Biology subjects

Akter, S.

Publications and source records attributed to Akter, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Green Synthesized Zinc Oxide Nanoparticles from Azadirachta indica Exhibit Enhanced Antibacterial, Antioxidant and Cytotoxic Activities

Green synthesis of zinc oxide nanoparticles (ZnO NPs) offers a sustainable strategy for developing multifunctional antimicrobial nanomaterials. In this study, ZnO NPs were synthesized using Azadirachta indica leaf extract and characterized by UV-vis spectroscopy, FTIR, XRD, SEM, and GC-MS. The nanoparticles exhibited a characteristic absorption peak at 352 nm, a direct band gap of 3.07 eV, and hexagonal wurtzite crystallinity with an average crystallite size of approximately 32 nm. The biosynthesized ZnO NPs showed concentration-dependent antibacterial activity against Erwinia carotovora, producing inhibition zones of up to 25.9 mm. Mechanistic studies revealed significant membrane damage, evidenced by 4.77-fold and 5.62-fold increases in extracellular protein and amino acid leakage, respectively, with marked alterations in bacterial protein profiles detected by SDS-PAGE. The nanoparticles also exhibited strong antioxidant activity, achieving 89.4% DPPH radical scavenging, and induced dose-dependent cytotoxicity in HepG2 cells with an estimated IC50 of 124.8 g/mL. These findings demonstrate that neem mediated ZnO nanoparticles possess potent antibacterial activity through membrane disruption while exhibiting promising antioxidant properties, highlighting their potential as eco-friendly nanomaterials for the management of bacterial soft rot and other phytopathogenic diseases.

microbiology↗

bioRxiv2026

Cervicovaginal Dysbiosis in HPV-Negative Women: Metagenomic Evidence Implicates Achromobacter in Female Infertility

The cervicovaginal microbiome is pivotal to reproductive health, yet its dynamics in HPV-negative women with gynaecological disorders remain underexplored. We investigated microbial diversity and taxonomic shifts in HPV-negative women from Bangladesh using 16S rRNA gene sequencing and shotgun metagenomics. Of 224 women screened, 136 were HPV-negative; 29 underwent 16S profiling, and three infertility-associated cases were further analyzed by shotgun metagenomics. Healthy controls exhibited low alpha diversity and a Lactobacillus-dominated profile (98.2%), reflecting ecological stability. In contrast, pathological cases displayed significantly elevated richness and evenness, reduced Lactobacillus (28.0%), and enrichment of anaerobic and opportunistic taxa, including Bifidobacterium (23.4%), Achromobacter (12.9%) and Sneathia (7.5%). Distinct microbial signatures emerged across clinical subgroups: pelvic inflammatory disease was enriched in Bifidobacterium, intra-menstrual bleeding retained moderate Lactobacillus, while infertility exhibited prominent dominance of Achromobacter (45.5%). Shotgun metagenomics confirmed Achromobacter spp. (A. ruhlandii, A. dolens, A. xylosoxidans) as the predominant taxa (84.9%) in infertility cases, accompanied by depletion of protective Lactobacillus. Functional inference revealed conserved metabolic backbones but disease-specific enrichment of stress-response and biosynthetic pathways, particularly in infertility and PID. Co-occurrence network analysis identified condition-specific microbial consortia, with Achromobacter forming infertility-associated clusters. This study represents the first integrated application of amplicon and shotgun metagenomic approaches to profile the cervicovaginal microbiota in HPV-negative women. It identifies Achromobacter as a potential microbial biomarker of infertility and highlights the urgent need for microbiome-informed diagnostics and targeted interventions to restore cervicovaginal homeostasis.

microbiology↗

bioRxiv2026

Dietary Lees Supplementation Enhances Poultry Health Performance Through Gut Ecosystem Reprogramming

The search for sustainable alternatives to in-feed antibiotics has intensified with the global antimicrobial resistance crisis. While microbial by-products show potential, their mechanisms remain elusive. This study reveals that spent yeast lees, a fermentation by-product, profoundly reprograms the chicken gut ecosystem to enhance growth. We investigated the differential effects of live spent lees versus autoclaved spent lees from a molasses fermenter with Saccharomyces cerevisiae. In a 14-day controlled trial, 0-day-old poultry chicks (n=15) were assigned to a control diet (n=5), a live spent Lees-supplemented diet (n=5), or an autoclaved spent Lees-supplemented diet (n=5). Through the feeding trial with either live spent Lees or autoclaved spent Lees, we demonstrate significant enhancement of growth performance, with autoclaved spent Lees achieving the highest final body weight (573.4 {+/-} 17.2 g). Using deep shotgun metagenomic sequencing of faecal samples, we demonstrate that both spent Lees forms induced a dramatic ecological shift, driving the gut microbiome to a state of monodominance by Bacteroides fragilis (reaching 74.83% with live spent Lees). This was accompanied by the near-complete eradication of enteropathogens like like Enterococcus faecium and Escherichia coli. Crucially, live spent Lees supplementation effectively countered a natural age-dependent expansion of the gut resistome, eliminating the high-risk oxazolidinone resistance gene o23S and restructuring the virulome away from offensive effector systems. However, this beneficial restructuring came at the cost of significantly reduced microbial diversity and suppression of beneficial commensals. A key finding was that autoclaved spent Lees, while inducing a less extreme microbial shift, yielded superior final body weight, suggesting its lysed cells provide enhanced nutritional availability. Our work establishes spent yeast Lees not as mere waste, but as a potent, multi-functional supplement that enhances growth through gut ecosystem engineering, yet necessitates a strategic choice between its live and autoclaved forms based on production priorities.

microbiology↗

bioRxiv2025

Exploration of diuretic potential of different parts (flower, bark, leaf) of Butea Monosperma

Hypertension (HTN) or high blood pressure poses major global health concerns, and the conventional synthetic antihypertensive drugs are effective, though their long-term use is often limited due to adverse effects. Butea monosperma (B. monosperma), commonly known as the Flame of the Forest, the traditional use as medicinal plant for diuresis and other usage in rural areas in South Asia suggests a role for its antihypertensive potential. The study aimed, first to identify the diuretic constituents present from different parts (flower, bark, and leaf) of B. monosperma and to evaluate their diuretic activity through in vivo experimentation. The chemical profiling of the extracts of different parts were performed using Liquid Chromatography Mass Spectrometry (LC-MS/MS), while diuretic efficacy was assessed in Swiss Albino wistar rats. Urinary volume and electrolyte excretion (Na{square}, K{square}, and Cl{square}) were measured to elucidate the possible mechanism of action. Statistical analyses were conducted using one-way ANOVA followed by multiple comparison test, with significance set at p < 0.05. LC MS/MS analysis confirmed the presence of chlorthalidone, a thiazide-like diuretic compound, in all three plant parts under selective ionization mode. In vivo results demonstrated a significant, dose dependent increase in urine output and electrolyte excretion in treated rats compared to controls (p < 0.05). These findings provide both phytochemical and pharmacological evidence that B. monosperma possesses potent diuretic activity, supporting its traditional use and highlighting its potential as a natural source for the development of novel antihypertensive and diuretic therapeutics.

biochemistry↗

bioRxiv2025

Hydrogen sulfide modulates plant hypoxic responses through the persulfidation of Plant Cysteine Oxidases

Hydrogen sulfide (H2S) is a gaseous molecule historically regarded as toxic. Nevertheless, increasing evidence has brought to light important physiological roles in both animals and plants. In plants, H2S is involved in environmental and developmental responses, such as stomatal closure and seed germination, and in tolerance mechanisms to different stress conditions like salinity, drought and waterlogging. In this study, we report a function of H2S as a modulator of hypoxic responses in Arabidopsis thaliana. A combination of biochemical and genetic evidence demonstrates that H2S inhibits the activity of Plant Cysteine Oxidases, the molecular sensors of oxygen, through protein persulfidation to modulate hypoxia-associated responses. Furthermore, we show that H2S physiology contributes to responses to low oxygen, as disturbing H2S production impaired activation of hypoxia-responsive genes and submergence tolerance. Overall, this work introduces H2S as signalling modulator in plant hypoxic responses and adds a regulatory layer to the plant oxygen-sensing mechanism.

plant biology↗

bioRxiv2025

In silico reconstruction of primary and metastatic tumor architecture using GIS-augmented spatial transcriptomics

The tumor microenvironment (TME) comprises different cell populations that interact, contributing to tumor heterogeneity and therapy response. Spatial transcriptomics offers valuable insights into transcriptional complexity and heterogeneity of the TME. We established Geographic Information System (GIS)-augmented In-Silico Reconstruction of Tumor Architecture (GIS-ROTA), a biologically informed analytic framework that integrates pathway or cell type-based enrichment analysis with local Morans I to uncover functional spatial domains. In our Visium dataset of primary and metastatic estrogen receptor-positive breast tumor samples, GIS-ROTA revealed extensive co-localization of estrogen response with metabolic pathway gene sets and mutual exclusivity with metastasis-related and specific immune-related pathway gene sets. The novelty of our approach lies in considering biological functions prior to identifying any spatial domains, providing direct interpretability and minimizing the subjectivity of interpreting clusters observed from conventional analytic methods. Overall, our GIS-ROTA framework integrates biological knowledge first, yielding spatial patterns with functional relevance and enabling identification of novel targets for development of therapeutic strategies.

cancer biology↗

bioRxiv2025

Metabolic Versatility of Lysinibacillus capsici BCSIR-Raj-01 Underpins Its Multifunctionality in Biocontrol, Bioremediation, and Plant Growth Promotion

Microbial inoculants that integrate plant growth promotion, pathogen suppression, and pollutant degradation are central to sustainable agriculture. Here, we report the genomic and phenotypic characterization of Lysinibacillus capsici BCSIR-Raj-01, an endophyte isolated from citrus leaves in Bangladesh. The 4.62 Mb genome encodes 4,699 coding sequences and displays an open pangenome with loci linked to stress adaptation, xenobiotic degradation, and secondary metabolite biosynthesis. Genome mining revealed complete pathways for indole-3-acetic acid (IAA) production, siderophore biosynthesis, and phosphate metabolism, alongside gene clusters for bacteriocins, lantibiotics, terpenes, and polyketides. Nitrogen cycling genes indicated diazotrophic growth potential and a truncated denitrification pathway. Phenotypic assays validated these predictions: L. capsici BCSIR-Raj-01 solubilized phosphate, produced IAA and siderophores, grew on hydrocarbons, and exhibited diazotrophic activity. Notably, the strain showed potent larvicidal activity against Culex and Anopheles larvae, suggesting ecological roles beyond plant association. Together, these results establish L. capsici BCSIR-Raj-01 as a multifunctional bacterium with potential applications in crop improvement, bioremediation, and biological vector control. IMPORTANCEThe challenges of modern agriculture and environmental sustainability demand microbial solutions that deliver multiple functions. Lysinibacillus species are increasingly recognized for such versatility, but their genomic basis remains poorly resolved. Our study provides the first genome-enabled framework for understanding multifunctionality in L. capsici. By combining whole-genome sequencing with phenotypic validation, we show that BCSIR-Raj-01 harbors biosynthetic clusters, stress adaptation loci, and xenobiotic degradation genes while also expressing experimentally confirmed traits, including phosphate solubilization, IAA and siderophore production, nitrogen fixation, hydrocarbon utilization, and larvicidal activity. This integration of plant growth promotion, biocontrol potential, and pollutant degradation positions L. capsici BCSIR-Raj-01 as a next-generation bioinoculant. Beyond broadening the functional scope of Lysinibacillus, our findings highlight how genome-guided approaches can identify microbes with cross-sectoral applications in agriculture, bioremediation, and vector management.

microbiology↗

bioRxiv2025

Reelin Controls the Directional Orientation, Apical Localization and Length of Primary Cilia in Principal Neurons in the Cerebral Cortex

The primary cilia of pyramidal neurons in inside-out laminated regions orient predominantly toward the pia, reflecting reverse soma movement during postnatal neurodevelopment. However, the mechanisms underlying the directional cilia orientation are unknown. Here we show that the primary cilia of pyramidal neurons are localized near the base of the apical dendrites and aligned on the nuclear side opposite to the axon initial segment (AIS). However, this pattern is not observed in atypical pyramidal neurons in the deep neocortex, excitatory neurons in non-laminated regions, interneurons, or astrocytes, where cilia are irregularly positioned around the nuclei and lack preferred orientation. In Reelin-deficient mice (reeler), the directional orientation and apical location of cilia in late-born neocortical and CA1 neurons are disrupted. However, the initial impairments are partially corrected during postnatal development, along with a realignment of apical-basal orientation. In contrast, loss of Reelin drastically disrupts the directional orientation of cilia in early-born neocortical neurons and principal neurons in evolutionarily conserved cortical regions, which lack postnatal correction. Consistently, their cilia do not preferably localize to the apical side. Additionally, Reelin deficiency increases the cilia length of principal neurons across the cerebral cortex at a developmental stage when cilia stabilize in wild-type mice, but this effect is not observed in interneurons, astrocytes, or excitatory neurons in non-laminated regions. Together, Reelin controls the directional orientation, apical localization, and length of primary cilia in principal neurons in the cerebral cortex, underscoring the cilium as a key apical domain particularly prominent in late-born neurons.

neuroscience↗

bioRxiv2025

Metatranscriptomic Insights into Host-Microbiome Interactions Underlying Asymptomatic COVID-19 Cases

In recent years, the research on Coronavirus disease 2019 (COVID-19) has surged rapidly due to its infectious nature and epidemiological importance as a pandemic. Association of other pathogenic microbes or different human microbiomes with COVID-19 severity is well established. While much is known about COVID-19, studies exploring how host-pathogen interactions at the transcriptomic level influence disease severity are still limited. This research focuses on metatranscriptomic perspective of COVID-19 patients from different Bangladeshi cohorts. Metatranscriptomic sequencing was performed using the extracted RNA of forty different nasopharyngeal samples. After preprocessing and assembly of the genome sequence data, taxonomic identification and diversity along with antibiotic resistance pattern was analyzed using different bioinformatic pipelines. COVID-19 positive and asymptomatic positive patients had a higher abundance of pathogenic and multidrug resistant bacteria whereas the Healthy or recovered patients had higher fungal population. Differential gene expression analysis was also performed to identify the upregulated and downregulated genes responsible for different biological and immunological pathways of humans. Here, immunological response related genes were mostly upregulated in positive cases which was also evident in the proinflammatory cytokines upregulation. Moreover, asymptomatic positive cases showed low TLR-4 expression, which is key to recognizing pathogen-associated molecular patterns (PAMPs) and triggering pro-inflammatory immune responses. This study can clarify the gene expression and signaling pattern of COVID-19 patients with different severity. This may also suggest that some populations exhibit reduced basal expression of TLR-4, which may suppress innate immune activation following infection and contribute to asymptomatic clinical outcomes; however, this hypothesis requires further investigation. Future studies should aim to validate these associations using larger, ethnically diverse cohorts with comprehensive clinical and demographic data.

microbiology↗

bioRxiv2025

Immunoinformatics Approach to Engineer a Multi-Epitope Vaccine Against SdrG in Skin Commensal Staphylococcus epidermidis

The human skin serves as a dynamic ecosystem for beneficial commensal bacteria such as Staphylococcus epidermidis, which play a crucial role in maintaining skin barrier integrity and modulating immune responses. Remarkably, recent research has demonstrated that the skin can function as a natural vaccination site, producing specific antibodies against commensal microbes without inducing inflammation. However, S. epidermidis can transition into an opportunistic pathogen in clinical settings, forming resilient biofilms on medical implants and exhibiting increasing resistance to antibiotics (MRSE), posing a significant healthcare challenge. To address this challenge, advanced immunoinformatics strategies were leveraged to design a novel multi-epitope vaccine targeting the SdrG protein, a key mediator of S. epidermidis biofilm formation. The vaccines binding dynamics with Toll-like receptor 4 (TLR4) were evaluated through computational analyses, including molecular docking and 500-nanosecond molecular dynamics (MD) simulations. Stability assessments via Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Radius of Gyration (Rg) confirmed that the vaccine-TLR4 complex achieved structural equilibrium, with TLR4 maintaining rigidity while the vaccine exhibited adaptive flexibility for optimal binding. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) method revealed a strong binding affinity, with a peak free energy of -52.73 kcal/mol and an average of -24.72 {+/-} 9.5989 kcal/mol over the last 50 ns, indicating a thermodynamically favorable interaction. Furthermore, in silico cloning validated the vaccines expressibility, with successful integration into the pET-Sangamo-His vector (8560 bp) for optimal E. coli production. These findings underscore the vaccines potential to elicit a robust immune response by stably engaging TLR4, a critical step in innate immune activation. By combining computational precision with immunological insights, this study lays a foundation for developing an effective prophylactic strategy against S. epidermidis biofilm-associated infections.

immunology↗

bioRxiv2025

An atlas of cell type specific regulatory effects in cattle

Understanding the genetic and molecular architecture of complex traits and artificial selection is crucial for advancing sustainable precision breeding in cattle and other livestock. Yet, how genetic variation affects cellular gene expression remains elusive in cattle. Here, by integrating 8,866 bulk RNA-seq samples and 999,192 single cells of 81 cell types in 22 bovine tissues, we presented a comprehensive atlas of regulatory variants at the cell type resolution in cattle. By colocalizing with bulk-tissue expression quantitative trait loci (beQTL), we detected 57,043 novel cell-type stratified eQTL and cell-type/state interaction eQTL in 18,153 genes, which also exhibited a stronger tissue/cell-type specificity than beQTL. By examining genome-wide associations (GWAS) of 44 complex traits, these cell-resolved eQTL were colocalized with 505 (24%) additional GWAS loci compared to beQTL. Through integrating this resource with selection signatures between dairy and beef cattle, we provided tissue/cell-specific regulatory insights into cattle breeding. Overall, the current atlas of cell-type-specific regulatory variants will serve as an invaluable resource for cattle genomics and selective breeding.

genetics↗

bioRxiv2025

Identification of novel therapeutic inhibitors against E6 and E7 oncogenes of HPV-16 associated with cervical cancer

BackgroundHuman Papilloma Virus type 16 (HPV-16) is highly oncogenic with the E6 and E7 oncogenes playing crucial roles in the pathogenesis of HPV-related cervical carcinogenesis. Targeting these oncoproteins with specific inhibitors offers a promising approach for therapeutic intervention. ObjectiveThis study aimed to identify potential inhibitors of the HPV-16 E6 and E7 oncoproteins through an in silico approach, providing a foundation for the development of targeted therapies against HPV associated malignancies. MethodologyWe performed virtual screening on a library of 1000 compounds to identify promising candidates. Subsequent molecular docking studies were conducted to assess the binding affinities of the promising candidates. The top-scoring compounds for oncoproteins were then subjected to molecular dynamics simulations to evaluate their stability and interaction profiles. ResultsThe virtual screening identified 14 promising candidates followed by docking studies. Among these Galangin was identified as a promising inhibitor for the E6 oncogene, while Neoechinulin showed potential as an inhibitor of the E7 oncogene. ConclusionOur findings suggest Galangin and Neoechinulin with high potential as therapeutic inhibitors of HPV-16 E6 and E7 oncogenes respectively. These inhibitors could contribute significantly to the development of targeted therapies against HPV associated malignancies. However, further in vitro and in vivo investigations are required to use these phytochemicals as antiviral agents against HPV-16.

cancer biology↗

bioRxiv2024

Prevalence of Key Spike Protein Mutations and Their Limited Effect on COVID-19 Clinical Manifestations in Sylhet, Bangladesh

SARS-CoV-2 is the virus responsible for the COVID-19 pandemic, which has spread rapidly around the world and had a significant impact on public health and the economy worldwide. This study investigated the correlation between SARS-CoV-2 spike protein mutations, clinical outcomes and patient demographics in the Sylhet region of Bangladesh. We looked at the full genome sequences of 37 SARS-CoV-2 samples that were collected between January and June 2020. Specifically, we looked at five major spike protein mutations: D614G, A570D, D1118H, A222V, and P681R. The D614G mutation was the most prevalent (94.6%), followed by A570D and D1118H (both 32.4%), A222V (29.7%), and P681R (13.5%). Despite their high prevalence, we found no statistically significant associations between these mutations and clinical outcomes or demographic variables, except for possible trends for the P681R mutation. We found that age played a decisive role in recovery from COVID-19, with older patients exhibiting slower recovery rates. In terms of predictors of outcome, gender differences were observed: clinical symptoms and viral genetic mutations were more influential for men, while age and disease progression were more important for women. Common nucleotide substitutions (A23403G, C3037T, and C14408T) associated with European strains were identified, suggesting possible routes of transmission. This study contributes to our understanding of the genetics, clinical manifestations and epidemiology of SARS-CoV-2 in the Sylhet region and emphasizes the need for continuous genomic surveillance and adaptive public health strategies.

microbiology↗

bioRxiv2024

H2O2 repurposes the plant oxygen-sensing machinery to control the transcriptional response to oxidative stress

Plants sense reduced oxygen availability (hypoxia) through Plant Cysteine Oxidases (PCOs). Reduced PCO activity in hypoxia, as seen during submergence, stabilises Group VII Ethylene Response Factors (ERFVIIs), master regulators of adaptive metabolic and anatomic responses. Equally important is timely arrest of these responses upon reoxygenation, assumed to occur through ERFVII degradation. Reoxygenation involves reactive oxygen species (ROS) production. Here, we report that instead of degradation, reoxygenation results in ERFVII nuclear stabilisation, an effect mimicked by direct H2O2 treatment. Interestingly, typical hypoxia marker genes are repressed while genes involved in ROS homeostasis and oxidative stress protection are upregulated. Using in planta, heterologous and biochemical assays, we reveal that ROS-related ERFVII stabilisation is caused by PCO inactivation. Stabilised ERFVIIs are retained at hypoxia-responsive promoters but become repressors. Our findings suggest that by responding to both oxygen and ROS, PCOs coordinate ERFVII stability to regulate timely responses to damaging fluctuations in oxygen availability.

plant biology↗

bioRxiv2024

Arf GTPase-Activating proteins ADAP1 and ARAP1 regulate incorporation of CD63 in multivesicular bodies

Arf GTPase-Activating proteins (ArfGAPs) mediate the hydrolysis of GTP bound to ADP-ribosylation factors. ArfGAPs are critical for cargo sorting in the Golgi-to-ER traffic. However, the role of ArfGAPs in sorting into intralumenal vesicles (ILVs) in multivesicular bodies (MVBs) in post-Golgi traffic remains unclear. Exosomes are extracellular vesicles (EVs) of endosomal origin. EVs mediate cell-to-cell communication, and CD63 is an EV marker. CD63 is enriched in intralumenal vesicles (ILVs) in MVBs of cells. However, the secretion of CD63 positive EVs has not been consistent with the data on CD63 localization in MVBs, and how CD63-containing EVs are formed is yet to be understood. To elucidate the mechanism of CD63 transport to ILVs, we focused on CD63 localization in MVBs and searched for the ArfGAPs involved in CD63 localization. We observed that ADAP1 and ARAP1 depletion inhibited CD63 localization to enlarged endosomes after Rab5Q79L overexpression. We tested epidermal growth factor (EGF) and CD9 localization in MVBs. We observed that ADAP1 and ARAP1 depletion affected the localization of EGF and CD9 differently. Our results indicate that there may be different populations of MVBs and that ADAP1 and ARAP1 regulate CD63 incorporation into ILVs in different MVBs. Summary StatementADAP1 and ARAP1 regulate CD63 localization in endosomes.

cell biology↗

bioRxiv2023

Phylogenetic diversity and functional potential of large and cell-associated viruses in the Bay of Bengal

The Bay of Bengal (BoB), the largest bay in the world, provides valuable ecosystem services such as fishing and recreation to millions of people living along its coast and has a significant economic value. The BoB is impacted by various environmental factors such as seasonal monsoons and multiple freshwater inputs, and this region is particularly vulnerable to sea-level rise and increased frequency of devastating cyclones that are predicted to be exacerbated due to global climate change. These factors are also compounded by anthropogenic influences from tourism and development, making it an important ecosystem to understand and study from a global change perspective. Despite its importance, microbial diversity and ecology have remained largely understudied in this region. In this study, we describe the diversity and putative functional importance of large and cell-associated (that is, originating from the cellular size fraction) viruses from two coastal sites in the BoB, with an emphasis on giant viruses and large phages. Sites chosen for this study include Coxs Bazar, a populated beach with multiple freshwater inputs, and Saint Martin Island, a resort island that has considerably less human influence compared to Coxs Bazar. Through metagenomic sequencing, we were able to identify a more abundant and more diverse viral community at Coxs Bazar consisting of many viruses that are indicators of freshwater intrusion and runoff. Overall, 1962 putative phage genome bins were obtained ranging from 10 - 655 kilobase pairs (kbp) in sizes. Of these genomes, 16 from Saint Martin were found to be larger than 100kbp which we deemed "large" phages, and we were able to reconstruct a phylogeny of these large phages using the TerL gene as a marker. This phylogeny revealed clades enriched in large phages and a high diversity of large phage candidates in the Bay of Bengal coast. Protein annotation analysis showed a wide variety of functionality from both sites with more auxiliary metabolic genes (AMGs) found in the Coxs Bazar viral community. Five giant virus (Phylum Nucleocytoviricota) genomes were also reconstructed from Coxs Bazar and identified as belonging to the orders Imitervirales and Pandoravirales. These genomes ranged from 83 - 876 kbp in size and contained a wide range of encoded functionalities. To the best of our knowledge, our study represents the first insights on the phylogenetic and functional diversity of viruses in the Bay of Bengal. These results thus provide an important foundation for further studies on the impact of host-virus interactions on biogeochemical cycles and microbial food web in this understudied marine environment.

microbiology↗

bioRxiv2023

Exploring Microbial Diversity and Functional Potential along the Bay of Bengal Coastline in Bangladesh: Insights from Amplicon Sequencing and Shotgun Metagenomics

Although the Bay of Bengal (BoB) is the worlds largest bay, possessing distinct physiochemical properties, it has garnered little research focus concerning its microbial diversity and ecological importance. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoBs eastern coast, viz., Saint Martin and Coxs Bazar, Bangladesh. From the 16S sequencing data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Coxs Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S sequencing data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Coxs Bazar. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh and lay the foundation for further in-depth assessment of microbial community dynamics and functional potential in the context of global change in this region.

microbiology↗

bioRxiv2022

The E2 glycoprotein holds key residues for Mayaro virus adaptation to the urban Aedes aegypti mosquito

Adaptation to mosquito vectors suited for transmission in urban settings is a major driver in the emergence of arboviruses. To better anticipate future emergence events, it is crucial to assess their potential to adapt to new vector hosts. In this work, we used two different experimental evolution approaches to study the adaptation process of an emerging alphavirus, Mayaro virus (MAYV), to Aedes aegypti, an urban mosquito vector of many arboviruses. We identified E2-T179N as a key mutation increasing MAYV replication in insect cells and enhancing transmission by live Aedes aegypti. In contrast, this mutation decreased viral replication and binding in human fibroblasts, a primary cellular target of MAYV in humans. We also showed that MAYV E2-T179N was attenuated in vivo in a mouse model. We then used structural and experimental analyses to show that MAYV E2-T179N bound less efficiently to human cells, though the decrease in replication or binding was not mediated through interaction with one of the host receptors, Mxra8. When this mutation was introduced in the closely related chikungunya virus, which has caused major outbreaks globally in the past two decades, we observed increased replication in both human and insect cells, suggesting E2 position 179 is an important determinant of alphavirus host-adaptation, although in a virus-specific manner. Collectively, these results indicate that adaptation at the T179 residue in MAYV E2 may result in increased vector competence - but coming at the cost of optimal replication in humans - and may represent a first step towards a future emergence event. Author SummaryMosquito-borne viruses must replicate in both mosquito and vertebrate hosts to be maintained in nature successfully. When viruses that are typically transmitted by forest dwelling mosquitoes enter urban environments due to deforestation or travel, they must adapt to urban mosquito vectors to transmit effectively. For mosquito-borne viruses, the need to also replicate in a vertebrate host like humans constrains this adaptation process. Towards understanding how the emerging alphavirus, Mayaro virus, might adapt to transmission by the urban mosquito vector, Aedes aegypti, we used natural evolution approaches to identify several viral mutations that impacted replication in both mosquito and vertebrate hosts. We show that a single mutation in the receptor binding protein increased transmission by Aedes aegypti but simultaneously reduced replication and disease in a mouse model, suggesting that this mutation alone is unlikely to be maintained in a natural transmission cycle between mosquitoes and humans. Understanding the adaptive potential of emerging viruses is critical to preventing future pandemics.

microbiology↗