ITS-2 rDNA Nemabiome Metabarcoding in two Isolated Populations of Wild Roe Deer (Capreolus Capreolus) Reveals Variation in Gastrointestinal Nematode Community Composition Between Regions and Among Age Classes

Abstract

BackgroundGastrointestinal nematodes are ubiquitous for both domestic and wild ungulates which have varying consequences to health and fitness. They exist as complex communities of multiple co-infecting species and we have a very limited understanding of how these communities vary in different hosts, regions and circumstances or on how this affects their impacts. MethodsWe have undertaken ITS-2 rDNA nemabiome metabarcoding on populations of nematode larvae isolated from fecal samples of roe deer of different sex and age classes in the two isolated populations of Chizé and Trois Fontaines in France not co-grazing with any domestic ungulate species. ResultsWe identified 100 Amplified Sequence Variants (ASVs) that assigned to 14 gastrointestinal nematode taxa overall either at genus (38%), or species (62%) level. These taxa were dominated by parasites classically found in cervids - e.g., Ostertagia leptospicularis, Spiculopteragia spp. Higher parasite species diversity was present in the Trois Fontaine than in the Chize populations including the presence of some species more typically seen in domestic livestock, (Haemonchus contortus, Bunostomum trigonocephalum, Cooperia punctata, Teladorsagia circumcincta). No differences in parasite species diversity or community composition was seen in the samples collected from three zones of differing habitat quality within the Chize region. Young roe deer hosted the highest diversity of gastrointestinal nematodes, with more pronounced effects of age apparent in Trois Fontaines. The effect of host age differed between gastrointestinal nematode species, e.g. there was little effect on Ostertagia leptospicularis but a high effect on Trichostrongylus spp. No effect of host sex was detected in either site. ConclusionsThe presence of some livestock parasite species in the Trois Fontaine roe deer popualtions was surprising given the isolation of this population away from grazing domestic livestock. However, it should be noted that a small group of sheep were resident in the region, albeit separately fenced, which raises some interesting questions regarding the introduction of non-native parasite species into wildlife populations. Overall, our results suggest complex interactions between hosts, environments and parasites and illustrate the power of the nemabiome metabarcoding approach to elucidate the composition of gastrointestinal nematode communities in wildlife.

Cross-transmission of resistant gastrointestinal nematodes between wildlife and transhumant sheep

“…; Northen chamois; domestic goat, Capra hircus; red deer, Cervus elaphus; and roe deer, Capreolus capreolus) (Zaffaroni et al, 2000). In our study, only a few domestic goats Contrary to results obtained on roe deer Capreolus capreolus (Beaumelle et al, 2021), we found higher diversity of nematodes in adult males compared to females and kids/yearlings. In fact, ibex have high sexual dimorphisms and male are certainly more susceptible to parasitism (Markle and Fish, 2014).…”

“…We also checked for the presence of low abundant parasite propagules with a 14 mL tube filled with the remaining solution and covered with a coverslip before centrifugation (5 min at 1200 rpm) and microscopical observation ('control slide'). We attributed the value of 7.5 epg for parasites with no egg observed on the McMaster, but at least one egg observed on the control slide (for a similar procedure see Beaumelle et al, 2021).…”

“…The dada2 pipeline returns Amplicon Sequence Variants (ASV) which are sequence variants differing by as little as one nucleotide (Callahan et al, 2017). Following Beaumelle et al (2021), gastrointestinal nematodes were identified with four different methods of assignationdatabases: BLASTn (Altschul et al, 1990) based on (1) the NCBI database (Accessed:…”

Instability of fecal glucocorticoid metabolites at 4°C: Time to freeze matters

“…Second, our experimental design (adult individuals only with highly skewed sex ratio) does not allow us to formally conclude and discuss whether the age or sex of individuals affects the rate of FCM degradation at 4°C, even though these factors were selected in the model selection procedure. However, given that gut microbial communities may significantly differ between males and females, or between different age classes, especially in cervids (Beaumelle et al, 2021;Minich et al, 2021), these questions are definitely of interest and would require future works to elucidate to which extent FCM degradation may be impacted by these two factors. Finally, our results were obtained under controlled conditions of constant +4°C temperature, but little information can be inferred about the rate of FCM degradation in feces held in natural conditions when exposed to other environmental factors.…”

Estimation of the impact of three different bioinformatic pipelines on sheep nemabiome analysis

“…Most of the recently published studies employing NGS to study the nemabiomes in various host animals have relied on the accurate evaluation of short reads produced by the Illumina sequencing platform [7,13,15,29]. In fact, to our knowledge few studies exist on nematode parasites wherein the employed sequencing platform used has been PacBio [6].…”