Biology subjects

Mach, N.

Publications and source records attributed to Mach, N..

15 recordsLinked to original sources

bioRxiv2026

Gut and nasal microbiome trajectories shape respiratory disease severity in calves exposed to antibiotic and pathogen challenge

Bovine respiratory disease complex (BRDC) is a multifactorial syndrome resulting from interactions among pathogens, host responses, and environmental stressors. However, substantial variation in disease severity persists among animals exposed to similar infectious challenges. To assess the contribution of the respiratory and gut microbiota to BRDC severity, we experimentally inoculated 28 calves with Mycoplasma bovis, bovine coronavirus (BCoV), and influenza D virus (IDV), with half receiving metaphylactic tilmicosin. Clinical trajectories were classified into mild, moderate, and severe phenotypes using unsupervised clustering of longitudinal health scores. Severe BRDC was associated with higher and more persistent nasal IDV loads, yet pathogen burden alone failed to explain the marked inter-individual variability in clinical outcomes. Tilmicosin-treated calves developed substantially milder disease despite comparable pathogen loads, coinciding with lower systemic inflammation, suggesting that host-pathogen interactions, rather than pathogen replication alone, influenced disease severity. Neither nasal nor faecal microbiota diversity consistently explained BRDC severity. However, calves that later developed severe disease displayed a more homogeneous nasal microbiota before infection, indicating that early microbial community structure may influence susceptibility. In contrast, the strongest disease-associated microbial signatures were observed in the faecal microbiota. Gut antibiotic-induced dysbiosis revealed associations between BRDC severity, specific intestinal bacterial taxa, systemic inflammation, and faecal short-chain fatty acid (SCFA) profiles. Notably, Chlamydia was strongly associated with disease severity, while several other taxa were linked to inflammatory biomarkers and SCFA concentrations. Collectively, these findings support a holobiont-driven model of BRDC in which disease severity emerges from interactions among pathogens, host inflammatory responses, and microbiota-associated functions. The stronger associations observed in the intestinal microbiota, along with links between gut bacteria, SCFAs, and disease outcomes, provide evidence for a functional gut-lung axis in calves and highlight microbial metabolism as a potential target for strategies to improve respiratory health and reduce antibiotic use.

microbiology↗

bioRxiv2026

Mucosal architecture, microbiota resilience and metabolic disruption reveal holobiont dynamics during bovine respiratory disease

The gut-airway axis is increasingly recognised as an important determinant of respiratory health in livestock. However, the interactions among respiratory infections, microbial communities, mucosal barrier function, and microbial metabolism that underpin this axis remain poorly understood. Here, we combined longitudinal immunological, mucosal, microbiological, and metabolic analyses to characterise host-microbiota interactions during antibiotic treatment and experimental bovine respiratory disease (BRD). We found that the bovine respiratory tract is organised as a hierarchically structured mucosal ecosystem, with compartment-specific mucin expression patterns associated with distinct microbial communities. Within this framework, increasing respiratory pathogen loads were associated with greater clinical severity, oxidative stress, acute inflammation, and targeted alterations in mucosal regulation and microbial composition, while serum amyloid A emerged as the host biomarker most closely reflecting infection intensity. Although infection altered host and microbial states, antimicrobial treatment represented the dominant ecological perturbation. Antibiotic exposure reshaped both respiratory and intestinal microbial communities, reducing diversity, increasing community drift, and driving coordinated ecological transitions across the gut-airway axis that exceeded the effects of infection alone. Importantly, these compositional changes were accompanied by profound reductions in acetate, propionate, butyrate, and valerate, identifying short-chain fatty acids as a major functional consequence of gut microbiota disruption. Integrative multi-omics analyses revealed that mucosal organisation, microbial diversity, microbial metabolism, and immune activity were embedded within a highly structured gut-airway network. Together, these findings support a holobiont view of BRD in which disease outcomes emerge not only from pathogen-host interactions but also from ecological disturbances that propagate across interconnected mucosal compartments. Notably, antimicrobial treatment affected ecosystem structure and function more than infection itself, highlighting potential trade-offs between pathogen control and microbiota stability. Preserving microbial resilience and its metabolic functions may therefore represent an important component of future strategies to improve respiratory health and disease resilience in cattle.

systems biology↗

bioRxiv2026

Strain-level diversity shapes competitive outcomes in Fusarium: a multi-omic synthesis of fungal warfare

Fusarium head blight (FHB) is driven by co-occurring Fusarium species. Yet the molecular bases of their competitive interactions, particularly at the strain level, remain largely unknown. We performed an integrated multi-omic investigation of four Fusarium isolates cultivated in monoculture, self-confrontation (SC) and inter-specific confrontation (C) assays: two Fusarium graminearum strains FgrI349 and FgrPH-1, and two Fusarium avenaceum strains FaveI494 and FaLH03. Light microscopy and quantitative colorimetry revealed marked phenotypic heterogeneity. the F. graminearum strains formed expansive, red-pigmented colonies with rapid radial growth, whereas the F. avenaceum isolates grew more slowly and displayed distinct colony morphologies and pigmentation patterns. Untargeted LC-HRMS detected 1,008 metabolites in monocultures and 938 metabolites in confrontation zones. Species-level chemical signatures were confirmed, and strain-specific metabolite sets were identified, with FaLH03 producing more than 60 % of the metabolites being made exclusively by a single strain, highlighting its exceptionally unique metabolic profile. RNA-seq uncovered extensive transcriptional reprogramming during competition. In self-confrontations, strain-specific differences persisted but no major morphological or metabolic shifts were observed. Inter-specific confrontations elicited partner-dependent responses: FgrI349 up-regulated 1,492 genes against FaveI494 (including secondary-metabolite biosynthesis, oxidoreductase activity and transport) but only 407 genes against FaLH03, while down-regulating secondary-metabolite genes in the conspecific confrontation. Conversely, the F. avenaceum isolates showed opposite trends; FaLH03 strongly repressed ribosome-biogenesis and cell-wall genes while inducing oxidative-metabolism pathways, whereas FaveI494 displayed a modest transcriptional response dominated by down-regulation of cell-division and chromosome-segregation genes. Gene-ontology enrichment highlighted an opponent-specific reversal of the secondary-metabolite biosynthetic process category in F. graminearum: down-regulated in intra-specific confrontation but up-regulated in both inter-specific encounters. Collectively, our results demonstrate that competitive outcomes are shaped more by strain identity than by species identity, with each strain deploying a distinct molecular arsenal, ranging from metabolite-mediated antagonism to targeted transcriptional shutdown, when confronted with a specific opponent. These findings refine our understanding of Fusarium community dynamics and provide a framework for developing strain-targeted biocontrol strategies against FHB.

microbiology↗

bioRxiv2026

Nutritional Anthelmintics: Chicory Reconfigures the Equine Holobiont Across Microbial, Parasitic, and Host Scales

Anthelmintic resistance in cyathostomins is escalating worldwide, threatening equine health and highlighting the need for sustainable, ecology-based parasite control strategies. Chicory (Cichorium intybus, Puna II) has emerged as a promising antiparasitic forage, yet its broader effects on the equine holobiont, parasites, microbiota, and host physiology remain poorly understood. We conducted a 32-day longitudinal grazing trial in young horses to assess how chicory affects parasitological outcomes, gut microbial ecology, nemabiome composition, behaviour, and host physiological and immune responses. Twenty-six naturally infected Anglo-Arabian horses were monitored weekly, with 13 grazing a chicory-based sward and 13 grazing a permanent pasture. Clinical parameters, body weight, and serum biochemistry remained stable across treatments, indicating that chicory was well tolerated. Immune profiles showed limited variation, although IL-10 increased in chicory-fed horses, suggesting subtle immune modulation. Behavioural observations revealed no signs of discomfort and indicated slightly enhanced social interactions in the chicory group. Chicory grazing produced a marked reduction in cyathostomin egg excretion, accompanied by species-specific shifts in nemabiome composition. Several cyathostomin taxa, including Cylicocyclus ashworthi, C. leptostomus, and C. nassatus, declined in chicory-fed horses, whereas certain Cylicostephanus spp increased, indicating differential sensitivity rather than uniform suppression. Concomitantly, chicory induced profound ecological changes in the gut microbiota, including reduced alpha diversity, increased beta dispersion, and destabilised individual microbial trajectories. Several bacterial lineages, particularly Oscillospiraceae, Clostridiaceae, Lachnospiraceae, and Bacteroidales, were differentially enriched, reflecting a functional reorganisation of the intestinal ecosystem. Together, these findings demonstrate that chicory reduces parasite fitness, reshapes nemabiome composition, and alters gut microbial ecology while maintaining host physiological stability. Chicory thus emerges as a promising ecological tool for parasite control, capable of modulating the equine holobiont in ways that complement and potentially reduce reliance on conventional anthelmintic strategies. However, because its effects on gut microbial ecology remain uncertain, and may include shifts resembling dysbiosis, future studies are needed to monitor microbial dynamics more closely and clarify the long-term ecological consequences of chicory grazing. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/737212v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@7b7367org.highwire.dtl.DTLVardef@d5914aorg.highwire.dtl.DTLVardef@135ad65org.highwire.dtl.DTLVardef@10b0322_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2026

Effects of a temporary period on pasture on the transcriptomic signature of horses housed in individual boxes

AO_SCPLOWBSTRACTC_SCPLOWPasture access is widely recognized for its welfare, behavioural, and health benefits in horses compared to individual stabling. Our recent studies have shown that even short-term pasture exposure enhances welfare and induces lasting changes in gut microbiota, promoting health-associated bacterial populations. This study investigated the transcriptomic signature of 22 horses following a standardized pasture protocol, with peripheral blood gene expression analysed before pasture access (T0) and three months after returning to individual stabling (T1). First, using sPLS regression, we correlated gene expression profiles with behavioural welfare indicators measured at T0 and T1. Horses with pasture access exhibited significantly altered blood transcriptome compared to controls, with aggressiveness towards humans emerging as the strongest behavioural correlate of gene expression. Bioinformatic analyses revealed that aggressiveness-associated genes were linked to inflammation, apoptosis, and cell differentiation/growth. Then, horses with pasture access were divided in resilient and non-resilient according to the improvement of their behaviour after time on pasture. Differentially expressed genes post versus pre- pasture, compared between resilient and non-resilient horses for aggressiveness showed that inflammatory signals were downregulated in both subgroups, with a more pronounced effect in resilient horses. This suggests that resilient individuals are better equipped to modulate inflammatory responses in low-stress environments like pasture. Surprisingly, for unresponsiveness to the environment--a trait linked to depressive-like states--resilient horses displayed increased inflammatory signaling (e.g., IRF and CD40 activation) post-pasture, while non-resilient horses showed activation of anti-inflammatory PPAR signaling. Notably, non-resilient horses exhibited molecular signatures associated with organismal death, morbidity, and growth failure, indicating maladaptive physiological states. In contrast, resilient horses demonstrated activation of growth-related pathways (e.g., BMP2 and BMPR1A), suggesting a shift toward anabolic and developmental processes. This study underscores the behavioural and molecular benefits of pasture access for horses, particularly in reducing aggressiveness and inflammatory signaling in resilient individuals. The findings highlight the complex interplay between behaviour, inflammation, and resilience, with pasture access promoting adaptive physiological and molecular responses. Further research is needed to elucidate the long-term implications of these transcriptomic changes and their broader relevance to equine welfare.

animal behavior and cognition↗

bioRxiv2026

AI-Powered Acoustic Surveillance for Early Detection of Calf Respiratory Disease

Effective management of Bovine Respiratory Disease Complex (BRDC) requires timely, non-invasive diagnostic tools to protect calf health and welfare. Among early clinical signs, coughing stands out as both frequent and informative. To explore its potential for early BRDC detection, we deployed an artificial intelligence (AI)-driven acoustic monitoring system that recorded over 2,730 hours of audio during a 30-day period. Four experimental pens, each housing seven calves and stratified by infection status and antibiotic treatment, were equipped with a dedicated microphone to enable targeted acoustic surveillance. This configuration enabled pen-specific detection of cough events, which were subsequently classified using an AI HuBERT-based model trained on 1,045 labelled clips. The classifier achieved 92% accuracy. Temporal patterns in cough frequency aligned with infection dynamics, treatment responses, and circadian patterns. Notably, AI-detected coughs consistently preceded clinical scores by 1-2 days, confirming the systems sensitivity to early respiratory disorders. These findings support the use of acoustic surveillance as a valid, scalable, and autonomous tool for continuous monitoring and early warning of respiratory diseases in calves. ImplicationsThis study demonstrates that AI-powered acoustic monitoring enables real-time, non-invasive detection of coughs in calves for early warning of respiratory diseases, outperforming traditional veterinarian clinical scoring by 1-2 days. Its high accuracy and sensitivity to respiratory infection dynamics and treatment effects position it as a scalable tool for precision livestock farming.

zoology↗

bioRxiv2025

Nucleoside Binding by a Surface Lipoprotein Governs Conjugative ICE Acquisition in Ruminant Mycoplasmas

Integrative and conjugative elements (ICEs) are major mediators of horizontal gene transfer (HGT) in bacteria. However, the role of recipient cells in their acquisition has received little attention. Using the ruminant pathogens Mycoplasma agalactiae and Mycoplasma bovis as minimal models, we combined genome-wide transposon mutagenesis with high-throughput mating assays to identify recipient factors required for ICE acquisition. The surface lipoprotein P48 emerged as the primary determinant of ICE uptake in both species. Structural and functional analyses revealed that P48 is the substrate-binding component of an ABC transporter with nucleoside-binding capacity. A single point mutation that abolished nucleoside binding drastically reduced ICE acquisition, demonstrating that P48-mediated nucleoside recognition is essential for conjugative transfer. However, ICE uptake did not require nucleoside transport, as inactivation of the transporter permease blocked nucleoside analog toxicity but not ICE invasion. Loss of P48 also triggered transcriptional activation of vestigial ICE genes, suggesting that surface recognition affects the intracellular state of the recipient. Remarkably, ICE transmission from recipient-derived donors was unaffected by P48 loss, underscoring its acquisition-specific role. Together, these results reveal a previously unrecognized, surface-exposed recipient factor critical for efficient ICE transfer in mycoplasmas and identify nucleotide binding as a central function in conjugation. By demonstrating that recipient-encoded functions can directly control ICE dissemination, this work challenges the donor-centric paradigm of bacterial conjugation and suggests new strategies to restrict horizontal gene flow in pathogenic and synthetic mycoplasmas. IMPORTANCEIntegrative and conjugative elements (ICEs) are mobile DNA elements that drive bacterial conjugation, a major process by which bacteria exchange genes. Although conjugation has been studied for decades, the focus has been almost exclusively on donor cells and the ICE itself, leaving the role of recipient cells largely overlooked. Using the wall-less ruminant pathogens Mycoplasma agalactiae and Mycoplasma bovis as minimal models, we discovered that a single recipient lipoprotein is required for efficient ICE uptake. Our data show that nucleoside recognition by P48, but not transport, is critical for conjugation, revealing an unexpected mechanistic link between nutrient sensing and gene acquisition. These findings shift the paradigm of conjugation from a donor-driven process to one jointly determined by donor and recipient functions. By identifying a recipient-encoded determinant of ICE transfer, this work opens new avenues to control horizontal gene flow in both pathogenic and engineered bacteria. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/677790v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@f7cc15org.highwire.dtl.DTLVardef@77a34eorg.highwire.dtl.DTLVardef@82699corg.highwire.dtl.DTLVardef@1e3be93_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Arp2/3 complex contributes to the actin-dependent uptake of Aspergillus terreus conidia by alveolar epithelial cells

Aspergillus terreus is an opportunistic fungal pathogen associated with high mortality rates and intrinsic resistance to amphotericin B. Its ability to persist within host tissues without inducing strong immune responses was suggested to contribute to poor clinical outcomes. The cellular mechanisms underlying A. terreus interactions with host cells remain largely unexplored. In this study, we have used a micropattern-based infection model to investigate the early interactions between A. terreus conidia and alveolar epithelial cells, focusing on the role of Arp2/3-dependent actin remodeling. This system allows quantitative analysis of conidia-cell interactions under defined spatial conditions. We show that A. terreus conidia rapidly bind to micropatterned A549 cell islands, with conidial numbers increasing over time. Conidia were found in actin- and Lamp1-positive vesicles already after one hour of infection. Inhibition of the Arp2/3 complex significantly impaired conidial binding and disrupted the formation of actin-positive vesicles, confirming the essential role of Arp2/3-mediated actin remodeling in early stages of conidial uptake. A subset of internalized conidia was localized to Lamp1-positive phagolysosomes and accumulated over time. Interestingly, we have identified a small but consistent population of phagolysosomes decorated with actin patches, potentially resembling actin flashes. These structures were entirely abolished upon Arp2/3 inhibition, indicating active cytoskeletal remodeling at the phagolysosomal interface. Our findings provide the first mechanistic insights into A. terreus internalization by alveolar epithelial cells and establish Arp2/3-mediated actin dynamics as a key process in early host-pathogen interactions. This cellular pathway may contribute to intracellular persistence and help understand the delayed onset of A. terreus infections.

microbiology↗

bioRxiv2022

Evaluation of the nemabiome approach for the study of equine strongylid communities

Basic knowledge on the biology and epidemiology of equine strongylid species remains insufficient although it would contribute to the design of better parasite control strategies. Nemabiome is a convenient tool to quantify and to identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA cistron and its predictive performance and associated biases both remain unaddressed. This study aimed to bridge this knowledge gap using cyathostomin mock communities and comparing performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. The effects of bioinformatic parameters were investigated to determine the best analytical pipelines. Subsequently, barcode predictive abilities were compared across various mock community compositions. The replicability of the approach and the amplification biases of each barcode were estimated. Results were also compared between various types of biological samples, i.e. eggs, infective larvae or adults. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, a reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types, although infective larvae may remain the most tractable in the field. Additional strategies to improve the COI barcode performances are discussed. These results underscore the critical need of mock communities for metabarcoding purposes.

ecology↗

bioRxiv2022

The first horse gut microbiome gene catalog reveals that rare microbiome ensures better cardiovascular fitness in endurance horses

Emerging evidence indicates that the gut microbiome contributes to endurance exercise performance, but the extent of their functional and metabolic potential remains unknown. Using elite endurance horses as a model system for exercise responsiveness, we built the first equine gut microbial gene catalog comprising more than 25 million non-redundant genes representing 4,696 genera spanning 95 phyla. The unprecedented resolution unrevealed functional pathways relevant for both the structure of the microbiome and the host health and recovered 369 novel metagenome-assembled bacterial genomes, providing useful reference for future studies. Integration of microbial and host omic datasets suggested that microbiomes harboring rare species were functionally dissimilar from those enriched in Lachnospiraceae taxa. Moreover, they offered expanded metabolic pathways to fine-tune the cardiovascular capacity through mitochondria-mediated mechanisms. The results identify an associative link between horse endurance capability and its microbiome gene function, laying the basis for nutritional interventions that could benefit endurance athletes.

microbiology↗

bioRxiv2021

Species turnover between age groups of horses and positive network of co-occurrences define the structure of horse strongylid communities: a meta-analysis

Grazing horses are infected by a wide range of strongylid species mostly located in the large intestine. Despite their impact on equine health and the emergence of drug resistant isolates, the phenology of these nematodes has been poorly characterized and the rules structuring their assembly as a community are not understood. Here, we compiled data on 46 equine strongylid species collected worldwide at the regional or horse scales (upon deworming or after necropsy) to analyse their richness, diversity and associated factors of variation. Worldwide, twelve species from the Cylicocyclus (n = 4), Cylicostephanus (n = 3), Coronocyclus (n = 2) and Cyathostomum (n = 2) genera were found in at least 75% of sites. Geoclimatic conditions had a limited effect on strongylid communities, but reduced species richness was found under the temperate European area. The recovery method did not affect species richness and differences on the temporal and sampling effort scales between studies applying either methods underpinned heterogeneous variances in community diversity. At the horse level, rarefaction curves correlated poorly to parasite egg excretion, suggesting little contribution of community diversity to this trait. Using a diversity partitioning approach, we found that within-host diversity represented half of overall diversity underscoring the importance of host density and environmental contamination to the diversity of strongylid communities. While this is expected to erase diversity across communities, species turnover between age classes was the second most important contributor to overall diversity (23.9%). This was associated with a network of positive co-occurrences between the four most prevalent genera that we resolved at the anatomical niche level. Altogether this pattern of {beta}-diversity maintenance across age classes combined with positive co-occurrences may be grounded by priority effects between major species. Our findings set the first assembly rules of equine strongylid communities.

ecology↗

bioRxiv2021

Integrative biology defines novel biomarkers of resistance to strongylid infection in horses

The widespread failure of anthelmintic drugs against nematodes of veterinary interest requires novel control strategies. Selective treatment of the most susceptible individuals could reduce drug selection pressure but requires appropriate biomarkers of the intrinsic susceptibility potential. To date, this has been missing in livestock species. Here, we selected Welsh ponies with divergent intrinsic susceptibility to cyathostomin infection and found that their potential was sustained across a 10-year time window. Using this unique set of individuals, we monitored variations in their blood cell populations, plasma metabolites and faecal microbiota over a grazing season to isolate core differences between their respective responses under worm-free or natural infection conditions. Our analyses identified the concomitant rise in plasmatic phenylalanine level and faecal Prevotella abundance and the reduction in circulating monocyte counts as biomarkers of the need for drug treatment. This biological signal was replicated in other independent populations. We also unravelled an immunometabolic network encompassing plasmatic beta-hydroxybutyrate level, short-chain fatty acid producing bacteria and circulating neutrophils that forms the discriminant baseline between susceptible and resistant individuals. Altogether our observations open new perspectives on the susceptibility of equids to cyathostomin infection and leave scope for both new biomarkers of infection and nutritional intervention.

systems biology↗

bioRxiv2021

Understanding the holobiont: crosstalk between gut microbiota and mitochondria during endurance

Endurance exercise has a dramatic impact on the functionality of mitochondria and on the composition of the intestinal microbiome, but the mechanisms regulating the crosstalk between these two components are still largely unknown. Here, we sampled 20 elite horses before and after an endurance race and used blood transcriptome, blood metabolome and fecal microbiome to describe the gut-mitochondria crosstalk. A subset of mitochondria-related differentially expressed genes involved in pathways such as energy metabolism, oxidative stress and inflammation was discovered and then shown to be associated with butyrate-producing bacteria of the Lachnospiraceae family, especially Eubacterium. The mechanisms involved were not fully understood, but through the action of their metabolites likely acted on PPAR{gamma}, the FRX-CREB axis and their downstream targets to delay the onset of hypoglycemia, inflammation and extend running time. Our results also suggested that circulating free fatty acids may act not merely as fuel but drive mitochondrial inflammatory responses triggered by the translocation of gut bacterial polysaccharides following endurance. Targeting the gut-mitochondria axis therefore appears to be a potential strategy to enhance athletic performance.

systems biology↗

bioRxiv2017

Metagenomic signature of natural strongyle infection in susceptible and resistant horses

Gastrointestinal strongyles are a major threat to horses' health and welfare. Given that strongyles inhabit the same niche as the gut microbiota, they may interact with each other. These beneficial or detrimental interactions are unknown in horses and could partly explain contrasted susceptibility to infection between individuals. To address these questions, an experimental pasture trial with 20 worm-free female Welsh ponies (10 susceptible (S) and 10 resistant (R) to parasite infection) was implemented for five months. Fecal egg counts (FEC), hematological and biochemical data, body weight and gut microbiota composition were studied in each individual after 0, 24, 43, 92 and 132 grazing days.\n\nThe predicted R ponies exhibited lower FEC after 92 and 132 grazing days, and showed higher levels of circulating monocytes and eosinophils, while S ponies developed lymphocytosis by the end of the trial. Although the overall microbiota diversity remained similar between the two groups, R and S ponies exhibited sustained differential abundances in Clostridium XIVa, Ruminococcus, Acetivibrio and unclassified Lachnospiracea at day 0. These bacteria may hence contribute to the intrinsic pony resistance towards strongyle infection. Moreover, Paludibacter, Campylobacter, Bacillus, Pseudomonas, Clostridium III, Acetivibrio, members of the unclassified Eubacteriaceae and Ruminococcaceae and fungi loads were increased in infected S ponies, suggesting that strongyle and fungi may contribute to each others success in the ecological niche of the equine intestines. In contrast, butyrate-producing bacteria such as Ruminococcus, Clostridium XIVa and members of the Lachnospiraceae family decreased in S relative to R ponies. Additionally, these gut microbiota alterations induced changes in several immunological pathways in S ponies, including pathogen sensing, lipid metabolism, and activation of signal transduction that are critical for the regulation of immune system and energy homeostasis. These observations shed light on a putative implication of the gut microbiota in the intrinsic resistance to strongyle infection.\n\nOverall, this longitudinal study provides a foundation to better understand the mechanisms that underpin the relationship between host susceptibility to strongyle infection, immune response and gut microbiota under natural conditions in horses and should contribute to the development of novel biomarkers of strongyle susceptibility and provide additional control options.

systems biology↗

bioRxiv2017

Development of a high-density, 2M SNP genotyping array and 670k SNP imputation array for the domestic horse

BackgroundTo date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.\n\nResultsUsing whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of [~]5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of [~]2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of [~]670 thousand SNPs (MNEc670k), was designed for genotype imputation.\n\nConclusionsHere, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

genomics↗