U.S. Department of Agriculture: Agricultural Research Service, Lincoln, Nebraska


Document Type


Date of this Version



Agric. Environ. Lett. 2:170016 (2017)


Copyright © American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.

Open access



Biological processes within beef cattle gastrointestinal tracts (GIT) influence animal health, and the output (feces) is an important vector for zoonotic pathogens and antibiotic resistant bacteria. Historically, outside of the rumen, little attention was paid to the bacteria along the GIT, despite their essential role in catabolizing feed into feces. Here we characterize bacteria from 15 GIT sites within a beef steer and examine the proportion of bacteria contributed by upstream compartments. This animal displayed characteristic differences between tissue and digesta communities in gastric and large-intestine, but not small-intestine, samples. The GIT sites shared between 50 and 80% of the operational taxonomic units (OTUs) with their neighboring upstream compartment, with the exception of the ileum. The ileum shared only 11% with the jejunum but displayed a similar phylum-level taxonomic distribution with the jejunum. It is unclear whether the observed changes between compartments represent a nonrandom decrease in bacterial number or rapid multiplication of certain taxa.