Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations

Abstract

The fecal microbiome of cattle plays a critical role not only in animal health and productivity but also in food safety, pathogen shedding, and the performance of fecal pollution detection methods. Unfortunately, most published molecular surveys fail to provide adequate detail about variability in the community structures of fecal bacteria within and across cattle populations. Using massively parallel pyrosequencing of a hypervariable region of the rRNA coding region, we profiled the fecal microbial communities of cattle from six different feeding operations where cattle were subjected to consistent management practices for a minimum of 90 days. We obtained a total of 633,877 high-quality sequences from the fecal samples of 30 adult beef cattle (5 individuals per operation). Sequence-based clustering and taxonomic analyses indicate less variability within a population than between populations. Overall, bacterial community composition correlated significantly with fecal starch concentrations, largely reflected in changes in the Bacteroidetes, Proteobacteria, and Firmicutes populations. In addition, network analysis demonstrated that annotated sequences clustered by management practice and fecal starch concentration, suggesting that the structures of bovine fecal bacterial communities can be dramatically different in different animal feeding operations, even at the phylum and family taxonomic levels, and that the feeding operation is a more important determinant of the cattle microbiome than is the geographic location of the feedlot.The enteric microbiota of cattle affects animal health and food safety and is used as an indicator of fecal pollution, which can affect the types and concentrations of indicator organisms in recreational surface waters. The presence of pathogenic bacteria such as Escherichia coli O157:H7 in the bovine gastrointestinal tract has been linked to disease outbreaks due to the consumption of contaminated beef, milk, and drinking water (3). The average feedlot steer produces 1.62 kg of feces (dry matter) per day (2), resulting in more than 18 million metric tons of feces (dry matter) per year in the United States alone. When bovine fecal waste is moved from feedlot operations for land application as fertilizer or is accidentally discharged into the environment due to severe storms, hazardous events, or failure of onsite waste management practices, pathogenic members of this microbial community, such as E. coli O157:H7, Campylobacter jejuni, Salmonella spp., Leptospira interrogans, and Cryptosporidium parvum (5,14,22,41,44), can pose a serious public health risk.Because of the enormous influence the fecal bacterial community of cattle has on the beef and dairy industry, the economy, and public health, a great deal of research has been conducted to characterize the effects of animal age, disease state, feeding practices, and antibiotic treatments on cattle fecal microorganisms. Many of the most comprehensive studies use DNA-based methodologies, such as sequencing of the full-length 16S rRNA gen...

Rumen microbial (meta)genomics and its application to ruminant production

“…The community structure in the lower gastrointestinal tract is, as expected, different from that of the rumen (Callaway et al, 2010) but also greatly influenced by diet (Callaway et al, 2010;Durso et al, 2010;Shanks et al, 2011). The complexity of the feed seems to favour diversity.…”

“…The complexity of the feed seems to favour diversity. Rumen communities associated with bermudagrass diets, rich in structural carbohydrates and secondary compounds, were more diverse than those associated with growing wheat forage (Pitta et al, 2010), and the presence of highly degradable carbohydrates in the diet such as starch decreased bacterial diversity in faeces (Shanks et al, 2011). As in other mammalian gastrointestinal microbiomes (Ley et al, 2008b), the predominant phyla are the Bacteroidetes and the Firmicutes (Brulc et al, 2009;Callaway et al, 2010;Durso et al, 2010).…”

“…Deep sequencing produces useful and extensive coverage of the microbial diversity, allowing us to identify the prevalent 'core' members of the community but also 'rare' community members that could be associated with feeding practices (Shanks et al, 2011). The rare members are otherwise not detectable using less sensitive techniques (Pedros-Alio, 2006).…”

Next Generation Sequencing and Microbial Community Associated With Eukaryotes Including Parasitic Heliminths: A Review Article.

“…It is wellestablished that the microbial community structure and composition is affected by diet [54]. The feeding operation is a more essential determinant of the bovine microbiome than is the geographic location of the feedlot [55]. Probiotics/prebiotics have the ability to modulate the balance and activities of the GI microbial ecosystem in ruminants [56].…”

Development of Single-Nucleotide Polymorphism-Based Phylum-Specific PCR Amplification Technique: Application to the Community Analysis Using Ciliates as a Reference Organism

“…Recently, high-throughput sequencing methods such as pyrosequencing have been combined with a molecular survey to assess the entire spectrum of eukaryotes belonging to communities in environmental samples from various habitats (Blackwood et al, 2005;Nolte et al, 2010;Scheckenbach et al, 2010;Shanks et al, 2011). Conventional approaches use universal primers specific for an SSU rRNA gene targeting all organisms in an environmental sample.…”