Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

TLDR

The intestinal microbiota is crucial for animal health, productivity, and well‑being, yet livestock gut diversity remains poorly characterized due to costly methods. The study applies bTEFAP to analyze cattle fecal microbiota, aiming to enhance understanding of how gut bacteria affect animal health, productivity, and wellbeing. bTEFAP uses a novel tag‑priming strategy and streamlined bioinformatics to provide rapid, cost‑effective sequencing of fecal bacterial communities. Sequencing of 20 dairy cows revealed a diverse fecal microbiome dominated by Clostridium, Bacteroides, Porphyromonas, Ruminococcus, and others, with Salmonella detected in 4 cows and Campylobacter in 6, indicating the presence of foodborne pathogens.

Abstract

The microbiota of an animal's intestinal tract plays important roles in the animal's overall health, productivity and well-being. There is still a scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for this lack of data relates to the expense of methods needed to generate such data. Here we have utilized a bacterial tag-encoded FLX 16s rDNA amplicon pyrosequencing (bTEFAP) approach that is able to perform 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.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 detected in 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).Using bTEFAP we have examined the microbiota in the feces of cattle. As these methods continue to mature we will better understand the ecology of the major populations of bacteria the lower intestinal tract. This in turn will allow for a better understanding of ways in which the intestinal microbiome contributes to animal health, productivity and wellbeing.