Biology subjects

Ghasemian, E.

Publications and source records attributed to Ghasemian, E..

4 recordsLinked to original sources

bioRxiv2026

Microbial community profiles of the snake cloaca in the presence and absence of Chlamydiota

Chlamydiota are obligate intracellular bacteria detected in snake cloacal microbiota, yet their biological significance remains poorly understood. Members range from recognised pathogens, such as Chlamydia serpentis, to potential environmental symbionts, raising questions about whether they represent transient contaminants, persistent colonisers, or subclinical infectious agents. Despite the cloaca serving as a primary site of chlamydial shedding in snakes, its interaction with the broader cloacal microbiota remains unexplored. Following pan-Chlamydiota PCR screening of 137 captive snakes across five collections, 52 samples (caenophidian snakes) (27 Chlamydiota-positive, 25 Chlamydiota-negative) were retained after V3-V4 16S rRNA sequencing and quality filtering. Presence of Chlamydiota was not associated with significant differences in alpha diversity or overall community composition, though it was related to greater within-community compositional heterogeneity. Differential abundance and multivariate analyses identified several enriched and depleted genera, with Lachnospiraceae and Copromonas consistently negatively associated with Chlamydiota across all three methods. Co-occurrence network analysis recovered more associations and a higher proportion of positive edges in the presence of Chlamydiota, with an expansion of anaerobic taxa. Inferred functional composition did not differ globally between groups; however, elastic net stability selection identified subtle pathway-specific differences, including enrichment of proteolytic and mycobacterial pathways in infected snakes. Our findings suggest subtle infection-associated community shifts that do not fully conform to established mammalian paradigms in which Chlamydia species behave either as gastrointestinal commensals or as cervicovaginal pathogens, highlighting the need for multi-omics approaches in larger cohorts of caenophidian and henophidian wild and captive snakes to better characterise the mechanistic basis and generalisability of these associations.

microbiology↗

bioRxiv2026

Comparative analysis of cloacal microbiota in Henophidia (non-venomous) and Caenophidia (venomous) snakes

The evolutionary divergence between Henophidia (non-venomous) and Caenophidia (venomous) snakes has produced distinct cranial morphologies, digestive strategies, and presence of specialised venom systems in Caenophidia, yet the extent to which these long-standing diverging trajectories have shaped cloacal microbiota assembly remains poorly understood. We characterised cloacal microbiota in 70 captive snakes (52 Caenophidia, 18 Henophidia) by 16S rRNA amplicon sequencing. Beta diversity was tested by PERMANOVA, differential abundance by ANCOM-BC2, community types by Dirichlet Multinomial Mixture modelling (DMM), and microbial interactions by SparCC co-occurrence networks. Predicted functional potential (PICRUSt2) was analysed by ALDEx2 differential abundance testing and elastic net feature selection. Henophidia exhibited significantly higher bacterial richness and greater compositional variability than Caenophidia. Community composition showed clade-associated differences (PERMANOVA) and partitioned into two distinct DMM community types. The Henophidia network was 11.9-fold denser and more modular, with Burkholderiaceae as a keystone hub, whereas the Caenophidia network was sparse. Henophidia showed predicted enrichment in C1 metabolic pathways (ethylmalonyl-CoA, formaldehyde assimilation I, glycine betaine degradation I, methylaspartate cycle), aromatic compound catabolism, and nitrogen recycling, whilst Caenophidia showed enrichment in allantoin and glucuronate degradation. This multi-method analysis suggests Burkholderiaceae as a candidate keystone taxon in Henophidia and indicates that phylogenetic clade is a major contributor to cloacal microbiota structure. The lower richness in Caenophidia raises a testable hypothesis that broad-spectrum antimicrobial activity of their venom components may selectively filter susceptible microbial lineages, motivating future shotgun metagenomic studies in wild populations of snakes.

ecology↗

bioRxiv2025

Comparative transcriptomic profiling of human conjunctival epithelial cells and macrophages in response to Chlamydia trachomatis genovars A and B in early- and mid-infection cycles

Chlamydia trachomatis (Ct), an obligate intracellular bacterium, is the primary infectious cause of blindness through trachoma. Ct undergoes a unique biphasic developmental cycle between infectious elementary bodies and replicating reticulate bodies, manipulating host cells via secreted effector proteins. Whilst previous studies have characterised host-pathogen interactions including transcriptomes of urogenital Ct genovars E and L2, limited studies exist on ocular Ct genovars. This study examined transcriptomic responses of human conjunctival epithelial (HCjE) cells and PMA-differentiated THP-1 macrophages to infection with ocular Ct strains A/2497 or B/Tunis864 (live or heat-inactivated) at 4 and 24 hours post-infection (hpi). Transcriptomic profiling was performed using Lexogen QuantSeq 3 mRNA-Seq, with differential gene expression analysis conducted using DESeq2. Gene Ontology Biological Process and KEGG pathway enrichment analyses were performed using Gene Set Enrichment Analysis via clusterProfiler to identify strain-specific and cell type-specific transcriptional signatures. HCjE cells exhibited progressive transcriptional activation, with differentially expressed genes (DEGs) increasing from 4 to 24 hpi (144 to 259; P = 0.0458), whilst THP-1 macrophages showed temporal attenuation (391 to 154; P < 0.0001). B/Tunis864 consistently elicited higher responses than A/2497 in HCjE cells at both time points (4 hpi: 152 vs. 54, P = 0.0003; 24 hpi: 259 vs. 83, P < 0.0001). Conversely, THP-1 macrophages showed higher responses to A/2497 than B/Tunis864 at both time points (4 hpi: 599 vs. 376, P < 0.0001; 24 hpi: 166 vs. 114, P = 0.0221). HCjE cells demonstrated markedly higher proportions of strain-specific DEGs and pathways compared to macrophages. B/Tunis864 infection in HCjE cells induced pronounced interferon-stimulated gene signatures, particularly at 24 hpi. This study revealed contrasting temporal patterns: THP-1 macrophages showed peak-then-decline responses, whilst HCjE cells exhibited progressive activation to 24 hpi. HCjE cells demonstrated predominantly strain-specific responses, whereas macrophages deployed strain-invariant programmes. B/Tunis864s enhanced interferon-stimulated gene and inflammatory pathway activation in HCjE cells may suggest molecular hints for genovar B-associated trachoma severity.

microbiology↗

bioRxiv2023

Genomic insights into local scale evolution of ocular Chlamydia trachomatis strains within and between individuals in Gambian trachoma-endemic villages

Trachoma, a neglected tropical disease caused by Chlamydia trachomatis (Ct) serovar A-C, is the leading infectious cause of blindness worldwide. Its impact is substantial, with approximately 1.9 million individuals suffering from visual impairment. Africa bears the highest burden, accounting for over 86% of global trachoma cases. We investigated Ct serovar A (SvA) and serovar B (SvB) whole genome sequences prior to the induction of mass antibiotic drug administration in The Gambia. Here, we explore the factors contributing to Ct strain diversification and implications for Ct evolution within the context of ocular infection. A cohort study in 2002-2003 collected ocular swab samples across nine Gambian villages during a six-month follow-up study. To explore the genetic diversity of Ct within and between individuals, we conducted Whole-Genome Sequencing (WGS) on a limited number (n=43) of Ct positive samples. WGS was performed using target enrichment with SureSelect and Illumina paired-end sequencing. Out of 43 WGS samples, 41 provided sufficient quality for further analysis. ompA analysis revealed that 11 samples had a highest identity to Ct strain A/HAR13 (NC_007429) and 30 had a highest identity to Ct strain B/Jali20 (NC_012686). While SvB genome sequences formed two distinct village-driven subclades, the heterogeneity of SvA sequences led to the formation of many individual branches within the Gambian SvA subclade. Comparing the Gambian SvA and SvB sequences with their reference strains; Ct A/HAR13 and Ct B/Jali20 indicated a single nucleotide polymorphism accumulation rate of 2.4 {xi} 10^-5/site/year for the Gambian SvA and 1.3 {xi} 10^-5/site/year for SvB variants (p<0.0001). Variant calling resulted in a total of 1,371 single nucleotide variants (SNVs) with a frequency > 25% in SvA sequences, and 438 SNVs in SvB sequences, from which 740 (62.8%), and 241 (66.4%) were non-synonymous, respectively. Of note, in SvA variants, highest evolutionary pressure was recorded on genes responsible for host cell modulation and intracellular survival mechanisms, whereas in SvB variants this pressure was mainly on genes essential for DNA replication/ repair mechanisms and protein synthesis. A comparison of the sequences between observed separate infection events (4-20 weeks between infections) suggested that the majority of the variations accumulated in genes responsible for host-pathogen interaction such as CTA_0166 (phospholipase D-like protein), CTA_0498 (TarP), and CTA_0948 (deubiquitinase). This comparison of Ct SvA and SvB variants within a trachoma endemic population focused on their local evolutionary adaptation. We found a different variation accumulation pattern in the Gambian SvA chromosomal genes compared with SvB hinting at the potential of Ct serovar-specific variation in diversification and evolutionary fitness. These findings may have implications for optimizing trachoma control and prevention strategies. Impact StatementChlamydia trachomatis (Ct) is a globally significant pathogen. It is the leading infectious cause of blindness--a disease called trachoma. In addition, Ct causes the majority of bacterial sexually transmitted infections. Current control measures for trachoma are based on the "SAFE" strategy; Surgery for trichiasis (S), Antibiotics (A), Facial cleanliness (F) and Environmental improvement (E). Whilst this strategy has achieved remarkable success, the target date for the global elimination of blinding trachoma as a public health problem has been pushed back from 2020 to 2030. Prior studies demonstrated evidence indicating variations in infection loads and severity among different ocular Ct serovars. However, there remains a significant knowledge gap regarding the specific genes and mechanisms responsible for these variations. We generated genetic data from two main serovars of Ct that infect human eyes: Serovar A (SvA) and Serovar B (SvB) variants collected from four villages in two different administrative regions on opposing sides of the river Gambia to elucidate (i) the factors driving the diversification of ocular Ct strains; (ii) disparities in mutation frequency/accumulation profiles; (iii) selective pressures between serovar A and B; and (iv) the dynamics of mutation accumulation within the Gambian ocular Ct positive population over a short timeframe. Our findings suggest a different variation accumulation pattern in SvA chromosomal genes compared with SvB hinting at the potential of Ct serovar-specific variation in diversification and evolutionary fitness. These findings may have implications for optimizing trachoma control and prevention strategies.

genomics↗