Biology subjects

Hill, M. S.

Publications and source records attributed to Hill, M. S..

5 recordsLinked to original sources

bioRxiv2026

Temporal stability and niche partitioning of bacterial communities in paired residential sink P-traps

Sink P-traps harbor microbial communities derived from environmental and human sources, yet longitudinal studies examining their stability and assembly dynamics remain limited. Here, we present, to our knowledge, the longest continuous characterization of bacteria collected from residential sink P-traps, with daily sampling over two months (n = 61 days). Samples were collected from paired sinks in a shared bathroom to identify dominant taxa, quantify temporal stability, and determine how occupant usage patterns influence community assembly. Using full-length 16S rRNA gene sequencing, we identified 3,865 unique taxa, with both sinks dominated by common sink-associated genera, including Pseudomonas, Citrobacter, Klebsiella, and Arcobacter. Despite sharing identical plumbing, environmental conditions, and cleaning regimes, the two sinks maintained distinct communities (p < 0.001). Temporal stability analyses revealed notable differences: Sink A (male; hand washing, toothbrushing, shaving) exhibited deterministic dynamics with low variability (CV = 4.9%), significant temporal autocorrelation (p = 0.001), and predictable trajectories, with time explaining 49.9% of community variation. In contrast, Sink B (female; hand washing, toothbrushing, face washing, mouthwash use) displayed stochastic dynamics with high volatility (CV = 26.5%), no significant autocorrelation (p = 0.53), and minimal temporal predictability. Differential abundance analysis revealed that Sink B was enriched in anaerobes, biofilm-forming taxa, oral microbiome associates, and preservative-resistant and lipid-degrading bacteria, while Sink A harbored a more aerobic, skin-associated community. These findings demonstrate that individual usage patterns (particularly exposure to biocidal agents) can alter P-trap community structure and temporal dynamics, with implications for microbial community prediction in residential and healthcare settings. ImportanceSink drains are increasingly recognized as reservoirs for antimicrobial-resistant pathogens, yet we lack fundamental knowledge about what drives bacterial community dynamics in these environments. By sampling paired residential sink P-traps daily for two months, we show that individual-specific behaviors, such as using products with a biocidal effect, can alter community composition from a stable, predictable state to one characterized by stochastic fluctuations. The sink exposed to mouthwash and face wash harbored more anaerobes, biofilm formers, and oral bacteria, suggesting that repeated exposure promotes disturbance-tolerant taxa rather than reducing bacterial colonization. These results provide a baseline ecological framework for understanding P-trap microbiomes and suggest that predictive monitoring of sink-associated pathogens might be feasible in stable environments but more difficult when there is variable antimicrobial exposure -- a finding directly relevant to hospital infection control.

microbiology↗

bioRxiv2025

Spatiotemporal Microbial Ecoevolutionary Dynamics on the International Space Station

This study presents the most comprehensive spatiotemporal analysis of the ISS microbiome to date. Over a seven-year period, 184 surface samples were collected for live/dead metagenomic profiling, phenotypic characterization of antimicrobial resistance (AMR) and virulence among 102 cultured isolates, and metagenome-assembled genome (MAG) analysis to evaluate evolutionary selection pressures. Despite ecological stability, comparative genomics revealed ongoing microevolution through lateral gene transfer and selection for traits (e.g., radiation resistance and biocide tolerance). Importantly, predictions of AMR and virulence frequently misaligned with experimental outcomes, underscoring the need for functional validation. This dataset highlights a stable core microbiome that persists across years, punctuated by localized adaptation and gene flow. The ISS microbiome exemplifies both ecological resilience and microevolutionary innovation that can inform risk management for long-duration spaceflight.

microbiology↗

bioRxiv2023

Genomic evolution of non-small cell lung cancer patient-derived xenograft models

Patient-derived xenograft (PDX) models of cancer, developed through injection of patient tumour cells into immunocompromised mice, have been widely adopted in preclinical studies, as well as in precision oncology approaches. However, the extent to which PDX models represent the underlying genetic diversity of a patients tumour and the extent of on-going genomic evolution in PDX models are incompletely understood, particularly in the context of heterogeneous cancers such as non-small cell lung cancer (NSCLC). To investigate the depiction of intratumour heterogeneity by PDX models, we derived 47 new subcutaneous multi-region PDX models from 22 patients with primary NSCLC enrolled in the clinical longitudinal cohort study TRACERx. By analysing whole exome sequencing data from primary tumours and PDX models, we find that PDX establishment creates a genomic bottleneck, with 76% of PDX models being derived from a single primary tumour subclone. Despite this, multiple primary tumour subclones were capable of PDX establishment in regional PDX models, indicating that PDX libraries derived from multiple tumour regions can capture intratumour heterogeneity. Acquisition of somatic mutations continued during PDX model expansion, and was associated with APOBEC- or mismatch repair deficiency-induced mutational signatures in a subset of models. Overall, while NSCLC PDX models retain truncal genomic alterations, the absence of subclonal heterogeneity representative of the primary tumour is a major limitation. Our results emphasise the importance of characterising and monitoring intratumour heterogeneity in the context of pre-clinical cancer studies.

cancer biology↗

bioRxiv2021

Insights into early stages of the establishment of host:algal endosymbioses: Genetic responses to live versus heat-killed algae and bacterial prey in a sponge host

The freshwater sponge Ephydatia muelleri and its Chlorella-like green algal partner is an emerging model for studying animal:algal endosymbiosis. The sponge host is a highly tractable laboratory organism, and the symbiotic algae are easily cultured. We took advantage of these traits to experimentally interrogate fundamental questions about cellular mechanisms that govern the establishment of durable intracellular partnerships between hosts and symbionts in facultative symbioses. We modified a classical experimental approach to discern the phagocytotic mechanisms that might be co-opted to permit persistent infections, and identified genes differentially expressed in E. muelleri sponges early in the establishment of endosymbiosis. We exposed algal-free E. muelleri to live native algal symbionts, native heat-killed algae, and bacteria, and then performed RNASeq so we could compare patterns of gene expression in each treatment. We contrasted differential gene expression patterns between potential food items (bacteria and heat-killed algae) and the live native Chlorella-like symbiont. We found a relatively small but interesting suite of genes that are uniquely and differentially expressed in the host exposed to live algal symbionts, and a larger number of genes uniquely triggered by host exposure to heat-killed algae. One of the host genes, an ABC transporter that is downregulated in response to live algal symbionts, was further evaluated for its possible role in establishment of the algal symbiosis. We discuss the gene expression profiles associated with host responses to living algal cells in the context of conditions necessary for long-term residency within host cells by phototrophic symbionts as well as the genetic responses to sponge phagocytosis and immune driven pathways.

evolutionary biology↗

bioRxiv2017

Sexual antagonism exerts evolutionarily persistent genomic constraints on sexual differentiation in Drosophila melanogaster

The evolution of sexual dimorphism is constrained by a shared genome, leading to sexual antagonism where different alleles at given loci are favoured by selection in males and females. Despite its wide taxonomic incidence, we know little about the identity, genomic location and evolutionary dynamics of antagonistic genetic variants. To address these deficits, we use sex-specific fitness data from 202 fully sequenced hemiclonal D. melanogaster fly lines to perform a genome-wide association study of sexual antagonism. We identify ~230 chromosomal clusters of candidate antagonistic SNPs. In contradiction to classic theory, we find no clear evidence that the X chromosome is a hotspot for sexually antagonistic variation. Characterising antagonistic SNPs functionally, we find a large excess of missense variants but little enrichment in terms of gene function. We also assess the evolutionary persistence of antagonistic variants by examining extant polymorphism in wild D. melanogaster populations. Remarkably, antagonistic variants are associated with multiple signatures of balancing selection across the D. melanogaster distribution range, indicating widespread and evolutionarily persistent (>10,000 years) genomic constraints. Based on our results, we propose that antagonistic variation accumulates due to constraints on the resolution of sexual conflict over protein coding sequences, thus contributing to the long-term maintenance of heritable fitness variation.

evolutionary biology↗