Biology subjects

Trivedi, U.

Publications and source records attributed to Trivedi, U..

15 recordsLinked to original sources

bioRxiv2026

Evolutionary history and microbial cross-feeding shape lifestyle-stratified dominance of Bifidobacterium longum subspecies in infants

Bifidobacterium longum (Bl.) is a key early-life gut symbiont, yet its evolutionary origin and mechanisms underlying the global biogeographic distribution of its subspecies remain poorly resolved. Here, we compiled a global genomic atlas of >7,000 MAGs/genomes from infants, domesticated animals, non-human primates, and ancient humans. High-resolution phylogenomic and functional analyses expanded infant-associated subspecies to five. Compared with non-human primates, B. longum was more prevalent in domesticated animals and ancient humans dating from 150 to 1,500 years ago. Moreover, human- and livestock-derived lineages from the same geographic regions clustered together, suggesting potential host-associated transmission. Ecologically, Bl. infantis and Bl. longum predominated in non-Western and Western infants, respectively, independent of breastfeeding, delivery mode, or antibiotic exposure. Instead, their distribution was associated with co-occurring microbes and HMO-driven cross-feeding interactions. These findings explain subspecies differentiation in the gut microbiota of Western and non-Western infants and provide a framework for community-mediated interventions in early life.

microbiology↗

bioRxiv2025

Micro-scale spatial metagenomics: revealing high-resolution spatial biogeography of gut microbiomes

Spatial organisation is a fundamental yet poorly resolved aspect of gut microbial ecology. Conventional shotgun metagenomics provides rich functional information but relies on homogenised, macro-scale samples that obscure the micron-scale distributions critical for understanding microbial community dynamics. Here, we introduce Micro-Scale Spatial Metagenomics (MSSM), a new methodological framework that couples laser micro-dissection of tissue sections, ultra-low-input library preparation, and genome-resolved bioinformatics to reconstruct microbial communities from intestinal microsamples measuring as little as [~]500 {micro}m{superscript 2} ({approx}100 bacterial cells). We describe a fully optimised laboratory and computational pipeline that enables quantitative, strain-resolved, and functionally informed spatial profiling directly from intact gut tissue. Using chicken intestinal samples, we validated MSSM through combinatorial single-cell fluorescence in situ hybridisation (FISH) imaging and comparisons with macro-scale metagenomics, demonstrating its robustness and accuracy. MSSM captured fine-scale heterogeneity in taxonomic and functional composition across intestinal cryosections, hinting at spatially structured assemblages and segregation of metabolic capacities. Strain-level analyses uncovered coexisting Lawsonibacter lineages exhibiting distinct spatial distributions and host-specific occurrence patterns, while SNP-level microdiversity analyses showed that genetically coherent clonal populations cluster at spatial scales below [~]200 {micro}m. By enabling shotgun metagenomics at micron resolution, MSSM closes a longstanding methodological gap and provides a scalable platform for studying microbial ecosystems in situ. This approach unlocks a previously inaccessible view of microbial biogeography, offering new opportunities to investigate host-microbe and microbe-microbe interactions, and the spatial principles governing gut ecosystems. Significance statementUnderstanding how microbial communities are organised in space is essential to explaining their ecological and functional roles, yet microbiome research still relies overwhelmingly on bulk, spatially averaged measurements. We introduce micro-scale spatial metagenomics (MSSM), the first method that brings shotgun metagenomics to the microscale, enabling direct measurement of functional and taxonomic variation across regions containing as few as [~]100 cells. Unlike existing spatial approaches, MSSM reconstructs complete genomes and resolves strain-level diversity within intact tissue, allowing researchers to map metabolic potential, microdiversity, and community structure in situ. By coupling high-resolution sequencing with spatial context, MSSM reveals a previously inaccessible layer of microbial organisation, transforming how host-associated ecosystems can be studied.

microbiology↗

bioRxiv2025

The reference-free pangenome of Arabidopsis thaliana

For several decades, scientists relied on unique reference genomes as the basis for various genomic studies. This methodology presents multiple drawbacks, particularly for variation studies, often yielding unrepresentative and incomplete observations regarding the diversity of the species or group under study. Pangenomes are collections of genomic sequences from several individuals of a species or population, which allow to overcome the limitations of studies based on a single reference genome. In this study, we produced a 93-assembly pangenome of the model plant Arabidopsis thaliana using the reference-free method PanGenome Graph Builder (PGGB). The aim was to investigate the diversity within this species using this novel methodology, encompassing genomic sequences, genes, and pseudogenes. The pangenome exhibited a total length of 488.78 Mb, consisting of 30,391,243 nodes and 7,189,634 edges. We mapped a total of 2,325,577 genes and 23,894 pseudogenes across 93 assemblies, of which 36% and 0.9%, respectively, were classified as core. The observed variation in terms of genes and especially pseudogenes related to the geographical distance between sampling sites. Since the simulated pangenome growth curve based on gene did not reach a plateau, new accessions could potentially expand the represented diversity. This study enriches our understanding of intra-specific variation in A. thaliana and provides a new viewpoint on the potential applications of pangenomes in diversity research.

genomics↗

bioRxiv2025

Addressing efficacy of everyday hygiene cleansing products in context of sustainable handwashing behavior in the post-pandemic era

Simple hygiene behaviour such as washing hands is key to improving health of individuals and reducing community transmission of communicable diseases such as respiratory and enteric infections. Consistent and relentless messaging by global and local health authorities had resulted in heightened hygiene awareness amongst the public during the COVID-19 pandemic. Unfortunately, many of the hygiene behaviours practiced during the pandemic have proven to be unsustainable in the immediate period following the pandemic. While CDC guidelines suggest washing hands with soap for a minimum of 20 seconds to prevent the spread of germs, a hygiene interventions effectiveness must be evaluated in context of the prevalent hygiene behaviour. Here we report our findings from an observational study conducted across India, Pakistan, Saudi Arabia, and United Arab Emirates focusing on handwashing habit of individuals in the post-pandemic period. Across all geographies, the time spent for lathering product on skin (contact time) for a significant majority of individuals recruited for the study was found to be 10 seconds and less. To ensure that marketed hygiene formulations such as liquid cleansers and sanitizers are efficacious in inactivating pathogens under conditions practiced by the majority as a part of their daily hand washing practices, we have investigated the in-vitro antimicrobial efficacy of several hygiene cleansing formulations at 10 seconds of contact time. Our results show that well-formulated cleansing solutions can reduce the input titre of both bacterial and viral pathogens by 99.9% or more, even with brief contact. With the global resurgence of both existing and emerging pathogens in the post-pandemic world, promoting sustainable handwashing practices for infection prevention remains a challenge as it is deeply rooted in the socio-economic fabric of many countries. Therefore, it is crucial to conduct regular studies like this to reassure end-users and combat complacency regarding the composition of everyday hygiene products. HighlightsO_LIStudies of handwashing behavior in 4 countries reveals significantly short lathering duration C_LIO_LIAntimicrobial efficacy testing of marketed products was conducted against a range of pathogens C_LIO_LISuitably formulated hygiene products can inactivate pathogens at short durations of contact C_LI

microbiology↗

bioRxiv2024

Colora: A Snakemake Workflow for Complete Chromosome-scale De Novo Genome Assembly

BackgroundDe novo assembly creates reference genomes that underpin many modern biodiversity and conservation studies. Large numbers of new genomes are being assembled by labs around the world. To avoid duplication of efforts and variable data quality, we desire a best-practice assembly process, implemented as an automated portable workflow. ResultsHere we present Colora, a Snakemake workflow that produces chromosome-scale de novo primary or phased genome assemblies complete with organelles using PacBio HiFi, Hi-C, and optionally ONT reads as input. The source code of Colora is available on GitHub: https://github.com/LiaOb21/colora. Colora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/?usage=LiaOb21%2Fcolora). ConclusionColora is a user-friendly, versatile, and reproducible pipeline that is ready to use by researchers looking for an automated way to obtain high-quality de novo genome assemblies.

genomics↗

bioRxiv2024

A workflow for practical training in ecological genomics using Oxford Nanopore long-read sequencing

Long-read single molecule sequencing technologies continue to grow in popularity for genome assembly and provide an effective way to resolve large and complex genomic variants. However, uptake of these technologies for teaching and training is hampered by the complexity of high molecular weight DNA extraction protocols, the time required for library preparation and the costs for sequencing, as well as challenges with downstream data analyses. Here, we present a full long-read workflow optimised for teaching, that covers each stage from DNA extraction, to library preparation and sequencing, to data QC and genome assembly and characterisation, that can be completed in under two weeks. We use a specific case study of plant identification, where students identify an anonymous plant sample by sequencing and assembling the genome and comparing it to other samples and to reference databases. In testing, long-read genome skimming of nine wild-collected plant species extracted with a modified kit-based approach produced an average of 8Gb of Oxford Nanopore data, enabling the complete assembly of plastid genomes, and partial assembly of nuclear genomes. In the classroom, all students were able to complete the protocols, and to correctly identify their plant samples based on BOLD searches of barcoding loci extracted from the plastid genome, coupled with phylogenetic analyses of whole plastid genomes. We supply all the learning material and raw data allowing this to be adapted to a range of teaching settings.

genomics↗

bioRxiv2023

Benchmarking of Hi-C tools for scaffolding de novo genome assemblies

The implementation of Hi-C reads in the de novo genome assembly allows to order large regions of the genome in scaffolds, obtaining chromosome-level assemblies. Several bioinformatics tools have been developed for genome scaffolding with Hi-C, and all have pros and cons which need to be carefully evaluated before adoption. We developed assemblyQC, a bash pipeline that combines QUAST, BUSCO, Merqury and, optionally, Liftoff, plus a gene positioning validation script to evaluate and benchmark the performance of three scaffolders, 3d-dna, SALSA2, and YaHS, on two de novo assembly of Arabidopsis thaliana obtained from the same raw PacBio HiFi and ONT data. In our analysis, YaHS proved to be the best-performing bioinformatic tool for scaffolding of de novo genome assembly.

genomics↗

bioRxiv2023

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition

Even in the absence of antibiotic exposure, the gut microbiome of infants has been shown to contain numerous antibiotic resistance genes (ARGs), but the mechanism for this remains unclear. In environmental bacteria, the selective advantage of ARGs can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes. However, this phenomenon is unknown from the human gut microbiome during early life despite frequent exposures to biocides and metals from an early age. Here, we conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity, especially E. coli. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes located near other ARGs, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of virulence genes was associated with low gut microbial maturity and that virulence genes showed even higher potential for mobility than ARGs. Our study highlights important constraints that need to be considered when developing strategies to combat ARG dissemination.

microbiology↗

bioRxiv2020

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

BackgroundViruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a five-month period using short and long-read sequencing. ResultsHybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7,682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a five-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community. Including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut. ConclusionsThe cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment.

microbiology↗

bioRxiv2020

A telomere to telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes

Eukaryotic chromosomes have phylogenetic persistence. In many taxa, the number of chromosomes is related to the number of centromeres. However, in some groups, such as rhabditid nematodes, centromeric function is distributed across multiple sites on each chromosome. These holocentric chromosomes might, a priori, be expected to be permissive of large-scale chromosomal rearrangement, as chromosomal fragments could still partition correctly and fusions would not generate lethal conflict between multiple centromeres. Here, we explore the phylogenetic stability of nematode chromosomes using a new telomere-to-telomere assembly of the rhabditine nematode Oscheius tipulae generated from nanopore long reads. The 60 Mb O. tipulae genome is resolved into six chromosomal molecules. We find evidence of specific chromatin diminution at all telomeres. Comparing this chromosomal O. tipulae assembly with chromosomal assemblies of diverse rhabditid nematodes we identify seven ancestral chromosomal elements (Nigon elements), and present a model for the evolution of nematode chromosomes through rearrangement and fusion of these elements. We identify frequent fusion events involving NigonX, the element associated with the rhabditid X chromosome, and thus sex-chromosome associated gene sets differ markedly between species. Despite the karyotypic stability, gene order within chromosomes defined by Nigon elements is not conserved. Our model for nematode chromosome evolution provides a platform for investigation of the tensions between local genome rearrangement and karyotypic evolution in generating extant genome architectures.

genomics↗

bioRxiv2020

Adaptive evolution of phenotypic switching during environmental change

Microbes are faced with environmental fluctuations and it is therefore important to understand how change affects bacterial evolution and population dynamics. Here, we evolved a model bacterium, Pseudomonas aeruginosa PA14, under both constant and changing conditions where settlement by biofilm formation or migration by swimming motility was induced. In changing environments, a heterogeneous population evolved with both specialists and generalists. Interestingly, over time, generalists were outcompeted despite being better at both phenotypes compared to the ancestor. However, generalists became dominant when faced with local competition after resettlement. Reintroduction into a burn wound model, the environment PA14 originally was isolated from, further suggested a tradeoff between niche breadth and peak fitness in agreement with the evolution experiments. Mutations in the c-di-GMP system were key for adaptation of the phenotypes. No mutants lost their ability to regulate c-di-GMP, but generalists acquired mutations that optimized their phenotypic response by efficiently adjusting c-di-GMP levels.

evolutionary biology↗

bioRxiv2020

The microbiome of captive hamadryas baboon

Hamadryas baboon is a highly social primate that lives in complex multilevel societies exhibiting a wide range of group behaviors akin to humans. Here, we report the comprehensive 16s rRNA gene analyses of group-living baboon microbiota across different body sites. Additionally, we compared the baboon and human microbiome of the oral cavity, gut and vagina. Our analyses show that the baboon microbiome is distinct from the human and baboon cohabitants share similar microbial profiles in multiple body sites. The oral, gut and vagina shared more bacterial ASVs in group-living baboons than in humans. The shared ASVs in baboons had significantly positive correlations, suggesting a potential bacterial exchange throughout the body. No significant differences in baboon gut microbiome composition within the maternity line and between maternity lines were detected, suggesting that the offspring acquire their gut microbiota primarily through bacterial exchange among cohabitants. Besides, Lactobacillus was not so predominant in baboon vagina as in the human vagina but was the most abundant genus in baboon gut. These data and findings can form the basis of future microbiome studies in baboons and be used as a reference to research where the microbiome is expected to impact human modeling with baboons.

microbiology↗

bioRxiv2018

Silent crickets reveal the genomic footprint of recent adaptive trait loss

Secondary trait loss is widespread and has profound consequences, from generating diversity to driving adaptation. Sexual trait loss is particularly common1. Its genomic impact is challenging to reconstruct because most reversals occurred in the distant evolutionary past and must be inferred indirectly2, and questions remain about the extent of disruption caused by pleiotropy, altered gene expression and loss of homeostasis3. We tested the genomic signature of recent sexual signal loss in Hawaiian field crickets, Teleogryllus oceanicus. Song loss is controlled by a sex-linked Mendelian locus, flatwing, which feminises male wings by erasing sound-producing veins. This variant spread rapidly under pressure from an eavesdropping parasitoid fly. We sequenced, assembled and annotated the T. oceanicus genome, produced a high-density linkage map, and localised flatwing on the X chromosome. We characterised pleiotropic effects of flatwing, including changes in embryonic gene expression and alteration of another sexual signal, chemical pheromones. Song loss is associated with pleiotropy, hitchhiking and genome-wide regulatory disruption which feminises flatwing male pheromones. The footprint of recent adaptive trait loss illustrates R. A. Fishers influential prediction that variants with large mutational effect sizes can invade genomes during the earliest stages of adaptation to extreme pressures, despite having severely disruptive genomic consequences.

evolutionary biology↗

bioRxiv2018

Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation

The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to their ecological specialism from other sources of selection and more random changes is a challenge. Here we describe the genome of Drosophila montana, the most extremely cold-adapted Drosophila species. We describe the genome, which is similar in size and gene content to most Drosophila species. We look for evidence of accelerated divergence from a previously sequenced relative, and do not find strong evidence for divergent selection on coding sequence variation. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. We also re-sequenced three populations of D. montana representing its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.

genomics↗

bioRxiv2017

Signatures of the evolution of parthenogenesis and cryptobiosis in the genomes of panagrolaimid nematodes

Most animal species reproduce sexually, but parthenogenesis, asexual reproduction of various forms, has arisen repeatedly. Parthenogenetic lineages are usually short lived in evolution; though in some environments parthenogenesis may be advantageous, avoiding the cost of sex. Panagrolaimus nematodes have colonised environments ranging from arid deserts to arctic and antarctic biomes. Many are parthenogenetic, and most have cryptobiotic abilities, being able to survive repeated complete desiccation and freezing. It is not clear which genomic and molecular mechanisms led to the successful establishment of parthenogenesis and the evolution of cryptobiosis in animals in general. At the same time, model systems to study these traits in the laboratory are missing.\n\nWe compared the genomes and transcriptomes of parthenogenetic and sexual Panagrolaimus able to survive crybtobiosis, as well as a non-cryptobiotic Propanogrolaimus species, to identify systems that contribute to these striking abilities. The parthenogens are most probably tripoids originating from hybridisation (allopolyploids). We identified genomic singularities like expansion of gene families, and selection on genes that could be linked to the adaptation to cryptobiosis. All Panagrolaimus have acquired genes through horizontal transfer, some of which are likely to contribute to cryptobiosis. Many genes acting in C. elegans reproduction and development were absent in distant nematode species (including the Panagrolaimids), suggesting molecular pathways cannot directly be transferred from the model system.\n\nThe easily cultured Panagrolaimus nematodes offer a system to study developmental diversity in Nematoda, the molecular evolution of parthenogens, the effects of triploidy on genomes stability, and the origin and biology of cryptobiosis.

evolutionary biology↗