Microbial communities inhabit many environmental niches including the nutrient-rich gut
systems of animals, where they are involved in a number of important processes. Insect gut
microbiota may assist the host with several functions including synthesis of nutritional
components lacking from the host diet and digestion of lignocellulosic materials. It is generally
believed that the diet of the host plays an important role in the structure of the gut microbiome.
Numerous studies have focused on insects feeding on lignocellulosic diets such as termites,
as well as medically and agriculturally important insect species. Few studies have researched
the gut microbiota of adult dung beetles. Most scarab beetle species feed on the liquid
component of wet dung, whereas Pachysoma spp. may feed on lignocellulosic materials within
their diet of dry dung, plant detritus or both. This feeding behaviour makes Pachysoma an
ideal candidate for studying the role that diet has on gut microbiome assembly.
Plant detritus feeding P. endroedyi and the dry dung feeding P. striatum were collected
from Namaqualand, South Africa. The mid- and hindgut of each individual were dissected and
mDNA extracted using a phenol-chloroform method. Amplicon sequencing of the bacterial 16S
rRNA gene and the fungal ITS region was used to determine inter- and intra-specific
differences in microbial community structures. Shotgun sequencing of the entire gut
metagenome was carried out on mDNA extracted from whole gut samples. Shotgun
sequencing was used for both taxonomic and functional annotation of the Pachysoma gut
Both amplicon and shotgun sequencing detected substantial differences in bacterial and
fungal diversity between the two Pachysoma species. Amplicon sequencing showed the
number of bacterial phyla ranged from 6-11 and 4-7 (total 14 phyla) for P. endroedyi and P.
striatum, respectively. Furthermore, a minimal core microbiome was detected with only 2.57%
of the bacterial OTUs shared between the two Pachysoma species studied. Large intraspecific
variations were also noted within both Pachysoma species. Fungal communities could
not be detected in the gut of P. endroedyi, while only two fungal phyla were detected P. striatum gut samples. Metagenome shotgun sequencing detected a greater bacterial diversity
(total of 39 phyla) than the 16S rRNA gene amplicon study, although large differences were
noted between the two species. Furthermore, shotgun sequencing demonstrated that fungal
communities were present in the guts of both Pachysoma species. Archaea, viruses and other
eukaryotic microorganisms were also present in the gut metagenomes of both Pachysoma
The functional capacity of the Pachysoma spp. gut microbiomes was analysed using
shotgun sequencing. Both species had the genetic capacity to degrade cellulose and
hemicellulose but not lignin, supporting the suggestion that P. striatum feeds on plant material
in the dry dung. Furthermore, the functional capacity of the microbiomes of both Pachysoma
species were comparable, suggesting the ability for both species to feed on either dry dung or
plant detritus. The similarity of the functional profiles of the two Pachysoma species suggests
the existence of a functional rather than phylogenetic core microbiome
This primary study has successfully characterised the phylogenetic and functional
profiles of the gut microbiomes of two Pachysoma species feeding on different substrates.
However, it is still unclear if diet is the primary driver in gut microbiome assembly.