Biology subjects

Jaspan, H. B.

Publications and source records attributed to Jaspan, H. B..

16 recordsLinked to original sources

bioRxiv2026

A sensitive and specific microchimerism detection method using custom designed genotyping and companion qPCR assays

Since first reports of the presence of a small number of cells from one individual persisting in another, researchers have developed a number of methods to detect microchimerism. Molecular based detection platforms range from gel electrophoresis to quantitative PCR to Next-Gen Sequencing. Central to all approaches is the need for informative polymorphic loci to effectively distinguish microchimeric cells from the host. However, we observed in our studies of maternal microchimerism that currently published approaches can limit the number of samples available for assessment due to the inability to identify an informative marker of the donor in the recipient. This was most striking in our studies of populations of African descent in which the use of HLA-based markers, a common approach, prevented the testing of 30-50% of participants. Other potential options were cost prohibitive or lacked sufficient sensitivity. To address this challenge, we developed a novel, simple, and low-cost approach that leverages global population frequency databases for polymorphism selection, reduces cost by amplifying multiple targets in one multiplex assay to complete genotyping, and has high sensitivity and specificity using rigorously designed qPCR assays to quantify microchimerism. Herein, we outline our design process, detailed assay protocol, and assessment of maternal microchimerism using this approach in two different populations of infants from the United States and South Africa.

molecular biology↗

bioRxiv2026

Relatedness of Gardnerella prophages and their endolysins

The Gardnerella genus includes a complex sub-taxonomy of bacterial species and subgroups which have been implicated in bacterial vaginosis. We analyzed G. leopoldii, G. swidsinski, G. piotii, and G. vaginalis genomes available in public databases and predicted proviral sequences using Cenote-Taker3. We clustered 266 prophage sequences into 140 viral genera level groupings that encode four distinct gene clusters and 19 different lysin proteins. Analysis of the bacterial and prophage sequence phylogenies reveals that while there were no specific prophage sequence lineages that infected each bacterial host, there is clustering of the prophage sequences by bacterial species within the Gardnerella genus.

microbiology↗

bioRxiv2026

Urea is a dynamic and functional component of mammalian breast milk

Urea is a constituent of human milk, yet its regulation and interactions with the infant gut microbiome remain unclear. Combining three human cohorts, a controlled mouse model, and complementary microbiome analyses, we show that milk urea increases across lactation, is conserved across mammals, and is not explained by circulating urea levels or maternal diet. Instead, we identify lactation-dependent remodeling of mammary urea-metabolism and transport pathways, including dynamic AQP3 localization in secretory epithelium, indicative of regulated transfer of circulating urea into breast milk. Alongside urea, maternal milk and stool provide complementary reservoirs of urea-metabolizing bacteria that help establish the infant "ureabiome", whose urea-utilization capacity is supported by metagenomics. This maternal-infant axis is context-dependent: infant formulas provide substantially higher urea levels than human milk, while functional assays show that urea supports both commensal and opportunistic bacteria in a concentration-dependent manner. Together, these findings define a maternal nitrogen axis through which lactation can shape the assembly and function of the infant gut microbiome.

microbiology↗

bioRxiv2026

Benchmarking virus identification tools on vaginal metagenomes

The vaginal microbiome is associated with reproductive and sexual health, yet its viral component remains understudied. A recent vaginal genome catalogue reported that 85.8% of its species-level viral groups were absent from all five viral databases examined. Viral identification tools depend on reference sequences, either directly or through their training data. Previous benchmarks used simulated or non-vaginal datasets. How well these tools generalise to vaginal metagenomes therefore remains unclear. We benchmarked 14 tools spanning five methodological approaches. Evaluations used controlled genome fragments, viral spike-in co-assemblies and virus-like particle (VLP)-enriched co-assemblies. A multi-evidence benchmark assessed 13 vaginal shotgun assemblies (primary cohort). An independent 30-sample cohort provided external validation. geNomad ranked first or second by Matthews correlation coefficient (MCC) in every ranked evaluation. VIBRANT achieved similar MCC to geNomad on the primary assemblies. It made eight false-positive calls among 11,577 negatives but recovered only 22% of viral contigs. VIBRANT ranked first in the independent cohort. Tool rankings agreed closely between cohorts (Spearman rho = 0.952; 95% CI 0.921 - 0.960). Detection of sequences lacking reference homologues differed substantially between tools. Two phage genomes without detectable reference homologues provided a controlled novelty test. Each evaluated composition-based tool recovered at least 74% of their 1,500-bp fragments. Marker- or reference-dependent tools recovered at most 31%. A separate analysis examined 48 unconfirmed candidate viral contigs lacking detectable nucleotide or protein homologues. Jaeger flagged 41, compared with four for VIBRANT and one for geNomad. On short fragments, attention-based tools achieved 4.0-5.5 times the mean area under the precision-recall curve of feature-based tools. ViraLM accounted for most of this difference. ViraLM also had the highest recall (sensitivity) of eukaryote-infecting viruses in the evaluated panel. VirSorter2 achieved the highest MCC on VLP-enriched contigs. These results support geNomad when prioritising overall classification performance and VIBRANT when minimising false-positive phage calls is the priority. ViraLM supports short-contig and eukaryote-infecting-virus detection. VirSorter2 supports identification in VLP-enriched assemblies, and Jaeger supports screening for candidate novel phages. These findings guide tool selection for studies investigating the vaginal virome in reproductive and sexual health.

microbiology↗

bioRxiv2026

Characterisation of vaginal Lactobacillus isolates from South African women towards the development of a biotherapeutic to optimise the vaginal microbiome

HIV remains among the worlds most serious healthcare challenges, with adolescent girls and young women in sub-Saharan Africa at particularly high risk of infection. Bacterial vaginosis (BV) is a key risk factor for HIV acquisition, however current treatment strategies are limited. Optimal vaginal Lactobacillus spp. protect against BV and HIV, largely through immunoregulatory and antimicrobial activities mediated in part by lactic acid. Towards the development of a Lactobacillus-containing live biotherapeutic for African women, we sampled 181 vaginal Lactobacillus isolates from 25 BV-negative South African women. Fifty isolates were selected for evaluation of inflammatory responses using vaginal epithelial cells, D- and L-lactate and lactic acid production and culture acidification. Aside from a single Lactobacillus salivarius strain, L. crispatus isolates acidified the culture media the most and produced the most D- and L-lactic acid. Inflammatory cytokine responses to Lactobacillus strains were variable, with L. crispatus eliciting the lowest levels of cytokine production. When all properties were evaluated collectively, L. crispatus strains exhibited the most desirable biotherapeutic characteristics. Whole genome sequence analysis of ten L. crispatus isolates showed that the majority were more closely related to one another than to isolates from other geographical regions. This supports the need for live biotherapeutics to be tailored for the population of intended use. No antimicrobial resistance elements were detected, while putative bacteriocins and intact prophage sequences were identified in all isolates. L. crispatus isolates displayed characteristics essential for optimal live biotherapeutic performance, however additional analysis is required to determine the functionality of identified putative prophages. ImportanceHIV is a leading cause of morbidity and mortality in sub-Saharan Africa, where adolescent girls and young women are three times more likely to acquire HIV than their male counterparts. A key risk factor for HIV is bacterial vaginosis (BV), a condition characterised by the loss of beneficial Lactobacillus species and increased abundance of non-optimal, inflammatory bacteria. Although BV affects approximately 25% of women in sub-Saharan Africa, effective therapeutics are lacking. Live biotherapeutics containing optimal Lactobacillus spp. represent a promising strategy to improve BV treatment outcomes and reduce HIV infection risk. We isolated 181 vaginal Lactobacillus spp. from 25 BV-negative South African women and characterized 50 selected isolates. This led to the identification of live biotherapeutic candidates for African women with distinct genomes compared to isolates from other geographical regions. This study contributes to current knowledge of the characteristics that should be considered when screening novel isolates for this purpose.

microbiology↗

bioRxiv2025

Circulating Chlamydia trachomatis-specific T Cell Immunity Reflects Widespread Exposure in South African Adolescents and Young Women

Chlamydia trachomatis remains the most prevalent bacterial sexually transmitted infection worldwide, with adolescent girls and young women (AGYW) disproportionately affected. Despite this, vaccine development is hindered by our limited understanding of protective immunity, particularly in the context of recurrent infections and immune-mediated pathology. Here, we characterised mucosal inflammation and systemic immune responses to C. trachomatis in South African AGYW (n=145), stratified by exposure history based on nucleic acid amplification testing (NAAT) and anti-C. trachomatis IgG levels. Cervicovaginal cytokines were quantified from menstrual cup secretions, and cervical and peripheral blood T cell activation assessed by flow cytometry. CD4+ T cell responses to recombinant MOMP were measured in a subset of 46 women who were NAAT-positive and/or seropositive. Untreated or recurrent C. trachomatis infection (NAAT+/IgG+) was associated with increased cervical T cell activation. All women with untreated or recurrent infections had detectable circulating C. trachomatis-specific CD4+ T cells in blood; however, response magnitude was 2.4-fold lower than in women with cleared or primary infections. Women with cleared infection had the highest proportions of C. trachomatis-specific multifunctional CD4+ T cells, while those with untreated or recurrent infections had almost none. Notably, systemic C. trachomatis-specific Th1 responses were inversely correlated with genital tract concentrations of inflammatory cytokines including IL-1{beta}, TNF, and IL-17. These findings demonstrate that both the magnitude and quality of the systemic CD4+ T cell responses are critical components of protective immunity to C. trachomatis, and may limit mucosal immunopathology, which has important implications for vaccine strategies and evaluation in high-risk populations.

immunology↗

bioRxiv2024

Diminished placental Factor XIIIA1 expression associates with long term ART and preterm birth in pregnant people living with HIV.

We previously showed a link between maternal vascular malperfusion and pre-term birth (PTB) in pregnant people living with HIV (PPLH) initiating antiretroviral treatment (ART) before pregnancy, indicating poor placental vascularisation. After measuring antenatal plasma angiogenic factors to seek mechanistic insights, low levels of plasma Factor XIIIA1 (FXIIIA1) and vascular-endothelial-growth-factor (VEGF) was significantly associated with PTB at the time closest to delivery (median 34 weeks) in PPLH initiating ART before pregnancy. Knowing that FXIIIA1 is crucial for haemostasis, angiogenesis, implantation and pregnancy maintenance and that expression is found on placental macrophages (Hofbauer cells), we examined placentae at delivery from matching participants who either initiating ART before pregnancy or during gestation. Highest FXIIIA1 expression was on Hofbauer cells but was significantly lower in PTB regardless of HIV infection, but was significantly lower in PPLH in PTB from women who initiated ART before pregnancy. To test the hypothesis that antiretroviral drugs may disrupt vascularisation in the placenta, we used a human umbilical vein endothelial cell (HUVEC) matrigel angiogenesis assay. We identified that addition of pre-treated FXIIIA1-expressing MCSF-and IL-10-induced placenta-like macrophages with physiological concentrations of tenofovir, 3TC, and efavirenz resulted in significantly inhibited angiogenesis; akin to the inhibition observed with titratable concentrations of ZED1301, an inhibitor of FXIIIA1. Overall, an efavirenz-containing ART combination inhibits vasculogenesis without causing toxicity and likely does so through inhibition of a FXIIIA1-mediated-placental macrophage pathway.

immunology↗

bioRxiv2024

Exposure to HIV alters the composition of maternal microchimeric T cells in infants

Infants exposed to HIV but uninfected (iHEU) display altered cellular immunity and are at increased risk of infection through poorly understood mechanisms. We previously reported that iHEU have lower levels of maternal microchimerism (MMc), maternal cells transferred to the offspring in utero/during breastfeeding. We evaluated MMc levels in T cell subsets in iHEU and HIV unexposed infants (iHU) to determine whether a selective deficiency in MMc may contribute to altered cellular immunity. Across all infants, MMc levels were highest in CD8+ T cells; however, the level of MMc in the CD8 T cell subset was significantly lower in iHEU compared to iHU.

immunology↗

bioRxiv2023

A novel non-invasive method to sample immune cells in the lower female genital tract

T cells in the human female genital tract (FGT)2 are key mediators of susceptibility to and protection from infection, including HIV and other sexually transmitted infections. There is a critical need for increased understanding of the distribution and activation of T cell populations in the FGT, but current sampling methods require a healthcare provider and are expensive, limiting the ability to study these populations longitudinally. To address these challenges, we have developed a method to sample immune cells from the FGT utilizing disposable menstrual discs which are non-invasive, self-applied, and low-cost. To demonstrate reproducibility, we sampled the cervicovaginal fluid (CVF)3 of healthy, reproductive-aged individuals using menstrual discs over three sequential days. CVF was processed for cervicovaginal cells, and high parameter flow cytometry was used to characterize immune populations. We identified large numbers of live, CD45+ leukocytes, as well as distinct populations of T cells and B cells. Within the T cell compartment, activation and suppression status of T cell subsets were consistent with previous studies of the FGT utilizing current approaches, including identification of both tissue resident and migratory populations. In addition, the T cell population structure was highly conserved across days within individuals but divergent across individuals. Our approach to sample immune cells in the FGT with menstrual discs will decrease barriers to participation and empower longitudinal sampling in future research studies.

immunology↗

bioRxiv2023

Disrupted memory T cell expansion in HIV-exposed uninfected infants is preceded by premature skewing of T cell receptor clonality.

While preventing vertical HIV transmission has been very successful, the increasing number of HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared to HIV-unexposed and uninfected infants (iHUU). Immune developmental differences between iHEU and iHUU remains poorly understood and here we present a longitudinal multimodal analysis of infant immune ontogeny that highlights the impact of HIV/ARV exposure. Using mass cytometry, we show alterations and differences in the emergence of NK cell populations and T cell memory differentiation between iHEU and iHUU. Specific NK cells observed at birth were also predictive of acellular pertussis and rotavirus vaccine-induced IgG and IgA responses, respectively, at 3 and 9 months of life. T cell receptor V{beta} clonotypic diversity was significantly and persistently lower in iHEU preceding the expansion of T cell memory. Our findings show that HIV/ARV exposure disrupts innate and adaptive immunity from birth which may underlie relative vulnerability to infections.

immunology↗

bioRxiv2022

Bacterial Microbiome of Foreskin Tissue: Impact of Short-course PrEP and Host Inflammation

As part of the CHAPS randomized clinical trial, we sequenced a segment of the bacterial 16S rRNA gene from foreskin tissue of 144 adolescents from South Africa and Uganda collected during surgical penile circumcision after receipt of 1 to 2 doses of placebo, emtricitabine with tenofovir disoproxil fumarate, or emtricitabine with tenofovir alafenamide. We found a large proportion of Corynebacterium in addition to other anaerobic species. Cutibacterium acnes was more abundant among participants from South Africa than Uganda, though this made no difference in surgical recovery. We did not find a difference in bacterial populations by treatment received nor bacterial taxa that were differentially abundant between participants who received placebo versus active drug. Using RNAseq libraries from foreskin tissue of the same participants, we found negative correlations between the relative abundance of bacterial taxa and the expression of genes downstream of the innate response to bacteria and regulation of the inflammatory response. When participants were divided into clusters based on bacterial community composition, two main clusters emerged which were distinguished by high and low bacterial diversity. Random forest classification showed higher expression of NFATC3 and SELENOS and lower expression of STAP1 and NLRP6 in the higher diversity group compared to the lower. Our results show no difference in the tissue microbiome of the foreskin with short-course PrEP but that bacterial taxa were largely inversely correlated with gene expression, consistent with non-inflammatory colonization. Author SummaryWe investigated the bacterial community of the foreskin of the penis. Previous studies found increased inflammation with certain anaerobic bacteria from swabs taken under the foreskin, but we found that higher relative abundances of the bacteria were correlated with lower expression of inflammatory genes. We did not find different bacteria in participants who received medicine to prevent HIV. Understanding the relationship between bacteria and inflammation in the penis will help us to understand how interventions like penile circumcision reduce the risk of acquiring sexually transmitted infections such as HIV.

microbiology↗

bioRxiv2021

Stereotypic expansion of Tregulatory and Th17 cells during infancy is disrupted by HIV exposure and gut epithelial damage.

Few studies have investigated immune cell ontogeny throughout the neonatal and early paediatric period, where there is often increased vulnerability to infections. Here, we evaluated the dynamics of two critical T cell populations, regulatory (Treg) cells and Th17 cells, over the first 36 weeks of life. Firstly, we observed distinct CD4+ T cells phenotypes between cord blood and peripheral blood, collected within 12 hours of birth, showing that cord blood is not a surrogate for newborn blood. Secondly, both Treg and Th17 cells expanded in a synchronous fashion over 36 weeks of life. However, comparing infants exposed to HIV in utero, but remaining uninfected (iHEU), with HIV-unexposed uninfected control infants (iHUU), there was a lower frequency of peripheral blood Treg cells at birth, resulting in a delayed expansion, and then declining again at 36 weeks. Focusing on birth events, we found that Treg cells co-expressing CCR4 and 4{beta}7 inversely correlated with plasma concentrations of CCL17 (the ligand for CCR4) and intestinal fatty acid binding protein (iFABP), IL-7 and CCL20. This was in contrast to Th17 cells, which showed a positive association with these plasma analytes. Thus, despite the stereotypic expansion of both cell subsets over the first few months of life, there was a disruption in the balance of Th17 to Treg cells at birth likely being a result of gut damage and homing of newborn Treg cells from the blood circulation to the gut. Key pointsO_LIPhenotypic differences between cord and birth peripheral blood CD4 cells. C_LIO_LISynchronous increase of Th17-Treg cells is disrupted by HIV/ART exposure. C_LIO_LIIntrauterine HIV exposure was associated with epithelial gut damage. C_LI

immunology↗

bioRxiv2021

Factors influencing maternal microchimerism throughout infancy and its impact on infant T cell immunity

Determinants of the acquisition and maintenance of maternal microchimerism (MMc) during infancy and the impact of MMc on infant immune responses are unknown. We examined factors which influence MMc detection and level across infancy and the effect of MMc on T cell responses to BCG vaccination in a cohort of HIV exposed, uninfected and HIV unexposed infants in South Africa. MMc was measured in whole blood from 58 infants using a panel of quantitative PCR assays at day one and 7, 15, and 36 weeks of life. Infants received BCG at birth, and selected whole blood samples from infancy were stimulated in vitro with BCG and assessed for polyfunctional CD4+ T cell responses. MMc was present in most infants across infancy with levels ranging from 0-1,193/100,000 genomic equivalents and was positively impacted by absence of maternal HIV, maternal-infant HLA compatibility, infant female sex, and exclusive breastfeeding. Initiation of maternal antiretroviral therapy prior to pregnancy partially restored MMc level in HIV exposed, uninfected infants. Birth MMc was associated with an improved polyfunctional CD4+ T cell response to BCG. These data emphasize that both maternal and infant factors influence the level of MMc, which may subsequently impact infant T cell responses. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

immunology↗

bioRxiv2020

Microbial function and genital inflammation in young South African women at high risk of HIV infection

BackgroundFemale genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile, however, the relative importance of microbial activities has not been established. Since proteins are key elements representing actual microbial functions, this study utilized metaproteomics to evaluate the relationship between FGT microbial function and inflammation in 113 young and adolescent South African women at high risk of HIV infection. Women were grouped as having low, medium or high FGT inflammation by K-means clustering according to pro-inflammatory cytokine concentrations. ResultsA total of 3,186 microbial and human proteins were identified in lateral vaginal wall swabs using liquid chromatography-tandem mass spectrometry, while 94 microbial taxa were included in the taxonomic analysis. Both metaproteomics and 16S rRNA gene sequencing analyses showed increased non-optimal bacteria and decreased lactobacilli in women with FGT inflammatory profiles. However, differences in the predicted relative abundance of most bacteria were observed between 16S rRNA gene sequencing and metaproteomics analyses. Bacterial protein functional annotations (gene ontology) predicted inflammatory cytokine profiles more accurately than bacterial relative abundance determined by 16S rRNA gene sequence analysis, as well as functional predictions based on 16S rRNA gene sequence data (p<0.0001). The majority of microbial biological processes were underrepresented in women with high inflammation compared to those with low inflammation, including a Lactobacillus-associated signature of reduced cell wall organization and peptidoglycan biosynthesis. This signature remained associated with high FGT inflammation in a subset of 74 women nine weeks later, was upheld after adjusting for Lactobacillus relative abundance, and was associated with in vitro inflammatory cytokine responses to Lactobacillus isolates from the same women. Reduced cell wall organization and peptidoglycan biosynthesis were also associated with high FGT inflammation in an independent sample of ten women. ConclusionsBoth the presence of specific microbial taxa in the FGT and their properties and activities are critical determinants of FGT inflammation. Our findings support those of previous studies suggesting that peptidoglycan is directly immunosuppressive, and identify a possible avenue for biotherapeutic development to reduce inflammation in the FGT. To facilitate further investigations of microbial activities, we have developed the FGT-METAP application that is available at (http://immunodb.org/FGTMetap/).

microbiology↗

bioRxiv2019

crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyads

crAssphages are a class of bacteriophages that are highly abundant in the human gastrointestinal tract. Accordingly, crAssphage genomes have been identified in most human fecal viral metagenome studies. However, we currently have an incomplete understanding of factors impacting the transmission frequencies of these phages between mothers and infants, and the evolutionary pressures associated with such transmissions. Here, we use metagenome sequencing of stool-associated virus-like particles to identify the prevalence of crAssphage across ten South African mother-infant dyads that are discordant for HIV infection. We report the identification of a complete 97kb crAssphage genome, parts of which are detected at variable levels across each mother-infant dyad. We observed average nucleotide sequence identities of >99% for crAssphages from related mother-infant pairs but [~]97% identities between crAssphages from unrelated mothers and infants: a finding strongly suggestive of vertical mother to infant transmission. We further analyzed patterns of nucleotide diversity across the crAssphage sequences described here, identifying particularly elevated positive selection in RNA polymerase and phage tail protein encoding genes, which we validated against a crAssphage genome from previous studies. Using 16S rRNA gene sequencing, we found that the relative abundances of Bacteroides thetaiotaomicron and Parabacteroides merdae (Order: Bacteroidales) were differentially correlated with crAssphage abundance. Together, our results reveal that crAssphages may be vertically transmitted from mothers to their infants and that hotspots of selection within crAssphage RNA polymerase and phage tail protein encoding genes are potentially mediated by interactions between crAssphages and their bacterial partners.\n\nImportancecrAssphages are an ubiquitous member of the human gut microbiome and modulate interactions with key bacterial associates within the order Bacteroidales. However, the role of this interaction in the genomic evolution of crAssphage remains unclear. Across a longitudinally sampled cohort of ten South African mother-infant dyads, we use metagenome sequencing of the fecal virome and 16S rRNA gene sequencing of the fecal bacterial microbiota to elucidate the ecological and evolutionary dynamics of these interactions. Here, we demonstrate elevated levels of crAssphage average nucleotide identity between related mother-infant dyads as compared to unrelated individuals, suggesting vertical transmission. We report strong positive selection in crAssphage RNA polymerase and phage tail protein genes. Finally, we demonstrate that crAssphage abundance is linearly correlated (P < 0.014) with the abundance of two bacterial taxa, Bacteroides thetaiotaomicron and Parabacteroides merdae. These results suggest that phage-bacterial interactions may help shape ecological and evolutionary dynamics in the gut.

microbiology↗

bioRxiv2018

Effects of exclusive breastfeeding on infant gut microbiota: a meta-analysis across studies and populations

Literature regarding the differences in gut microbiota between exclusively breastfed (EBF) and non-EBF infants is meager with large variation in methods and results. We performed a meta-analysis of seven studies (a total of 1825 stool samples from 684 infants) to investigate effects of EBF compared to non-EBF on infant gut microbiota across different populations. In the first 6 months of life, overall bacterial diversity, gut microbiota age, relative abundances of Bacteroidetes and Firmicutes and microbial-predicted pathways related to carbohydrate metabolism were consistently increased; while relative abundances of pathways related to lipid, vitamin metabolism and detoxification were decreased in non-EBF vs. EBF infants. The perturbation in microbial-predicted pathways associated with non-EBF was larger in infants delivered by C-section than delivered vaginally. Longer duration of EBF mitigated diarrhea-associated gut microbiota dysbiosis and the effects of EBF persisted after 6 months of age. These consistent findings across vastly different populations suggest that one of the mechanisms of short and long-term benefits of EBF may be alteration in gut microbes.

microbiology↗