Biology subjects

Akter, A.

Publications and source records attributed to Akter, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Comprehensive Pan-Cancer Analysis Reveals the Prognostic, Molecular, and Immunological Significance of EPS8

Epidermal Growth Factor Receptor Pathway Substrate 8 (EPS8) is believed to function as a tumor driver; however, to understand its molecular characteristics across tumors, a comprehensive pan-cancer analysis of EPS8 is lacking. Objective: This study aimed to investigate the prognostic, molecular, and immunological significance of EPS8 across multiple human cancers. Methods: Comprehensive analyses were conducted using GEPIA2, UALCAN, TIMER2.0, cBioPortal, SMART, GSCA, Enrichr, and the TCGAplot R package to evaluate survival prognosis, gene expression, DNA methylation, immune infiltration, proteomic expression, tumor mutational burden (TMB), microsatellite instability (MSI), genetic alterations, drug sensitivity, and enriched pathways. Results: EPS8 overexpression in LGG (p=7.2x10-5) and PAAD (p=9.4x10-6) was significantly associated with poor overall survival and disease-free survival. Amplification was the most common genetic alteration, with alteration frequencies approaching 6% in TGCT and UCEC. In KIRC and PAAD, EPS8 expression correlated with tumor stage. Immune infiltration analysis revealed significant associations between EPS8 expression and immune cells. EPS8 expression also showed significant correlations with both TMB and MSI in STAD and ESCA. Enrichment analysis indicated an association between EPS8 and regulation of the actin cytoskeleton and similar pathways. Conclusion: These findings suggest that EPS8 has prognostic and immunological significance across multiple cancer types and may serve as a potential biomarker. The observed associations with immune-related features and drug response provide a basis for future experimental studies to evaluate its role in cancer biology and its potential relevance to immunotherapy.

cancer biology↗

bioRxiv2026

Human Gut Phageome Analysis Uncovers Thousands of Highly Modular Endolysins

The escalating threat of antimicrobial resistance has renewed global interest in bacteriophages as precise and powerful tools for controlling bacterial populations in the human gut. These viruses owe much of their antibacterial potential to phage-encoded endolysins, enzymes capable of rapidly degrading bacterial cell walls with high specificity and low potential for resistance development. Despite their therapeutic promise, the overall composition of the gut phageome and the structural modularity of its endolysins remain poorly understood. In this study, we performed a large-scale analysis of 9,141 human gut metagenomic samples from 34 independent studies. Using standardized workflows for assembly, genome clustering, host prediction, and protein domain annotation, we reconstructed 15,267 phage genomes and identified 3,794 corresponding endolysins. The recovered genomes showed substantial variation in size and coding density, with an average GC content of 43%. Host prediction indicated that most phages targeted bacterial members of the phyla Bacillota (41%) and Bacteroidota (23%). Endolysin sequences grouped into 296 protein families and displayed striking domain modularity. Catalytic domains such as Amidase_2 and Glyco_hydro_25 frequently co-occurred with cell wall-binding motifs including LysM and CW_7. Remarkably, one endolysin contained 15 distinct domains, the highest natural domain diversity reported to date. Collectively, this study represents the most comprehensive characterization of the human gut phageome and its encoded endolysins to date. The exceptional modular diversity uncovered highlights the gut phageome as a rich reservoir of endolysin variants, providing a strong foundation for developing next-generation therapeutics against multidrug-resistant bacterial pathogens.

genomics↗

bioRxiv2025

Genomic Insights into Wolbachia Strain wCin2USA1 Reveal Promising Cytoplasmic Incompatibility Potential and Next-Generation Dengue Biocontrol

Dengue fever poses a growing public health challenge globally, resulting in significant morbidity and economic burden. The use of Wolbachia-mediated biocontrol represents a promising, cost-effective, and environmentally sustainable strategy for managing dengue transmission. However, the susceptibility of existing Wolbachia strains utilized in controlling Aedes aegypti necessitates the investigation of novel strains to enhance dengue control efficacy. This study aimed to identify potential alternative Wolbachia strains for dengue control by comparing the genomes of seven Wolbachia pipientis strains: wMel, wAlbB, wlrr, wHm-C, wAnm, ant7, and a strain isolated from Aedes aegypti. We conducted comprehensive genomic analyses, including phylogenetic assessments, metabolic pathway evaluations, and characterization of the Cytoplasmic Incompatibility Factor (Cif) genes. Our analyses identified the strain wCin2USA1 as a strong candidate for alternative dengue control strategies. This strain demonstrated remarkable genomic similarities to wMel, an already established strain used as biocontrol for Aedes aegypti. Importantly, this strain presented two distinct pairs of Cif genes from different monophyletic types, each homologous to the Cif genes found in wMel and wAlbB. This genetic architecture suggests a high degree of compatibility and demonstrates promising potential for the suppression of Aedes aegypti populations through the induction of Cytoplasmic Incompatibility. The presence of multiple intact prophage regions also suggests greater adaptability compared to established strains. Our findings support the hypothesis that wCin2USA1 could serve as an effective biocontrol agent against dengue transmission. This work provides critical insights into developing innovative Wolbachia-based interventions aimed at mitigating the persistent threat posed by dengue fever. Future research should concentrate on optimizing release methodologies, evaluating ecological impacts, and assessing the strains effectiveness against the dengue virus. Author SummaryDengue fever is one of the fastest-growing mosquito-borne diseases in the world, causing illness and economic challenges in many countries. Current mosquito control methods, such as insecticides, are often costly, less effective over time, and harmful to the environment. An alternative approach uses naturally occurring bacteria called Wolbachia, which live inside insects. When certain Wolbachia strains are introduced into mosquitoes, they can reduce the insects ability to spread viruses like dengue. In our study, we compared the genetic makeup of several Wolbachia strains to identify new candidates that may work better for controlling dengue. We discovered that a strain called wCin2USA1 has strong potential because it shares important features with two strains already used successfully, while also having unique advantages. These include genes that help prevent mosquitoes from reproducing normally when carrying different Wolbachia strains, which can reduce mosquito populations. Our findings suggest that wCin2USA1 could be developed as a new, environmentally friendly tool to help reduce dengue transmission.

genomics↗

bioRxiv2024

Streptococcus Phage Genomes Reveal Extensive Diversity, New Taxonomic Insights, and Novel Endolysin-Derived Antimicrobial Peptides

The global rise of antibiotic-resistant bacteria, particularly among Streptococcus species, poses an escalating public health threat. Traditional antibiotic development has proven inadequate, making innovative approaches such as bacteriophage-based therapies promising alternatives. A deep understanding of phage biology at the genomic level is essential for advancing therapeutic applications. Here, we analyzed 709 Streptococcus phage genomes to bridge gaps in genomic diversity and propose revisions to Streptococcus phage taxonomy. The phage genomes were clustered based on shared proteins, resulting in 66 clusters and 35 singletons with significant variation in genome characteristics. Through proteome phylogeny, average nucleotide identity, and inter-cluster core genes, we propose 21 new family-level classifications and 296 genus-level subclusters, providing an updated framework for Streptococcus phage taxonomy. Further analysis revealed diverse domain architectures in Streptococcus phage endolysins, including previously unreported structures. Specific domains were associated with distinct streptococcal hosts, suggesting adaptive evolution. We also observed variation in endolysin gene organization, with purifying selection acting on most sites, though some were subject to diversifying selection. Additionally, 182 novel endolysin-derived antimicrobial peptides (AMPs) were identified, some exhibiting antifungal, antiviral, cell-penetrating and non-toxic properties. Molecular dynamics and docking simulations demonstrated high stability and strong binding affinity of peptides EP-39 and EP-121 to the Streptococcus pneumoniae virulence factor autolysin. This is the first comprehensive comparative study of Streptococcus phage genomes, providing critical insights into phage diversity and taxonomy. It also highlights the therapeutic potential of endolysin-derived AMPs against multidrug-resistant Streptococcus strains. Further experimental validation is required to assess their clinical potential.

genomics↗

bioRxiv2024

Comparative genomics reveals diversity and taxonomic relationships among Clostridioides difficile phages

Clostridioides difficile is associated with life-threatening antibiotic-associated diarrhea, colitis, and toxin-mediated infections. While antibiotics are the primary treatment against C. difficile infections, increasing resistance necessitates alternatives. Bacteriophages and bacteriophage-derived proteins such as endolysins hold promise as potential solutions. Understanding phage biology at the genomic level is crucial for their therapeutic use. We conducted a comparative genomic analysis of 44 C. difficile phage genomes from public databases, examining both whole genome and proteome levels and grouping them by shared protein content. Relationships within each group were observed, and core and highly conserved genes were identified. Using genome and proteome phylogeny, average nucleotide identity, and core gene identification, we proposed an updated taxonomic classification. Nine distinct clusters were identified, without any singleton. Cluster members exhibited similar genome architecture, genome sizes, GC content, number of coding sequences, presence of core genes, and high nucleotide identity. Additionally, we propose 23 new genera, three families and the elevation of currently assigned genera to subfamilies. The lytic module proteins, endolysins, and holins were also characterized, revealing four distinct endolysin organizations with diverse domain architectures. Notably, the amidase_3 and LysM domains were highly conserved and subjected to purifying selection within the C. difficile phage genomes. This is the first comprehensive comparative study regarding C. difficile phage genomes. Our study provides valuable genomic insights that add to the current understanding of the phages. Our taxonomic analysis may improve the classification scheme of C. difficile phages and aid in the future classification of newly isolated C. difficile phage genomes.

genomics↗

bioRxiv2023

Labile assembly of a tardigrade protein induces biostasis

Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins that form gels. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of gelation for CAHS D similar to that of intermediate filaments. We show that gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fiber-like condensates during osmotic stress. Condensation of CAHS D improves survival of osmotically shocked cells through at least two mechanisms: reduction of cell volume change and reduction of metabolic activity. Importantly, condensation of CAHS D is reversible and metabolic rates return to control levels after CAHS condensates are resolved. This work provides insights into how tardigrades induce biostasis through the self-assembly of CAHS gels.

physiology↗

bioRxiv2022

Nasopharyngeal competition dynamics are likely to be altered following vaccine introduction: bacteriocin prevalence and diversity among Icelandic and Kenyan pneumococci

Bacteriocins are antimicrobial peptides produced by bacteria to inhibit other bacteria in the surrounding environment. Streptococcus pneumoniae is a leading cause of disease worldwide and colonises the healthy human nasopharynx, where it competes for space and nutrients. Pneumococcal conjugate vaccines have reduced the incidence of disease, but they also restructure the bacterial population, and this restructuring likely alters the nasopharyngeal competition dynamics. Here, the distribution of bacteriocins was examined in over 5000 carriage and disease-causing pneumococci from Iceland and Kenya, recovered before and after the introduction of pneumococcal vaccination. Overall, up to eleven different bacteriocin gene clusters were identified per pneumococcus. Significant differences in the prevalence of bacteriocins were observed before and after vaccine introduction, and among carriage and disease-causing pneumococci, which were largely explained by the bacterial population structure. Genetically similar pneumococci generally harboured the same bacteriocins although sometimes different repertoires of bacteriocins were observed, which suggested that horizontal transfer of bacteriocin clusters had occurred. These findings demonstrated that vaccine-mediated changes in the pneumococcal population altered the prevalence and distribution of bacteriocins. The consequences of this for pneumococcal colonisation and disease remain to be determined.

genomics↗

bioRxiv2021

A Co-abundant Gene Analysis for Identification of Gut Microbial Strains Associated with Immune Responses to Oral Cholera Vaccine

The degree of protection conferred after receiving an oral cholera vaccine (OCV) varies based on age, prior exposure to Vibrio cholerae, and unknown factors. Recent evidence suggests that the microbiota may mediate some of the unexplained differences in oral vaccine responses. We used metagenomic sequencing of the microbiota at the time of vaccination, and then related microbial features to immune responses after OCV using a reference-independent gene-level analysis. We found that the presence of sphingolipid-producing bacteria was associated with the development of protective immune responses after OCV. We experimentally tested these results by stimulating human macrophages with Bacteroides xylanisolvens metabolites and found that sphingolipid-containing extracts increased innate immune responses to OCV antigens. Our findings demonstrate a new analytic method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome, and in validating this tool, we identified that microbe-derived sphingolipids impact in vitro immune responses to OCV antigens.

microbiology↗

bioRxiv2020

Interactive effects of temperature, water, and nitrogen availability on the growth, floral traits, and pollination of white mustard,

Changes in environmental conditions are likely to have a complex effect on the growth of plants, their phenology, plant-pollinator interactions, and reproductive success. The current world is facing an ongoing climate change along with other human-induced environmental changes. Most research has focused on the impact of increasing temperature as a major driving force for climate change, but other factors may have important impacts on plant traits and pollination too and these effects may vary between different seasons. In addition, it is likely that the effects of multiple environmental factors, such as increasing temperature, water stress, and nitrogen enrichment are not independent. Therefore, we tested the impact of three key factors - season, water, and nitrogen supply - on plant traits, pollination, and seed production in Sinapis alba (Brassicaceae). Plants were grown in three seasons with two levels of water and nitrogen supply in a factorial design. We collected data on multiple vegetative and floral traits and assessed the response of pollinators in the field. Additionally, we evaluated the effect of growing conditions on seed set in plants exposed to pollinators and in hand-pollinated plants. Our results show that water stress impaired vegetative growth, decreased flower production, reduced visitation by pollinators and seed set, while nitrogen availability played an important role in nectar production. Seasonality modulated the effect of water and nitrogen availability on vegetative and floral traits and strongly affected flowering phenology and flower production. We demonstrated that changes in water and nitrogen availability alter plant vegetative and floral traits, which impacts flower visitation and consequently plant reproduction. We conclude that ongoing environmental changes such as altered precipitation regimes and nitrogen enrichment may thus affect plant-pollinator interactions with negative consequences for the reproduction of wild plants and insect-pollinated crops.

ecology↗

bioRxiv2020

Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa and related species

Long noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression were analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels and when both were present, there were further increase in DNA methylation levels. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. Brassica rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events, but the detailed mechanism is not known. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of the B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and offers insights into the function of lncRNA in the Brassica genus.

plant biology↗

bioRxiv2020

Humans surviving cholera develop antibodies against Vibrio cholerae O-specific polysaccharide that inhibit pathogen motility

The mechanism of protection against cholera afforded by previous illness or vaccination is currently unknown. We have recently shown that antibodies targeting O-specific polysaccharide (OSP) of Vibrio cholerae correlate highly with protection against cholera. V. cholerae is highly motile and possesses a flagellum sheathed in O-specific polysaccharide (OSP), and motility of V. cholerae correlates with virulence. Using high speed video microscopy, and building upon previous animal-related work, we demonstrate that sera, polyclonal antibody fractions, and OSP-specific monoclonal antibodies recovered from humans surviving cholera block V. cholerae motility at both subagglutinating and agglutinating concentrations. This anti-motility effect is reversed by pre-adsorbing sera and polyclonal antibody fractions with purified OSP; and is associated with OSP-specific but not flagellin-specific monoclonal antibodies. F[ab] fragments of OSP-specific polyclonal antibodies do not inhibit motility, suggesting a requirement for antibody-mediated crosslinking in motility inhibition. We show that OSP-specific antibodies do not directly affect V. cholerae viability, but that OSP-specific monoclonal antibody highly protects against death in the murine cholera model. We used in vivo competitive index studies to demonstrate that OSP-specific antibodies impede colonization and survival of V. cholerae in intestinal tissues, and that this impact is motility-dependent. Our findings suggest that the impedance of motility by antibodies targeting V. cholerae OSP contributes to protection against cholera. IMPORTANCECholera is a severe dehydrating illness of humans caused by Vibrio cholerae. V. cholerae is a highly motile bacterium that has a single flagellum covered in lipopolysaccharide (LPS) displaying O-specific polysaccharide (OSP), and V. cholerae motility correlates with its ability to cause disease. The mechanisms of protection against cholera are not well understood; however, since V. cholerae is a non-invasive intestinal pathogen, it is likely that antibodies that bind the pathogen or its products in the intestinal lumen contribute to protection from infection. Here, we demonstrate that OSP-specific antibodies isolated from humans surviving cholera in Bangladesh inhibit V. cholerae motility and are associated with protection against challenge in a motility-dependent manner.

microbiology↗

bioRxiv2020

Increasing habitat loss and human disturbances in the world's largest mangrove forest: the impact on plant-pollinator interactions

The Sundarbans, the largest mangrove forest in the world and a UNESCO world heritage site has been facing an increasing pressure of habitat destruction. Yet, no study has been conducted to test how human disturbances are affecting plant-pollinator interactions in this unique ecosystem. Hence, we aimed to provide the first insight of the impact of habitat loss and human disturbances on the pollinator communities in the Sundarbans. We selected 12 sites in the North-Western region of the Sundarbans, along a gradient of decreasing habitat loss and human activities from forest fragments near human settlements to continuous pristine forest, where we studied insect pollinators of two mangrove plant species, Acanthus ilicifolius and Avicennia officinalis. Our results show that different pollinator groups responded to the disturbance gradient differently. For example, the abundance of Apis dorsata, one of the three local species of honey bees, increased gradually from the village area towards the deep pristine forest. On the other hand, A. cerana and A. florea were found in the village sites and completely absent in the deep forest. Although pollinator community composition changed along the disturbance gradient, their efficacy in pollination did not seem to be significantly affected. However, lower plant diversity and low understory plant cover in the forest patches nearby the village indicated that human disturbances not only affected pollinator community composition but also played a major negative role in the regeneration of the forest. Our study provides first insights into plant-pollinator interactions in the Sundarbans and demonstrates that more research is needed to inform conservation of this unique habitat.

ecology↗

bioRxiv2020

Proteome Exploration of Legionella pneumophila for Identifying Novel Therapuetics: A Hierarchical Subtractive Genomics and Reverse Vaccinology Approach

Legionella pneumophila, the causative agent of a serious type of pneumonia (lung infection) called Legionnaires disease. It is emerging as an antibacterial resistant strain day by day. Hence, the identification of novel drug targets and vaccine candidates is essential to fight against this pathogen. Herein attempts were taken through subtractive genomics approach on complete proteome of L. pneumophila to address the challenges of multidrug resistance. A total 2930 proteins from L. pneumophila proteome were investigated through diverse subtractive proteomics approaches, e.g., identification of human non-homologous and pathogen-specific essential proteins, druggability and anti-target analysis, prediction of subcellular localization, human microbiome non-homology screening, protein-protein interactions studies in order to find out effective drug and vaccine targets. Only 3 were identified that fulfilled all these criteria and proposed as novel drug targets against L. pneumophila. Furthermore, outer membrane protein TolB was identified as potential vaccine target with better antigenicity score and allowed for further in silico analysis to design a unique multiepitope subunit vaccine against it. Antigenicity and transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis, and molecular docking approach were adopted to generate the most potent epitopes. The final vaccine was constructed by the combination of highly immunogenic epitopes along with suitable adjuvant and linkers. The designed vaccine construct showed higher binding interaction with different MHC molecules and human immune TLR2 receptors with minimum deformability at molecular level. The translational potency and microbial expression of the vaccine protein was also analyzed using pET28a(+) vector. The present study aids in the development of novel therapeutics and vaccine candidates for efficient treatment of the infections caused by Legionella pneumophila. However, further wet lab-based investigations and in vivo trials are highly recommended to experimentally validate our prediction.

bioinformatics↗

bioRxiv2020

An empirical attack tolerance test alters the structure and species richness of plant-pollinator networks

Ecological network theory hypothesizes a link between structure and stability, but this has mainly been investigated in-silico. In an experimental manipulation, we sequentially removed four generalist plants from real plant-pollinator networks and explored the effects on, and drivers of, species and interaction extinctions, network structure and interaction rewiring. Our results indicate that cumulative species and interaction extinctions increased faster with generalist plant loss than what was expected by co-extinction models, which predicted the survival or extinction of many species incorrectly. In addition, network nestedness decreased, modularity increased, and opportunistic random interactions and structural unpredictability emerged, which are all indicators of network instability and fragility. Conversely, interaction reorganization (rewiring) was high, asymmetries between network levels emerged as plants increased their centrality. From the experimental manipulations of real networks, our study shows how plant-pollinator network structure has low stability and changes towards a more fragile state when generalist plants are lost.

ecology↗

bioRxiv2019

Does a strong reduction of colony workforce affect the foraging strategy of a social pollinator?

The way pollinators gather resources may play a key role for buffering their population declines. Social pollinators like bumblebees could adjust their foraging after significant workforce reductions to keep provisions to the colony optimal, especially in terms of pollen quality, diversity, and quantity. To test what effects a workforce reduction causes on the foraging for pollen, colonies of the bumblebee Bombus terrestris were experimentally manipulated in field by removing half the number of workers. The pollen pellets of the workers were taxonomically identified with DNA metabarcoding, a ROC approach was used to filter out underrepresented OTUs, and video cameras and network analyses were employed to investigate foraging strategies and behaviour. The results suggested that the plant diversity in the pollen pellets was high but plant identity and pollen quantity traits were influenced mainly by plant phenology. During the experiment, although the treated colonies increased foraging effort in relation to control nests, only minor changes in the diet breadth and in the other node-level and network-level indices were observed after workforce removal. Therefore, a consistency in the bumblebees feeding strategies emerges despite the lowered workforce, which questions the ability of social pollinators to adjust their foraging in the field.

ecology↗

bioRxiv2019

Oral immunization with a probiotic cholera vaccine induces broad protective immunity against Vibrio cholerae colonization and disease in mice

Oral cholera vaccines (OCVs) are being increasingly employed, but current killed formulations generally require multiple doses and lack efficacy in young children. We recently developed a new live-attenuated OCV candidate (HaitiV) derived from a Vibrio cholerae strain isolated during the 2010 Haiti cholera epidemic. HaitiV exhibited an unexpected probiotic-like activity in infant rabbits, preventing intestinal colonization and disease by wild-type V. cholerae before the onset of adaptive immunity. However, it remained unknown whether HaitiV would behave similarly to other OCVs to stimulate adaptive immunity against V. cholerae. Here, we orally immunized adult germ-free female mice to test HaitiVs immunogenicity. HaitiV safely and stably colonized vaccinated mice and induced known adaptive immune correlates of cholera protection within 14 days of administration. Pups born to immunized mice were protected against lethal challenges of both homologous and heterologous V. cholerae strains. Cross-fostering experiments revealed that protection was not dependent on vaccine colonization in or transmission to the pups. These findings demonstrate the protective immunogenicity of HaitiV and support its development as a new tool for limiting cholera. Author summaryVaccines for cholera are gaining acceptance as public health tools for prevention of cholera and curtailing the spread of outbreaks. However, current killed vaccines provide minimal protection in young children, who are especially susceptible to this diarrheal disease, and do not stimulate immunity against antigens that may only be expressed by live bacteria during infection. We recently developed HaitiV, an extensively engineered live-attenuated oral cholera vaccine candidate, derived from a clinical isolate from the Haiti cholera outbreak. Here, we found that the HaitiV induces immunological correlates of protection against cholera in germ free mice and leads to protection against disease in their offspring. Protection in this model was dependent on passively acquired factors in the milk of immunized dams and not transmission or colonization of HaitiV. Coupling the immunogenicity data presented here with our previous observation that HaitiV can protect from cholera prior to the induction of adaptive immunity, suggests that HaitiV may provide both rapid-onset short-term protection from disease while eliciting stable and long-lasting immunity against cholera.

microbiology↗

bioRxiv2018

Prophages and satellite prophages are widespread among Streptococcus species and may play a role in pneumococcal pathogenesis

Prophages (viral genomes integrated within a host bacterial genome) are abundant within the bacterial world and are of interest because they often confer various phenotypic traits to their hosts, such as by encoding genes that increase pathogenicity. Satellite prophages are parasites of parasites that rely on the bacterial host and another helper prophage for survival. We analysed >1,300 genomes of 70 different Streptococcus species for evidence of prophages and identified nearly 800 prophages and satellite prophages, the majority of which are reported here for the first time. We show that prophages and satellite prophages were widely distributed among streptococci, were two clearly different entities and each possessed a structured population. There was convincing evidence that cross-species transmission of prophages is not uncommon. Furthermore, Streptococcus pneumoniae (pneumococcus) is a leading human pathogen worldwide, but the genetic basis for its pathogenicity and virulence is not yet fully understood. Here we report that over one-third of pneumococcal genomes possessed satellite prophages and demonstrate for the first time that a satellite prophage was associated with virulence in a murine model of infection. Overall, our findings demonstrate that prophages are widespread components of Streptococcus species and suggest that they play a role in pneumococcal pathogenesis.

genomics↗

bioRxiv2018

Experimental loss of generalist plants reveals alterations in plant-pollinator interactions and a constrained flexibility of foraging

Species extinctions undermine ecosystem functioning but species do not disappear at random. Ecosystem dynamics are ruled by a subset of dominant species, but it is not clear how losing several of these key species would affect plant-pollinator interactions. We tested how the experimental loss of the most highly visited generalist plants would affect flower visitor abundances (visitation) and pollinator effectiveness (quantity of pollen-tubes within pistils) in several sites. Significant changes in the plant-pollinator communities were detected. Firstly, visitation decreased after removing 1-2 most visited plants, suggesting that these species mostly facilitate other plants by keeping high flower visitor abundances in the sites. Nevertheless, we recorded within-site variations of these trends, especially among sampled transects and among plant species, suggesting that complex facilitation-competition interactions occur among plants, but that these vary among transects within the same sites. Pollinator effectiveness fluctuated but not in a clear linear way and was not directly linked to changes of flower visitation. This suggests that fluctuations of pollinator effectiveness might be due to destabilization of the pollinators by the removal of key resources. In addition, we detected a constrained flexibility of the foraging of flower visitors because they did not switch among flower shapes and they favoured specific plant traits such as high sugar content, small inflorescences and taller plants. Indeed, these constraints would eventually limit utilisation of new resources after perturbations, possibly undermining the stability of the system. In conclusion, our work demonstrates that the loss of dominant, highly generalist plants alters plant-pollinator interactions with implications for pollination and insect foraging. Therefore, in order to preserve ecosystems, generalist plants should not get lost, because they sustain the complex pattern of interactions between plants and flower visitors.

ecology↗