Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer

Abstract

The gastrointestinal tracts (GIT) of herbivores harbor dense and diverse microbiota that has beneficial interactions with the host, particularly for agriculturally relevant animals like ruminants such as cattle. When assessing ruminant health, microbiological indicators are often derived from the rumen or feces. However, it is probable that ruminal and fecal microbiota do not reflect the microbial communities within the GIT of ruminants. To test this, we investigated the compartments of the GIT from a Brazilian Nelore steer and performed a 16S rRNA pyrosequencing analysis on the collected samples. Our results showed high intra-individual variation, with samples clustering according to their location in the GIT including the forestomach, small intestine, and large intestine. Although sequences related to the phyla Firmicutes and Bacteroidetes predominated all samples, there was a remarkable variation at the family level. Comparisons between the microbiota in the rumen, feces, and other GIT components showed distinct differences in microbial community. This work is the first intensive non-culture based GIT microbiota analysis for any ruminant and provides a framework for understanding how host microbiota impact the health of bovines.

Variability in microbial population and fermentation traits at various sites within the forestomach and along the digestive tract as assessed in goats fed either grass or browse

“…Copy numbers of fibrolytic bacteria decreased from the rumen to the hindgut to a much larger degree than total bacteria or were no longer detected in the hindgut at all, similar to findings from Koike and Kobayashi (2001). This implies that the three fibrolytic species were less abundant in the hindgut bacterial population than other gut bacteria, a phenomenon described before by de Oliveira et al (2013) for Fibrobacteres (in only one animal sampled). A likely explanation is that the fibre entering the hindgut does not promote the rumen fibrolytic bacteria, because it is much harder to degrade as all easily-degradable fibres have already been removed in the rumen and the time for degradation is shorter due to the difference in volume between rumen and hindgut (Gressley et al, 2011).…”

“…However, the actual fermentation intensity and the composition of the microbial population in the caecum, colon or faeces differ from those in the rumen content (Metzler-Zebeli et al, 2013;de Oliveira et al, 2013). It also depends on the substrate flow from the rumen, which is influenced by diet (Metzler-Zebeli et al, 2013).…”

“…It also depends on the substrate flow from the rumen, which is influenced by diet (Metzler-Zebeli et al, 2013). In studies where samples from different parts of the gastrointestinal tract have been collected, the animals were mostly fed on one diet only (Romero-Perez et al, 2011;de Oliveira et al, 2013) or concentrate-and forage-based diets were compared (Metzler-Zebeli et al, 2013). Studies investigating the differences in microbial population and fermentation traits in defined rumen compartments and along the lower part of the gastrointestinal tract (GIT) of ruminants comparing different forage types have not been performed so far.…”

Taxonomic Identification of Commensal Bacteria Associated with the Mucosa and Digesta throughout the Gastrointestinal Tracts of Preweaned Calves

“…In contrast to the adult beef steer, Bacteroidetes dominated the large intestines of preweaned calves. Despite the differences observed in the bacterial composition due to the host age, diet, and breed (15), both studies revealed a region-dependent bacterial community throughout the GIT of cattle. Moreover, de Oliveira and colleagues (15) reported more diverse rumen and large-intestinal bacterial communities than small-intestinal communities, and these communities clustered separately.…”

“…Analysis of the digesta-associated bacterial community along the GIT of a 2-year-old beef steer revealed a high prevalence of Bacteroidetes in the rumen and a high prevalence of Firmicutes in the small and large intestines (15). Similarly, Bacteroidetes dominated the rumen contents of preweaned calves, while Firmicutes dominated the small intestines.…”