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Abstract
Host-restricted lineages of gut bacteria often include many closely related strains,
but this fine-scale diversity is rarely investigated. The specialized gut symbiont
Snodgrassella alvi has codiversified with honeybees (Apis mellifera) and bumblebees
(Bombus) for millions of years. Snodgrassella alvi strains are nearly identical for
16S rRNA gene sequences but have distinct gene repertoires potentially affecting host
biology and community interactions. We examined S. alvi strain diversity within and
between hosts using deep sequencing both of a single-copy coding gene (minD) and of
the V4 region of the 16S rRNA gene. We sampled workers from domestic and feral A. mellifera
colonies and wild-caught Bombus representing 14 species. Conventional analyses of
community profiles, based on the V4 region of the 16S rRNA gene, failed to expose
most strain variation. In contrast, the minD analysis revealed extensive strain variation
within and between host species and individuals. Snodgrassella alvi strain diversity
is significantly higher in A. mellifera than in Bombus, supporting the hypothesis
that colony founding by swarms of workers enables retention of more diversity than
colony founding by a single queen. Most Bombus individuals (72%) are dominated by
a single S. alvi strain, whereas most A. mellifera (86%) possess multiple strains.
No S. alvi strains are shared between A. mellifera and Bombus, indicating some host
specificity. Among Bombus-restricted strains, some are restricted to a single host
species or subgenus, while others occur in multiple subgenera. Findings demonstrate
that strains diversify both within and between host species and can be highly specific
or relatively generalized in their host associations.