16S rRNA gene amplicons derived from six helminth species collected from four gut sections of 32 wild Apodemus flavicollis

The symbiotic relationship between bacteria and multicellular organisms is such that the collective of bacteria in the gut (microbiota) has been described as the second genome, or undiscovered organ, owing to the large collective of genes, and their associated impact on host health. All multicellular organisms are expected to play host to a microbiota, including parasitic helminths, another key component of the gut biome. We describe, for the first time, the diversity and taxonomic composition of microbiota associated with the parasitic helminth community (six species and 2,045 helminths) of 32 naturally infected wild rodents (Apodemus flavicollis), and compare this microbiota with that of the corresponding gut niche in which the helminths co-occurred using 16S rRNA sequencing. Bacterial diversity of each helminth species was lower than that of the respective gut section that it parasitised. The composition of helminth-associated microbiota was significantly different from that of the host gut (distance-based redundancy analyses), with helminths being dominated by the phyla Firmicutes (mean per pool: 27.48%), Proteobacteria (34.07%), Tenericutes (25.78%) and/or Deferribacteres (5.44%, 0 - 80.29%), while the host was dominated by Firmicutes (55.02%), Bacteroidetes (24.75%) and Proteobacteria (15.66%). Helminth microbiota contained more potentially pathogenic bacteria than their corresponding host gut niche. This study provides the first in depth analysis of bacteria associated with parasitic helminths from naturally infected wild rodent hosts. Since microbiota could impact helminth survival, the results discussed here provide insight into possible parasite control.