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).