Submitted to: BMC Microbiology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/15/2008
Publication Date: 7/24/2008
Citation: Dowd, S.E., Callaway, T.R., Sun, Y., McKeehan, T., Edrington, T.S. 2008. Evaluation of the bacterial diversity in the feces of cattle using bacerial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiology. 8:article 125. Interpretive Summary: The bacteria populations in the gut of animals are diverse and vital to the health and well-being of the animal. Alterations in management practices such as diet can positively or negatively affect the gut bacterial flora, thereby promoting dramatic effects in the productivity of the animal. USDA-ARS scientists in Lubbock, TX, have developed a novel genetic approach using next generation genetic sequencing to enable high-throughput evaluation of bacterial diversity in the animal. The gastrointestinal microbiota from cattle were evaluated using this novel method. Using this new method, we have identified the major populations that are common among the cattle. Several of the cattle were shown to be infected with Salmonella spp. and Campylobacter spp. This indicates a powerful potential of this technology in food safety, epidemiological applications, and other bacterial diversity applications. Using bTEFAP, we can expect to gain a much better understanding of how the microbiome of the animal contributes to their health and well-being.
Technical Abstract: Background: The microbiota of an animal's intestinal tract plays important roles in the animal's overall health, productivity, and well-being. There is currently a surprising scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for the scarcity of data on livestock gastrointestinal microbiomes relates to high costs of labor and those methods needed to generate such data. Here we have utilized a bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) approach that is able to perform deep diversity analyses of gastrointestinal populations. bTEFAP is relatively inexpensive in terms of both time and labor due to the implementation of a novel tag priming method and an efficient bioinformatics pipeline. We have evaluated the microbiome from the feces of 20 commercial lactating dairy cows. Results: Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were isolated from several of the cattle. A total of 4 cows were found to be positive for Salmonella spp (tentative enterica) and 6 cows were positive for Campylobacter spp. (tentative lanienae). Conclusions: Using bTEFAP, we have examined normal microbiota of cattle using modern molecular methods to understand the ecology of the lower intestinal tract which will confer a better understanding of how the intestinal microbiome contributes to animal health and well-being.