Microbial community composition along the digestive tract in forage- and grain-fed bison

Abstract

Background: Diversity and composition of microbial communities was compared across the 13 major sections of the digestive tract (esophagus, reticulum, rumen, omasum, abomasum, duodenum, jejunum, ileum, cecum, ascending colon, transverse colon, descending colon, and rectum) in two captive populations of American bison (Bison bison), one of which was finished on forage, the other on grain.

Results: Microbial diversity fell to its lowest levels in the small intestine, with Bacteroidetes reaching their lowest relative abundance in that region, while Firmicutes and Euryarchaeota attained their highest relative abundances there. Gammaproteobacteria were most abundant in the esophagus, small intestine, and colon. The forage-finished bison population exhibited higher overall levels of diversity, as well as a higher relative abundance of Bacteroidetes in most gut sections. The grain-finished bison population exhibited elevated levels of Firmicutes and Gammaproteobacteria. Within each population, different sections of the digestive tract exhibited divergent microbial community composition, although it was essentially the same among sections within a given region of the digestive tract. Shannon diversity was lowest in the midgut. For each section of the digestive tract, the two bison populations differed significantly in microbial community composition.

Conclusions: Similarities among sections indicate that the esophagus, reticulum, rumen, omasum, and abomasum may all be considered to house the foregut microbiota; the duodenum, jejunum, and ileum may all be considered to house the small intestine or midgut microbiota; and the cecum, ascending colon, transverse colon, descending colon, and rectum may all be considered to house the hindgut microbiota. Acid from the stomach, bile from the gall bladder, digestive enzymes from the pancreas, and the relatively low retention time of the small intestine may have caused the midgut's low microbial diversity. Differences in microbial community composition between populations may have been most strongly influenced by differences in diet (forage or grain). The clinical condition of the animals used in the present study was not evaluated, so further research is needed to establish whether the microbial profiles of some bison in this study are indeed indicative of dysbiosis, a predisposing factor to ruminal acidosis and its sequelae.

Keywords: Bison; Diet; Digestive tract; Microbiota.

Fig. 1

Microbial diversity along the length of the bison digestive tract. Letters above the chart indicate results of Tukey’s HSD test; sections marked with different letters were significantly different from one another. a Diversity of the gut microbiota in forage-finished bison, as measured by the Shannon index. b Diversity of the gut microbiota in grain-finished bison, as measured by the Shannon index

Fig. 2

Principal coordinates analysis (PCoA) of microbial operational taxonomic units (OTUs) for entire digestive tract in both populations (forage- and grain-fed) of captive bison. a Colors represent the seven bison used in the study. b Colors represent the 13 sections of the digestive tract. c Colors represent the three regions of the digestive tract. D) Colors represent the two bison populations sampled, each with a different diet

Fig. 3

Heat map showing bacterial families with a mean relative abundance of at least 3% across all samples, paired with hierarchical cluster analysis of Bray-Curtis similarity among digestive tract sections in forage-finished (Population A) and grain-finished (Population B) bison. These families represent 27–77% of the microbial community in each gut section

Fig. 4

Results of SIMPER analysis, showing average percent dissimilarity among the 13 sections of the digestive tract. Brighter tones of red represent higher levels of dissimilarity, while brighter tones of blue represent lower levels of dissimilarity

Fig. 5

Stacked area plots showing the eight most abundant genera on average in each of the 13 sections of the digestive tract. a Bison from Population A, which were grass-finished. b Bison from Population B, which were grain-finished. Eso = Esophagus, Ret = Reticulum, Rum = Rumen, Oma = Omasum, Abo = Abomasum, Duo = Duodenum, Jej = Jejunum, Ile = Ileum, Cec = Cecum, Asc = Ascending colon, Tra = Transverse colon, Des = Descending colon, and Rec = Rectum