Does the fecal pellet microbiome represent the endogenous
microbiome?
Even though fecal pellets and tissues were collected for different
studies and from different animals, we compare their microbial
communities descriptively. The three most abundant families in fecal
pellets (Lachnospiraceae , Ruminococcaceae , andBacteroidaceae ) combined made up an average of 60% of the fecal
microbial community, 43% of the upper intestine community, and less
than 1% of the cloacal community (Online Resource 1). The similarity
between fecal and the upper intestine communities is predominantly due
to the high abundance of Ruminococcaceae andBacteroidaceae in the upper intestine. However, despite the high
abundance of Lachnospiraceae in fecal pellets, only about 1% of
the upper intestine community was made up of Lachnospiraceae . At
the phylum level, fecal pellet communities averaged 62% Firmicutes,
18% Bacteroidetes, and 11% Proteobacteria (Fig 7). As we sampled down
the digestive and reproductive tracts, the percentage of Firmicutes and
Bacteroidetes steadily decreased and the percentage of Proteobacteria
increased, to the point of nearly totally dominating the cloacal
community at an average of 99% Proteobacteria found in cloacal tissues
(Fig 7).