Microtus agrestis microbiome reads, taxonomy and related animal metadata

Mammalian gastrointestinal microbiomes are highly variable, both within
individuals and across populations, with changes linked to time and ageing
being widely reported. Discerning patterns of change in wild mammal
populations can therefore prove challenging. We used high-throughput
community sequencing methods to characterise the microbiome of wild field
voles (Microtus agrestis) from faecal samples collected across 12
live-trapping field sessions, and then at cull. Changes in α- and
β-diversity were modelled over three timescales. Short-term differences
(following 1–2 days captivity) were analysed between capture and cull, to
ascertain the degree to which the microbiome can change following a rapid
change in environment. Medium-term changes were measured between
successive trapping sessions (12–16 days apart), and long-term changes
between the first and final capture of an individual (from 24 to 129
days). The short period between capture and cull was characterised by a
marked loss of species richness, while over medium- and long-term in the
field, richness slightly increased. Changes across both short and long
timescales indicated shifts from a Firmicutes-dominant to a
Bacteroidetes-dominant microbiome. Dramatic changes following captivity
indicate that changes in microbiome diversity can be rapid, following a
change of environment (food sources, temperature, lighting etc.). Medium-
and long-term patterns of change indicate an accrual of gut bacteria
associated with ageing, with these new bacteria being predominately
represented by Bacteroidetes. While the patterns of change observed are
unlikely to be universal to wild mammal populations, the potential for
analogous shifts across timescales should be considered whenever studying
wild animal microbiomes. This is especially true if studies involve animal
captivity, as there are potential ramifications both for animal health,
and the validity of the data itself as a reflection of a ‘natural’ state
of an animal.