Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle

Abstract

The intestinal microbiota of beef cattle are important for animal health, food safety, and methane emissions. This full-length sequencing survey of 11,171 16S rRNA genes reveals animal-to-animal variation in communities that cannot be attributed to breed, gender, diet, age, or weather. Beef communities differ from those of dairy. Core bovine taxa are identified.The gastrointestinal tracts (GIT) of beef cattle are colonized by microorganisms that profoundly impact animal physiology, nutrition, health, and productivity (5). The GIT microbiota potentially impact food safety via pathogen shedding (13) by interacting with organisms such as Salmonella and competing for resources in the GIT. Cattle intestinal microbiota also play an important role in methane emissions, with U.S. beef cattle alone contributing an estimated 3.87 million metric tons of methane into the environment each year, both from rumen and large-intestine fermentations (7). Although the bovine fecal microbiota have been well characterized using culture-based methods, these techniques are necessarily limited to characterizing bacteria that can be grown in the laboratory. Cultureindependent methods can reveal community members that are recalcitrant to culture. Only a handful of deep-sequencing studies have been done using culture-independent 16S rRNAbased methods (1,11,12,14), all with dairy cattle, which have a fundamentally different diet and metabolism from beef cattle. Despite the potential contributions of the beef cattle GIT microbiota to animal health, food safety, and global warming, these communities remain poorly characterized. With the advent of pyrosequencing technology, researchers now have the tools to characterize these important communities. Pyrosequencing will allow rapid characterization of large-sample data sets (1). However, the taxonomic information generated by rapid sequencing is approximate by necessity (9), and fulllength 16S-rRNA sequencing remains the "gold standard" method. Accordingly, we have characterized fecal bacteria from six feedlot cattle by full-length capillary sequence analysis of 11,171 16S rRNA gene clones (Fig.

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.…”

“…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). The microbial diversity in the gastrointestinal tract of ruminants is estimated to be higher than that of humans (Eckburg et al, 2005;Brulc et al, 2009;Durso et al, 2010), with a few predominant genera (20 to 25), representing up to 90% of the total number of sequences (Callaway et al, 2010;Durso et al, 2010). Depending on the anatomical site, rumen or caecum, and probably also on the technical approach, the relative proportion of genera may change.…”

“…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). The microbial diversity in the gastrointestinal tract of ruminants is estimated to be higher than that of humans (Eckburg et al, 2005;Brulc et al, 2009;Durso et al, 2010), with a few predominant genera (20 to 25), representing up to 90% of the total number of sequences (Callaway et al, 2010;Durso et al, 2010).…”

“…The number of clones analysed per study increased exponentially with the refinement and decreasing cost of the Sanger DNA sequencing technique, for example, from 133 sequences examined by Whitford et al (1998) in one of the first studies using clone libraries in the rumen to 11 171 produced by Durso et al (2010) from cattle faecal samples. However, the production of data has been revolutionised by the availability of second-generation sequencing techniques, particularly pyrosequencing.…”

Analysis of the bacterial diversity in the fecal material of the endangered Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis

“…Many cultivation independent studies have been conducted on human fecal material [14][15][16]. The bacterial diversity in the fecal material of other animals, such as polar bears (Ursus maritimus) [17], wolves (Canis lupus) [18], gorillas (Gorilla beringei) [19], rats [20] and cows [21], has been described. The bacterial diversity in ruminants, such as the Yah (Bos grunniens) [22], the Gayal (Bos frontalis) [23,24], and the Swamp buffalo (Bubalus bubalis) [24] has also been investigated.…”