Biology subjects

MacIntyre, D. A.

Publications and source records attributed to MacIntyre, D. A..

6 recordsLinked to original sources

bioRxiv2025

Multi-omic analysis of vaginal bacteria:host immune and metabolic interactions in adverse early pregnancy outcomes

Accurate and timely diagnosis of early pregnancy outcomes remains a clinical challenge, particularly in cases classified as pregnancy of unknown location, where ultrasound fails to confirm the location of the pregnancy. Delayed diagnosis can lead to serious complications, especially in ectopic pregnancies. This prospective cohort study aimed to characterise host-microbe interactions during early pregnancy in the vaginal mucosa by exploring the relationship between the bacterial community composition, immune response, and metabolic phenotype. We analyzed vaginal swabs from 91 women with pregnancy of unknown location, including 22 with viable intrauterine pregnancies and 69 with adverse outcomes. Metataxonomic profiling, immune assays, and direct on-swab metabolomics were performed. Adverse outcomes, especially ectopic pregnancies, were associated with reduced Lactobacillus abundance, increased bacterial diversity, mucosal inflammation, and elevated lipid species. Vaginal bleeding, a common symptom in PUL, significantly impacted immune and metabolic profiles and should be considered as a confounder in studies of the lower female reproductive tract. Multi-omic data integration highlighted metabolic phenotypes of immune response in the context of bacterial community composition, underscoring the influence of microbe-host interactions on mucosal health and pregnancy outcomes. IMPORTANCEEarly detection of complications in pregnancy is essential for improving maternal health outcomes, yet current diagnostic tools often fail to identify ectopic or failing pregnancies in a timely manner. This study highlights how changes in the vaginal microbiome, inflammation, and metabolic signals are closely linked to adverse outcomes in early pregnancy. By showing that metabolic profiling can predict microbial and immune states even in the presence of vaginal bleeding, the research provides a foundation for developing rapid, non-invasive diagnostic tools. These insights could pave the way for more personalized and effective early pregnancy care.

microbiology↗

bioRxiv2025

KODAMA enables self-guided weakly supervised learning in spatial transcriptomics

Spatial transcriptomics provides researchers with a powerful tool to investigate gene expression patterns within their native positional context in tissues, revealing intricate cellular relationships. However, analyzing spatial transcriptomics data presents unique challenges due to their high dimensionality and complexity. Several competitive tools have emerged, each aiming to integrate spatial dependencies into their workflow. Yet, the overall performance of these approaches remains constrained by limitations in prediction accuracy and compatibility with specific data types. Here, we introduce the third version of the KODAMA algorithm, specifically tailored for spatial transcriptomics analysis. This upgraded version incorporates a novel approach that effectively reduces data dimensionality while preserving spatial information. At its core, the KODAMA algorithm employs parallel iterations that enforce spatial constraints throughout an embedded clustering process. Our method provides the flexibility to simultaneously analyze multiple samples, streamlining analysis workflows. Additionally, it extends beyond traditional 2D analysis to accommodate multidimensional datasets, including 3D spatial information. KODAMA seamlessly integrates into various pipelines, such as Seurat and Giotto. Extensive evaluations of KODAMA on 10x Visium, Visium HD, and image-based 3D datasets demonstrate its high accuracy in spatial domain prediction. Comparative analyses against alternative dimensionality reduction techniques and spatial analysis tools consistently validate and highlight KODAMAs superior performance in unraveling the spatial organization of cellular components across both single and integrated tissue samples.

bioinformatics↗

bioRxiv2024

Lactobacillus crispatus S-layer proteins modulate innate immune response and inflammation in the lower female reproductive tract.

Lactobacillus species dominance of the vaginal microbiome is a hallmark of vaginal health. Pathogen displacement of vaginal lactobacilli drives innate immune activation and mucosal barrier disruption which increases the risks of STI acquisition and, in pregnancy, of preterm birth. Using cell reporter systems, we describe differential TLR mediated activation of the proinflammatory transcription factor NF-{kappa}B by vaginal pathogens and commensals. Vaginal Lactobacillus strains associated with optimal health were shown to selectively interact with anti-inflammatory innate immune receptors whereas species associated with suboptimal health including L. iners and Gardnerella vaginalis interacted with both pro- and anti-inflammatory receptors. Anti-inflammatory action of L. crispatus was regulated by surface layer protein (SLPs)-mediated shielding of TLR ligands and selective interaction with anti-inflammatory receptor, DC-SIGN. In pregnant women, cervicovaginal SLPs were predominately associated with Lactobacillus-enriched microbiota. These data offer new mechanistic insights into how vaginal microbiota modulate host immune response and influences risk of preterm birth.

microbiology↗

bioRxiv2024

Dynamic roles of ILC3 in endometrial repair and regeneration

Innate lymphoid cells (ILC) are prominent in the human uterine mucosa and play physiological roles in pregnancy. ILC3 are the second-most common ILC subset in the uterine mucosa, but their role remains unclear. Here we define two subsets of lineage-negative CD56+ CD117+ CRTH2-uterine ILC3, distinguished by their expression of CD127. The CD127-subset is most numerous and active during menstruation and immediately after parturition, suggesting a role in repair of the uterine mucosa (called endometrium outside of pregnancy); the CD127+ subset is most numerous and active immediately after menstruation, as the endometrium regenerates. In healthy endometrium, ILC3 are spatially associated with glandular epithelial and endothelial cells, which both express receptors for the ILC3-derived cytokines, IL-22 and IL-8. In the eutopic endometrium of people with endometriosis, ILC3 are located further from glandular epithelial and endothelial cells suggesting that these cells may be less exposed to ILC3 products, potentially with negative consequences for endometrial regeneration. Our findings highlight the dynamic nature of ILC3 in the uterine mucosa and suggest their primary role is in repair and regeneration. An improved understanding of uterine ILC3 will inform future research on endometrial health and disease.

immunology↗

bioRxiv2021

Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population

Vaginal microbiota-host interactions are linked to preterm birth (PTB), which continues to be the primary cause of global childhood mortality. Despite the majority of PTB occuring in Asia, studies of the pregnancy vaginal microbiota are largely limited to Northern American and European populations. Here, we characterised the vaginal microbiome of 2689 pregnant Chinese women using metataxonomics and in a subset (n=823), the relationship between vaginal microbiota composition, sialidase activity and leukocyte presence and pregnancy outcomes. Vaginal microbiota were most frequently dominated by Lactobacillus crispatus or L. iners, with the latter associated with vaginal leukocyte presence. Women with high sialidase activity were enriched for bacterial vaginosis-associated genera including Gardnerella, Atopobium and Prevotella. Vaginal microbiota composition, high sialidase activity and/or leukocyte presence was not associated with PTB risk suggesting underlying differences in the vaginal microbiota and/or host immune responses of Chinese women, possibly accounting for low PTB rates in this population. ImportanceSpecific vaginal microorganisms or vaginal microbiota, are associated with preterm birth, which is the primary cause of death in children under 5yrs of age worldwide. Despite most preterm births occuring in Asia, almost all studies of the pregnancy vaginal microbiota have been limited to Northern American and European women. Here, we studied the vaginal microbiota in a large cohort of 2689 pregnant Chinese women and showed that it was most frequently dominated by Lactobacillus crispatus or L. iners. The latter was associated with leukocyte infiltration of vaginal secretions. Women with high activity of the enzyme sialidase, were frequently colonised by species associated with the common condition bacterial vaginosis, including Gardnerella, Atopobium and Prevotella species. Vaginal microbiota, high sialidase activity and/or leukocyte presence was not associated with preterm birth risk indicating differences in the microbe-host immune responses of Chinese women, possibly explaining why preterm birth rates in this population are low.

systems biology↗

bioRxiv2020

Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome

Bacteria use protein receptors called lectins to anchor to specific host surface sugars. The role of lectins in the vaginal microbiome, and their involvement in reproductive tract pathophysiology is poorly defined. Here we establish a classification system based on taxonomy and protein 3D structure to identify 109 lectin classes. Hidden Markov Model (HMM) profiles for each class were used to search bacterial genomes, resulting in the prediction of >100 000 bacterial lectins available at unilectin.eu/bacteria. Genome screening of 90 isolates from 21 vaginal bacterial species showed that potential pathogens produce a larger variety of lectins than commensals indicating increased glycan-binding potential. Both the number of predicted bacterial lectins, and their specificities for carbohydrates correlated with pathogenicity. This study provides new insights into potential mechanisms of commensal and pathogen colonisation of the reproductive tract that underpin health and disease states.

bioinformatics↗