Biology subjects

Common, J.

Publications and source records attributed to Common, J..

11 recordsLinked to original sources

bioRxiv2026

Comparative Proteomics Across Tissues and Crop Agroecosystems Reveals Agricultural Stressor Responses in the Western Honey Bee

Maintaining honey bee health in crop production systems is increasingly difficult because worker bees encounter multiple chemical and biological pressures from pesticides and pathogens. How these field-realistic pressures affect molecular physiology across functionally distinct tissues remains poorly understood. Here, we tested whether tissue-resolved proteomics could separate stable tissue-specific patterns from crop-associated molecular changes. To do this, we profiled abdomen, gut, and head proteomes from honey bees collected across four Canadian crop ecosystems over two consecutive years, and integrated these data with pesticide-residue and pathogen-load measurements. Proteomic variation was structured by both tissue identity and crop environment. Tissue-specific proteomic profiles were characterized across samples, whereas crop-associated effects were detected in both years and were stronger in 2021, the second year of the study. Tissue-specific enrichment and network analyses linked the abdomen to lipid catabolism and ubiquitin-proteasome proteostasis, the gut to central carbon metabolism, membrane transport, vesicle trafficking, and cytoskeletal organization, and the head to neurosensory and mitochondrial functions, together with amino-sugar metabolism and vesicle-associated quality-control modules. Among the measured pesticide residues, boscalid was the most reproducible chemical correlate of proteomic variation, with the strongest signal in the gut. Cross-year validation associated boscalid exposure with reduced abundance of gut proteins involved in mitochondrial metabolism, protein quality control, vesicle trafficking, nutrient transport, and biosynthetic pathways. Additionally, integrated proteome-transcriptome-microbiome factor analysis further identified gut-centered components associated with measured stressor variables and linked protein-level variation to coordinated transcriptomic and microbial shifts. Independent-year validation showed that compact crop-associated protein signatures detected in 2020 were also present in 2021. Together, these results show that honey bee tissues maintain stable proteomic identities while showing tissue- and year-specific responses to pesticide and pathogen pressures encountered in crop ecosystems. The gut proteome may specifically provide a sensitive molecular indicator of pesticide-associated perturbation under field conditions.

bioinformatics↗

bioRxiv2026

Host recovery after skin barrier disruption is individual-specific and associated with microbial functions

The human skin is repeatedly exposed to mechanical and environmental stress, particularly in common skin diseases such as eczema, and yet the determinants of recovery remain poorly understood. Using longitudinal, multimodal profiling of skin physiology, structure (Raman spectroscopy), and microbial communities (shotgun metagenomics), we investigated in a human cohort (n=36 subjects, x2 sites, x6 timepoints) how host-microbe interactions could jointly shape recovery. Despite baseline variability in physiological parameters, we established that our protocol enables a defined disruption of the stratum corneum. While recovery trajectories for host attributes were notably consistent across age groups and body sites, individual-specific differences in recovery timelines were observed. To assess the role of the skin microbiome, several key time-dependent changes in microbial species were identified including enrichment of select Cutibacterium and Staphylococcus species and depletion of Corynebacterium and Malassezia species. Clustering of microbiome stability profiles across subjects and sites identified 6 distinct groups which associate with varying host-recovery patterns and microbial functions. Finally, joint hazards modelling of recovery timing revealed significant contributions from microbial taxa, functions and stability groups, highlighting the under-appreciated role of host-microbial interactions in response to skin stress and in the recovery process.

genomics↗

bioRxiv2026

Two orthogonal MAP3K-driven pathways of NLRP1 inflammasome activation revealed by poisonous beetles.

Environmental toxins that cause irritant dermatitis remain poorly understood as activators of innate immune pathways. Here, we identify rove beetle (Paederus) and blister beetle (Meloidae) toxins as previously unrecognized triggers of the human NLRP1 inflammasome in keratinocytes. Rove beetles, likely through the ribosome inhibitor pederin, activate NLRP1 via translational stalling and the ZAK-dependent ribotoxic stress response. In contrast, the phosphatase inhibitor cantharidin from blister beetles induces NLRP1 through TAK1-driven hyperphosphorylation of its linker region, independent of ZAK. In their hyperactivated states, ZAK and TAK1 share overlapping phosphosites on the NLRP1 disordered linker, including a common essential TZ motif. In addition, we show that TAK1 and ZAK are jointly responsible for NLRP1 linker phosphorylation and activation caused by dsRNA and CHIKV infection. These findings reveal medically relevant insect toxins as activators of NLRP1, and uncover parallel MAP3 kinase pathways as converging upstream activating signals for the human NLRP1 inflammasome. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=172 HEIGHT=200 SRC="FIGDIR/small/701189v1_ufig1.gif" ALT="Figure 1000"> View larger version (50K): org.highwire.dtl.DTLVardef@ee34b9org.highwire.dtl.DTLVardef@c79ec9org.highwire.dtl.DTLVardef@189c373org.highwire.dtl.DTLVardef@17ec853_HPS_FORMAT_FIGEXP M_FIG C_FIG KEY POINTSTwo dermatitis-causing beetle species induce NLRP1-driven pyroptosis of human keratinocytes Rove beetles, likely via pederin, activate NLRP1 via ribosome inhibition and ZAK[a]-driven RSR Cantharidin from blister beetles activates human via TAK1-, instead of ZAK[a]-driven hyperphosphorylation of the NLRP1 linker region Shared phosphosites by TAK1 and ZAK[a] on NLRP1 contribute to dsRNA-driven NLRP1 activation

immunology↗

bioRxiv2025

Malassezia and the Asian menopausal skin

BackgroundPost-menopausal women undergo significant dermatological changes, including thinning skin and reduced sebaceous gland activity, alongside increased incidence of dermatological diseases and hair loss. These changes reshape the skins ecological niche, influencing the skin mycobiome composition and behavior. Malassezia, a lipid-dependent human pathobiont and dominant fungal resident of skin, has been implicated in several dermatological disorders. We hypothesize that shifts in Malassezia populations contribute to post-menopausal skin disorders through altered host-microbe interactions. ResultsShotgun metagenomics of facial and scalp skin from 345 Asian women were stratified by menopausal stage (pre- [N=171], peri- [N=36], and post-menopausal [N=138]) and revealed the presence of seven out of the seventeen recognized Malassezia species: M. globosa, M. restricta, M. arunalokei, M. furfur, M. dermatis, M. japonica, and M. sympodialis. Detection frequencies of several species varied markedly across menopausal groups. Notably, M. globosa was detected 20% more frequently on the scalp of post- versus pre-menopausal women. Reduced sebum concentration on post-menopausal womens skin correlated with increased M. globosa abundance. In vitro co-culture of keratinocytes with Malassezia spp. showed cells tolerated fungal loads up to 104.5 CFU/cm{superscript 2}, but severe cytotoxicity was observed at [≥]105.5 CFU/cm{superscript 2}. M. globosa elicited the highest cytotoxicity towards keratinocytes. All Malassezia spp. tested invaded keratinocytes and triggered strong pro-inflammatory responses. Notably, IL-1, IL-1{beta}, IL-6, IL-8, IL-21, TNF-, GM-CSF, G-CSF, and MMP1 were significantly overproduced. Transcriptomics of keratinocytes exposed to toxic fungal loads revealed a gene expression profile characteristic of hyperproliferative and undifferentiated cells, alongside elevated expression of NLRP3, a key inflammasome sensor involved in pyroptosis. ConclusionsMenopause is associated with distinct shifts in Malassezia spp. prevalence and abundance. Reduced skin lipids and thickness may increase fungal burden relative to host cells, promoting inflammation and barrier dysfunction. Malassezias ability to invade keratinocytes suggests a mechanism for immune evasion and induction of chronic inflammation. Furthermore, keratinocytes exposed to high fungal loads exhibited a transcriptomic profile indicative of hyperproliferation and impaired differentiation, resembling patterns observed in psoriasis, seborrheic dermatitis, and other inflammatory skin conditions. Our co-culture model provides mechanistic insight into Malassezia-driven skin inflammation and offers a platform to develop targeted therapies for post-menopausal skin disorders.

microbiology↗

bioRxiv2025

Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites

While skin microbiome studies have increasingly highlighted its importance in health and disease, our understanding of inter-individual heterogeneity in structure and function remains limited, impacting the ability to develop microbiome-based stratification and therapeutics. Powered by comprehensive skin microbiome characterization in a multi-ethnic population-based cohort (>3,550 shotgun metagenomes across 18 sampling sites), we established significant undescribed inter-individual heterogeneity and the extensive prevalence of distinct microbial configurations (17 species-resolution dermotypes) in seven out of nine body sites. Combining functional in silico and in vitro studies revealed insights into how these dermotypes assemble as a function of niche-dependent microbial interactions (e.g. hypoxia-dependent inhibition of S. hominis by S. epidermidis/M. luteus) and metabolic resource utilization (e.g. differential galactose and histidine metabolism). Integration of demographic, skin physiological, and behavioral data further identified >30 significant associations with host attributes. Cross-site analysis revealed remarkable coordination across disparate skin regions (predictive AUC-ROC>0.8) and bilateral consistency (Pearson {pi}>0.95), emphasizing the role of specific microbial and host factors in shaping dermotypes. Finally, we provide multiple lines of evidence that dermotype states impact the risk for skin discomfort (e.g. irritation, itch) and diseases (e.g. eczema), that when combined with our highly accurate dermotype classifiers (AUC-ROC>0.98), provide a new paradigm for understanding skin microbiome function and stratifying patients in the context of skin and other diseases.

genomics↗

bioRxiv2024

Skin metatranscriptomics reveals landscape of variation in microbial activity and gene expression across the human body

The skin microbiome plays an important role in immune homeostasis and skin health, and yet our understanding of in vivo microbial gene activity is hindered by the lack of a robust, non-invasive protocol for metatranscriptomics across skin sites. Circumventing the challenges of low microbial biomass, host contamination, and RNA stability, we developed a clinically tractable skin metatranscriptomics workflow that provides high technical reproducibility of profiles (Pearson r>0.95), uniform coverage across gene bodies, and strong enrichment of microbial mRNAs (2.5-40x). Applying this protocol to a cohort of healthy adults (n=27) across five different skin sites (n=102, paired metatranscriptomes and metagenomes), identified a striking divergence between transcriptomic and genomic abundances, with Staphylococcus species and the skin fungi Malassezia having an outsized contribution to the metatranscriptomic landscape at most sites despite their modest representation in metagenomes. Species-level analysis showed skin site-specific enrichment of gene expression (e.g. increased levels of secreted fungal phospholipase C on cheeks relative to scalp), and revealed how key pathways were transcriptionally active in vivo (e.g. propionate and 4-aminobutyrate metabolism, potentially impacting skin barrier function). Gene-level analysis identified diverse antimicrobial genes transcribed by skin commensals in situ, including several uncharacterized bacteriocins, some of which are expressed at levels comparable to known antimicrobial genes. Correlation of microbial gene expression with organismal abundances uncovered >20 genes that putatively mediate interactions between microbes (e.g. a secreted Malassezia restricta protein with strongly negative in vivo association with Cutibacterium acnes; Spearman {rho}>0.7). This work showcases the potential for leveraging skin metatranscriptomics to identify microbes whose activities play an outsized role in the community, and for uncovering pivotal microbial pathways and biomarkers linked to skin health and disease.

genomics↗

bioRxiv2024

Pollen foraging mediates exposure to dichotomous stressor syndromes in honey bees

Recent declines in the health of honey bee colonies used for crop pollination pose a considerable threat to global food security. Foraging by honey bee workers represents the primary route of exposure to a plethora of toxins and pathogens known to affect bee health, but it remains unclear how foraging preferences impact colony-level patterns of stressor exposure. Resolving this knowledge gap is crucial for enhancing the health of honey bees and the agricultural systems that rely on them for pollination. To address this, we carried out a national-scale experiment encompassing 456 Canadian honey bee colonies to first characterize pollen foraging preferences in relation to major crops, then explore how foraging behaviour influences patterns of stressor exposure. We used a metagenetic approach to quantify honey bee dietary breadth and found that bees display distinct foraging preferences that vary substantially relative to crop type and proximity, and the breadth of foraging interactions can be used to predict the abundance and diversity of stressors a colony is exposed to. Foraging on diverse plant communities was associated with increased exposure to pathogens, while the opposite was associated with increased exposure to xenobiotics. Our work provides the first large-scale empirical evidence that pollen foraging behaviour plays an influential role in determining exposure to dichotomous stressor syndromes in honey bees. Significance StatementInsect-mediated pollination is an important ecological process that is crucial for food production. Managed honey bee colonies are one of the most important insect pollinators, but their health has been under threat from a variety of stressors. Bee workers are primarily exposed to stressors while foraging and understanding how bee foraging preferences are related to exposure risk could provide pivotal information to improve management efforts. Here, we studied honey bee foraging preferences in relation to prominent Canadian crops and across a gradient of modified environments. We found that honey bees show distinct, measurable foraging preferences and that dietary diversity is a strong predictor of the stressors that colonies are exposed to.

ecology↗

bioRxiv2024

Climatic predictors of prominent honey bee (Apis mellifera) disease agents: Varroa destructor, Melissococcus plutonius, and Vairimorpha spp.

Improving our understanding of how climate influences honey bee parasites and pathogens is critical as weather patterns continue to shift under climate change. While the prevalence of diseases vary according to regional and seasonal patterns, the influence of specific climatic predictors has rarely been formally assessed. To address this gap, we analyzed how occurrence and intensity of three prominent honey bee disease agents (Varroa destructor [-] hereon Varroa [-] Melissococcus plutonius, and Vairimorpha spp.) varied according to regional, temporal, and climatic factors in honey bee colonies across five Canadian provinces. We found strong regional effects for all disease agents, with consistently high Varroa intensity and infestation probabilities and high M. plutonius infection probabilities in British Columbia, and year-dependent regional patterns of Vairimorpha spp. spore counts. Increasing wind speed and precipitation were linked to lower Varroa infestation probabilities, whereas warmer temperatures were linked to higher infestation probabilities. Analysis of an independent dataset shows that these trends for Varroa are consistent within a similar date range, but temperature is the strongest climatic predictor of season-long patterns. Vairimorpha spp. intensity decreased over the course of the summer, with the lowest spore counts found at later dates when temperatures were warm. Vairimorpha spp. intensity increased with wind speed and precipitation, consistent with inclement weather limiting defecation flights. Probability of M. plutonius infection generally increased across the spring and summer, and was also positively associated with inclement weather. These data contribute to building a larger dataset of honey bee disease agent occurrence that is needed in order to predict how epidemiology may change in our future climate.

molecular biology↗

bioRxiv2024

Higher prevalence of sacbrood virus in highbush blueberry pollination units

Highbush blueberry pollination depends on managed honey bees (Apis mellifera) for adequate fruit set; however, beekeepers have raised concerns about poor health of colonies after pollinating this crop. Postulated causes include agrochemical exposure, nutritional deficits, and interactions with parasites and pathogens, particularly Melisococcus plutonius(the causal agent of European foulbrood disease), but other pathogens could be involved. To broadly investigate common honey bee pathogens in relation to blueberry pollination, we sampled adult honey bees from colonies at time points corresponding to before (t1), during (t2), at the end (t3), and after (t4) highbush blueberry pollination in British Columbia (BC), Canada, across two years (2020 and 2021). Nine viruses as well as M. plutonius, Vairimorpha ceranae and V. apis (formerly Nosema ceranae and N. apis) were detected by PCR and microscopy and compared among colonies located near and far from blueberry fields. We found a significant interactive effect of time and blueberry proximity on the multivariate pathogen community, mainly due to differences at t4 (corresponding to roughly six weeks after the beginning of the pollination period). Post-hoc comparisons of pathogens in near and far groups at t4 showed that detections of sacbrood virus (SBV), which was significantly higher in the exposed group, was the primary driver. The association of SBV with highbush blueberry pollination may be contributing to the health decline that beekeepers observe after pollinating this crop, likely in combination with other factors.

zoology↗

bioRxiv2024

Life stage impact on the human skin ecosystem: lipids and the microbial community

While research into gut-microbe interactions is common and advanced, with multiple defined impacts on human health, studies exploring the significance of skin-microbe interactions remain underrepresented. Skin is the largest human organ, has a vast surface area, and is inhabited by a plethora of microorganisms which metabolise sebaceous lipids. Sebaceous free fatty acids are metabolized into bioactive lipid mediators with immune-modulatory properties by skin-resident microbes, including Malassezia. Intriguingly, many of the same lipid mediators are also found on human skin, implying these compounds may have microbial or mixed microbial/human origin. To support this hypothesis, we isolated lipids and microbial DNA from the skin of prepubescent, adult, pre- and post-menopausal volunteers and performed correlational analyses using skin lipidomics and metagenomics to compare lipid mediator profiles and microbiome compositions on skin with either low or high sebaceous gland activity. We found that specific microbial taxonomies were positively and negatively correlated with skin lipid mediator species with high statistical significance. 2D in vitro co-cultures with Malassezia and keratinocytes also directly linked the production of specific lipid mediators, detected on healthy human skin, to secretion of immuno-stimulatory cytokines. Together, these findings further support the hypothesis that microbial-derived skin lipid mediators influence healthy skin homeostasis and skin disease development and progression, thereby spotlighting the relevance of the skin microbiomes footprint on human health.

microbiology↗

bioRxiv2019

Host resistance diversity protects susceptible genotypes by restricting pathogen spread and evolution

Diversity in host resistance often associates with reduced pathogen spread. This may result from ecological and evolutionary processes, likely with feedback between them. Theory and experiments on bacteria-phage interactions have shown that genetic diversity of the bacterial adaptive immune system can limit phage evolution to overcome resistance. Using the CRISPR-Cas bacterial immune system and lytic phage, we engineered a host-pathogen system where each bacterial host genotype could be infected by only one phage genotype. With this model system, we explored how CRISPR diversity impacts the spread of phage when they can overcome a resistance allele, how immune diversity affects the evolution of the phage to increase its host range, and if there was feedback between these processes. We show that increasing CRISPR diversity benefits susceptible bacteria via a dilution effect, which limits the spread of the phage. We suggest that this ecological effect impacts the evolution of novel phage genotypes, which then feeds back into phage population dynamics.

evolutionary biology↗