Association between the skin microbiome and MHC class II diversity in an amphibian.

Microbiomes play an important role in determining the ecology and behaviour of their hosts. However, questions remain pertaining to how host genetics shape microbiomes, and how microbiome composition influences host fitness. We explored the effects of geography, evolutionary history and host genetics on the skin microbiome diversity and structure in a widespread amphibian. More specifically, we examined the association between bacterial diversity and composition and the major histocompatibility complex class II exon 2 diversity in 12 moor frog (Rana arvalis) populations belonging to two geographical clusters that show signatures of past and ongoing differential selection. We found that while bacterial alpha diversity did not differ between the two clusters, MHC alleles/supertypes and genetic diversity varied considerably depending on geography and evolutionary history. Bacterial alpha diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. Furthermore, bacterial community composition showed significant variation between the two geographical clusters and between specific MHC alleles/supertypes. Our findings emphasize the importance of historical demographic events on hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.

A novel duplex ddPCR assay for detection and differential diagnosis of Ascaridia galli and Heterakis gallinarum eggs from chickens feces.

Since the EU ban on battery cages, many studies have listed Ascaridia galli and Heterakis gallinarum as the most common roundworms in the European laying hen population. A complicating factor is that the eggs of these parasites are almost identical. Thus, lack of molecular diagnostic approaches has driven epidemiological studies to take on necropsy for species discrimination, which is labor and cost intensive. Here, we describe a novel diagnostic tool based on droplet digital PCR for simultaneous identification and absolute quantification of the eggs of both of these ascarids in chickens' droppings using two different genus-specific primer-probe sets targeting the second internal transcribed spacer region (ITS-2) in the nuclear ribosomal (rRNA) gene array. No cross-reaction was observed when different combinations of DNA and species-specific primers and probes were tested. The lowest obtained frequency threshold for the detection of H. gallinarum in the presence of a constant A. galli DNA concentration was determined to be 0.8 %. After validation, we used the assay to analyze field samples collected from several Swedish laying hen farms. Out of 134 samples, 86 (64 %) were positive for A. galli while 11 (8.3 %) samples were positive for H. gallinarum. These samples were initially analyzed with flotation technique for detection of ascarid eggs. The results of the Cohen's kappa indicated substantial agreement (85.8 %) between the two tests. In conclusion, we have validated a novel molecular-based diagnostic tool for quantification and differentiation between intestinal parasites of major importance in chickens with high precision. Although this study focuses on identification of parasites of laying hens, the findings may well have a bearing on all types of chicken production systems. The present study lays the groundwork for future research into epidemiology of these two important chicken parasite species.

Developmental capacity of Ascaridia galli eggs is preserved after anaerobic storage in faeces.

The reliability of the results of in vitro studies such as detection of anthelmintic resistance often depends on the ability of the parasite eggs to develop under laboratory conditions. The aim of this study was to assess the embryonation capability of the chicken roundworm Ascaridia galli eggs after storage under different conditions. Two storage media for parasite eggs were used; faeces or water. Eggs in petri dishes (90 dishes in total) containing faces or water media were first exposed either to aerobic or anaerobic conditions at different temperatures (4 °C /+O2, 4 °C /-O2, 25 °C/-O2) for a maximum of 72 days. Every second week, materials from petri dishes in triplicates were recovered and incubated aerobically for two weeks at 25 °C. After the incubation, 200-300 eggs from each petri shish (sampling unit) were counted and the number of embryonated eggs was determined. Data was analyzed in R (version 3.4.3) A logistic regression model with the probability of an egg to embryonate as dependent variable and conditions, storage medium and time points as fixed effects with quasibinomial distribution was run. Least-square means were calculated and pairwise comparisons were made with the fixed effect factors (condition, storage medium and time point). Eggs in faeces had a significantly (p ˂ 0.05) higher embryonation than those in water, irrespective of storage conditions. At 4 °C embryonation tended to decline over time under aerobic conditions irrespective of the storage medium, whereas it remained constant following storage at anaerobic conditions. In contrast, anaerobic storage at the 25 °C negatively affected egg development in both media, except for day 14 in faeces. Our major finding was that eggs in faeces under anaerobic conditions and at 4 °C retained the highest rate of development, with a minimum decline in their developmental capacity over time compared to cleaned eggs stored in water.

A sensitive and reliable restriction enzyme assay to distinguish between the mosquitoes Culex torrentium and Culex pipiens.

Culex pipiens pipiens Linnaeus and Culex torrentium Martini (Diptera: Culicidae) are closely related vector species that exist sympatrically in Europe. The two species are morphologically almost identical and can only be distinguished with certainty by characters of the male genitalia. Hence, correct species identification and conclusions on distribution and vector status are very difficult and often neglected. Therefore, we developed a reliable and simple mitochondrial cytochrome c oxidase subunit I (COI) gene restriction enzyme assay to discriminate between Cx. pipiens and Cx. torrentium, based on the analysis of morphologically identified male specimens. We sequenced approximately 830 bp in the 3' region of the mitochondrial COI gene of 18 morphologically identified males of Cx. pipiens and Cx. torrentium. Two restriction enzymes (FspBI and SspI) that could distinguish between the two species according to species-specific differences in these sequences were chosen. The restriction enzymes were tested on 227 samples from Sweden and verified by sequencing 44 of them. The enzyme FspBI correctly identified all investigated samples; the enzyme SspI identified all samples except one Cx. torrentium. We hope the method and the findings presented here will help to shed light on the true distribution and relative proportions of the two species in Europe.