Biology subjects

Jasper, M.

Publications and source records attributed to Jasper, M..

6 recordsLinked to original sources

bioRxiv2024

Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion

Bacteria use invertible genetic elements known as invertons to generate heterogeneity amongst a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promising for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the result-ing inverton predictions. Here, we developed a customized bioinformatic workflow - PhaseFinderDC - to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons. Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes.

microbiology↗

bioRxiv2024

Gut microbiota gate host exposure to metabolites from dietary Solanums

Dietary plants are molecularly rich but the fates of these compounds post-ingestion and their implications for human health are largely unknown. Here, we systematically characterized the major chemical contributions of widely consumed Solanum species (nightshades) to the human metabolome. Using untargeted metabolomics, we found that a series of steroidal alkaloids resulting from glycoalkaloids tomatine, solanine, and chaconine are dominant diet-derived compounds in systemic circulation following ingestion of tomato and potato. By comparing serum and tissue metabolomes of colonized and microbiome-depleted mice, we determined that the gut microbiota modifies these compounds extensively, altering their absorption and gating host exposure. By screening the metabolic products in human urine and stool samples, we established that steroidal glycoalkaloid metabolism varies inter-individually in a population. Furthermore, using a collection of representative human commensal type strains, we found that a limited set of strains is responsible for steroidal glycoalkaloid metabolism, with the chemical output of a community determined by its strain-level composition. These findings enabled the rational design of complex synthetic microbial communities that controlled host exposure to steroidal alkaloid metabolites in vivo. Importantly, microbial metabolism of Solanum metabolites alters their acetylcholinesterase inhibition in vitro and gut motility in vivo. Our study provides insights into the molecular mechanisms of a diet-microbiome interactions and the effects of dietary metabolites on host physiology.

microbiology↗

bioRxiv2022

Genome-wide SNPs of vegetable leafminer, Liriomyza sativae: insights into the recent Australian invasion

Liriomyza sativae, the vegetable leafminer, is a serious agricultural pest originally from the Americas which has now colonized all continents except Antarctica. In 2015, L. sativae arrived on the Australian mainland and established on the Cape York Peninsula in the northeast of the country. Here, we assessed genetic variation in L. sativae based on genome-wide single nucleotide polymorphisms (SNPs) generated by double-digest restriction-site associated DNA sequencing (ddRAD-seq) to uncover the potential origin(s) of this pest in Australia and contribute to reconstructing its global invasion history. Our principal component analyses (PCA) results suggested that Australian mainland populations were genetically close to populations from the Torres Strait and had connections to Bali and Papua New Guinea (PNG), whereas populations from Asia and Africa were more distantly related. Hawaii was genetically distinct from populations from Asia, Africa and Australia. Co-ancestry analyses pointed to signals of gene flow from the Torres Strait into the Australian mainland, while Indonesia/PNG were the likely sources of the initial invasion into the Torres Strait. Admixture analyses further revealed that L. sativae from the Torres Strait had genetic diversity originating from multiple sources, which has now spread to the Australian mainland. The L. sativae lineages from Asia/Africa appear closely related and may share co-ancestry. Isolation by distance (IBD) was found at a broad global scale, but not within small regions, suggesting human-mediated factors contribute to the local spread of this pest. Overall, our findings highlight the challenges in quarantine measures aimed at restricting the distribution of this global pest.

bioinformatics↗

bioRxiv2020

Unbiased population heterozygosity estimates from genome-wide sequence data

O_LIHeterozygosity is a metric of genetic variability frequently used to inform the management of threatened taxa. Estimating observed and expected heterozygosities from genome-wide sequence data has become increasingly common, and these estimates are often derived directly from genotypes at single nucleotide polymorphism (SNP) markers. While many SNP markers can provide precise estimates of genetic processes, the results of downstream analysis with these markers may depend heavily on upstream filtering decisions. C_LIO_LIHere we explore the downstream consequences of sample size, rare allele filtering, missing data thresholds and known population structure on estimates of observed and expected heterozygosity using two reduced-representation sequencing datasets, one from the mosquito Aedes aegypti (ddRADseq) and the other from a threatened grasshopper, Keyacris scurra (DArTseq). C_LIO_LIWe show that estimates based on polymorphic markers only (i.e. SNP heterozygosity) are always biased by global sample size (N), with smaller N producing larger estimates. By contrast, results are unbiased by sample size when calculations consider monomorphic as well as polymorphic sequence information (i.e. genome-wide or autosomal heterozygosity). SNP heterozygosity is also biased when differentiated populations are analysed together, while autosomal heterozygosity remains unbiased. We also show that when nucleotide sites with missing genotypes are included, observed and expected heterozygosity estimates diverge in proportion to the amount of missing data permitted at each site. C_LIO_LIWe make three recommendations for estimating genome-wide heterozygosity: (i) autosomal heterozygosity should be reported instead of (or in addition to) SNP heterozygosity; (ii) sites with any missing data should be omitted; (iii) populations should be analysed in independent runs. This should facilitate comparisons within and across studies and between observed and expected measures of heterozygosity. C_LI

genomics↗

bioRxiv2019

An elusive endosymbiont: Does Wolbachia occur naturally in Aedes aegypti?

Wolbachia are maternally-inherited endosymbiotic bacteria found within many insect species. Aedes mosquitoes experimentally infected with Wolbachia are being released into the field for Aedes-borne disease control. These Wolbachia infections induce cytoplasmic incompatibility which is used to suppress populations through incompatible matings or replace populations through the reproductive advantage provided by this mechanism. However the presence of naturally-occurring Wolbachia in target populations could interfere with both population replacement and suppression programs depending on the compatibility patterns between strains. Aedes aegypti were thought to not harbor Wolbachia naturally but several recent studies have detected Wolbachia in natural populations of this mosquito. We therefore review the evidence for natural Wolbachia infections in Ae. aegypti to date and discuss limitations of these studies. We draw on research from other mosquito species to outline the potential implications of natural Wolbachia infections in Ae. aegypti for disease control. To validate previous reports, we obtained a laboratory population of Ae. aegypti from New Mexico, USA, that harbors a natural Wolbachia infection, and we conducted field surveys in Kuala Lumpur, Malaysia where a natural Wolbachia infection has also been reported. However, we were unable to detect Wolbachia infection in both the laboratory and field populations. Because the presence of naturally-occurring Wolbachia in Ae. aegypti could have profound implications for Wolbachia-based disease control programs, it is important to continue to accurately assess the Wolbachia status of target Aedes populations.

ecology↗

bioRxiv2019

A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito

Understanding past dispersal and breeding events can provide insight into ecology and evolution, and can help inform strategies for conservation and the control of pest species. However, parent-offspring dispersal can be difficult to investigate in rare species and in small pest species such as mosquitoes. Here we develop a methodology for estimating parent-offspring dispersal from the spatial distribution of close kin, using pairwise kinship estimates derived from genome-wide single nucleotide polymorphisms (SNPs). SNPs were scored in 162 Aedes aegypti (yellow fever mosquito) collected from eight close-set, high-rise apartment buildings in an area of Malaysia with high dengue incidence. We used the SNPs to reconstruct kinship groups across three orders of kinship. We transformed the geographical distances between all kin pairs within each kinship category into axial standard deviations of these distances, then decomposed these into components representing past dispersal events. From these components, we isolated the axial standard deviation of parent-offspring dispersal, and estimated neighbourhood area (129 m), median parent-offspring dispersal distance (75 m), and oviposition dispersal radius within a gonotrophic cycle (36 m). We also analysed genetic structure using distance-based redundancy analysis and linear regression, finding isolation by distance both within and between buildings and estimating neighbourhood size at 268 individuals. These findings indicate the scale required to suppress local outbreaks of arboviral disease and to target releases of modified mosquitoes for mosquito and disease control. Our methodology is readily implementable for studies of other species, including pests and species of conservation significance.

ecology↗