five cases of Vibrio paracholerae . Phenotypic testing revealed widespread multidrug resistance, while whole-genome sequencing (WGS) uncovered both known and atypical AMR determinants. Phylogenomic analysis showed diverse clustering patterns, with pan-genome comparisons identifying species-specific genomic regions despite overall high similarity. Notably, V. paracholerae lacked the canonical cholera toxin gene ( ctxAB ) but harbored alternative virulence factors, including hlyA , chxA , proteases, and type VI secretion system components, supporting its role as a non-cholera enteric pathogen of concern. Our study underscores the importance of long-term surveillance and comparative genomic profiling to understand AMR evolution and guide cholera management in endemic regions. IMPORTANCE: This study highlights how long-term environmental and antimicrobial pressures shape the evolution of Vibrio species, leading to multidrug resistance and genomic diversification. By analyzing 16 years of clinical isolates from a major cholera-endemic region in India, including emerging Vibrio paracholerae cases, we reveal both known and novel resistance mechanisms and virulence factors. These findings emphasize the need for sustained genomic surveillance to track evolving resistance trajectories and support effective control strategies for cholera and related enteric infections in endemic regions.

Antimicrobial resistance (AMR) has emerged as a critical global health challenge, supported in part by bacterial taxa that act as reservoirs of resistance determinants, facilitating their dissemination across microbial communities under antibiotic selective pressure. Among the diverse mechanisms underlying AMR, enzyme-mediated resistance plays a dominant role. These enzymes typically inactivate antibiotics or modify their targets by transferring specific functional groups or hydrolyzing the antibiotic molecules. Recent evolutionary pressures have fostered the emergence of bifunctional resistance enzymes, which provide simultaneous protection against multiple antibiotic classes and significantly enhance bacterial fitness. The remarkable diversity of these enzymes largely arises from divergent evolution, which has produced extensive enzyme superfamilies within bacterial systems. Collectively, they encompass a wide range of molecules that execute distinct resistance strategies, thereby fortifying microbial survival. To drive the discovery of novel therapeutics, it is essential to elucidate the expression patterns, structural dynamics, and functional mechanisms of these enzymes. Recent advances in omics technologies have transformed our capacity to investigate microbial defence systems, offering deep, high-throughput insights into the molecular underpinnings of resistance. This review provides an overview of critical resistance enzymes responsible for antibiotic modification and target protection in human-associated bacterial pathogens. Enhancing our understanding of these mechanisms is essential for developing next-generation therapeutics, including antibiotic potentiators, to effectively combat bacterial drug resistance.

Background: Lactobacillus crispatus is a dominant member of the healthy female reproductive tract microbiota, contributing to mucosal homeostasis and pathogen exclusion. Numerous studies have highlighted the protective effects of L. crispatus against both intestinal and genital infections. In the present study, we build on this foundation to investigate the broader health-promoting properties of L. crispatus , focusing on its antimicrobial and metabolic functions; and its protective roles in hepatic and cardiometabolic disorders. Methods: Three L. crispatus strains were selected from a panel of sixty isolates based on comprehensive genome mining analyses described in our previous publication. In the present study, we generated complete genome data for these three strains, and delineated biosynthetic pathways including their capacity for antimicrobial peptide production, lactic acid biosynthesis, short chain fatty acid synthesis and biogenic amine production. The antimicrobial activity of these isolates was assessed via agar well-diffusion assay and time-kill assay. Their ability to survive gastric pH and bile stress was evaluated through acid and bile salt tolerance assays. Further, to assess metabolic benefits, anti-steatotic and cardioprotective effects were examined in a preclinical diet-induced mouse model of cardiometabolic disorder. Results: Complete genome analysis of L. crispatus strains revealed multiple antimicrobial peptide (AMP) biosynthetic gene clusters, including several novel loci associated with bacteriocins. Metabolic profiling identified pathways for bile salt metabolism, folate biosynthesis and short chain fatty acids production. Cell-free culture supernatants exhibited broad-spectrum antibacterial activity, particularly against Escherichia coli , Enterobacter hormaechei, Staphylococcus aureus and Staphylococcus haemolyticus . Further, the strains tolerated gastric pH 2 and physiological bile stress of 0.3% suggesting potential for oral administration. In vivo, oral administration of L. crispatus (10 ⁸ CFU) daily for 2 weeks followed by twice-weekly for 12 weeks significantly reduced hepatic steatosis, improved insulin sensitivity and cardiac function in a diet-induced cardiometabolic disorder mouse model. This is the first report demonstrating the cardiometabolic protective potential of L. crispatus . Conclusions: L. crispatus confers diverse health benefits through pathogen resistance functions and modulation of host metabolic pathways. These findings support its potential as a novel biotherapeutic for preventing and managing hepatic and cardiometabolic disorders, extending its therapeutic relevance beyond reproductive health.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection profoundly impacts the upper respiratory tract, yet the dynamics of the resident virome across different stages of Coronavirus Disease 2019 (COVID-19) and recovery remain poorly understood. This study profiled virome and microbiome alterations in 143 SARS-CoV-2–positive adults, stratified by disease severity (Non-Severe, Severe, Critical), compared with 96 RT-PCR–negative controls. Nasal and oral swabs underwent targeted viral enrichment and next-generation sequencing, followed by virome profiling. The respiratory virome of SARS-CoV-2 positive individuals was dominated by SARS-CoV-2, with co-detected viruses such as Human Mastadenovirus C increasing with severity and persisting post-recovery. Alpha diversity was highest in Non-Severe cases and declined in Severe and Critical groups, indicating increasing virome disruption with disease severity. Beta diversity showed clear separation between controls and cases, and across severity levels. LEfSe identified distinct viral signatures differentiating infection status, and logistic regression of key viral taxa accurately classified Critical versus post-recovery samples (AUC = 0.91). Although the study focused on viruses, bacterial taxa including Rothia mucilaginosa and Haemophilus parahaemolyticus were also detected with severity-linked variation, highlighting viral–bacterial interactions. Longitudinal paired analysis revealed consistent post-recovery enrichment of Streptococcus-specific bacteriophages across all severity groups, suggesting restoration of Streptococcus-associated phage dynamics during convalescence. Overall, this study reveals SARS-CoV-2–associated alterations in the respiratory virome and microbiome and highlights specific microbial taxa with potential as biomarkers for disease severity and post-infection recovery.

The emergence and spread of antimicrobial resistance (AMR) in clinically important bacterial pathogens has severely compromised the effectiveness of commonly used antibiotics in healthcare. Acquisition and transmission of AMR genes (ARGs) are often facilitated by sublethal concentrations of antibiotics in microbially dense environments. In this study, we use sewage samples (n = 381) collected from six Indian states between June and December 2023 to assess the concentration of eleven antibiotics, microbial diversity, and ARG richness. We find antibiotics from seven drug classes and detect over 2000 bacterial amplicon sequence variants (ASVs). Metagenomic (n = 220) and isolated genome sequences (n = 305) of aerobic and anaerobic bacterial species identify 82 ARGs associated with 80 mobile genetic elements (MGEs). These MGEs are predominantly present in multidrug-resistant (MDR) bacterial pathogens. Comparative core genome analysis of MDR bacterial isolates (n = 7166) shows strong genetic similarity between sewage-derived strains and clinical pathogens. Our results highlight sewage as a significant reservoir for ARGs, where genetic exchanges occur and facilitate the evolution and spread of AMR pathogens in both community and healthcare settings. Additionally, the dipstick-based assay developed for ARGs detection can be used for sewage surveillance in low-resource settings for better understanding of resistance prevalence.