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Background  Growing evidence points towards a role of gastrointestinal (GI) helminth parasites of ruminants in modifying the composition of the host gut flora, with likely repercussions on the pathophysiology of worm infection and disease, and on animal growth and productivity. However, a thorough understanding of the mechanisms governing helminth-microbiota interactions and of their impact on host health and welfare relies on reproducibility and replicability of findings. To this aim, in this study, we analysed quantitative and qualitative fluctuations in the faecal microbiota composition of lambs vaccinated against, and experimentally infected with, the parasitic GI nematode  Teladorsagia circumcincta  over the course of two separate trials performed over two consecutive years.    Methods  Two trials were conducted under similar experimental conditions in 2017 and 2018, respectively. In each trial, lambs were randomly assigned to one of the following experimental groups: (i) vaccinated/infected, (ii) unvaccinated/infected and (iii) unvaccinated/uninfected. Faecal samples collected from individual animals were subjected to DNA extraction followed by high-throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene and bioinformatics and biostatistical analyses of sequence data.    Results  Substantial differences in the populations of bacteria affected by immunisation against and infection by  T. circumcincta  were detected when comparing data from the two trials. Nevertheless, the abundance of  Prevotella  spp. was significantly linked to helminth infection in both trials.    Conclusions  Despite the largely conflicting findings between the two trials, our data revealed that selected gut microbial populations are consistently affected by  T. circumcincta  infection and/or vaccination. Nevertheless, our study calls for caution when interpreting data generated from  in vivo  helminth-microbiome interaction studies that may be influenced by several intrinsic and extrinsic host-, parasite- and environment-related factors.Supplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04688-4.

parasites and vectors

Vaccination against the brown stomach worm, Teladorsagia circumcincta, followed by parasite challenge, induces inconsistent modifications in gut microbiota composition of lambs