ive abundance, representing 10.9% and 7.9% in the abomasal microbial communities of both groups, respectively. There were 10 
genera with their relative abundance $1.0% in the microbiota of control animals. Thirty two genera were shared by all samples tested, possibly representing the core microbiome of the bovine abomasal community. Infection in immune cattle seemingly had only a minor impact on genus-level abomasal microbiota composition. Five genera with a low level of abundance were marginally impacted by infection. These genera included Ethanoligenens and Subdoligranulum, two of 32 genera consisting of the core microbiota. Approximately 91.6%62.4% input 16S rDNA sequences can be positively assigned by the RDP Classifier to any phylum at a confidence threshold of 80%. However, under the same threshold, only approximately 38.9% of 16S sequences can be assigned to a genus. Up to 61.1% of the 16S rDNA sequences cannot be positively assigned to any genus and remained unknown, suggesting that a substantial portion of the abomasal microbial diversity remained unexplored. Species-level microbial composition in the bovine abomasal microbiota was analyzed using CD-HIT-OTU. A total of 90.362.9 OTU were identified in each abomasal microbial community. Seventy two OTU were present in the abomasal microbial communities of all 6 immune animals and likely represented the core microbiome of the abomasal microbial community. The community was dominated by 4 OTU, 3 September 2011 | Volume 6 | Issue 9 | e24417 The Bovine Abomasal Microbiota Richness indices ACE and Chao1 as well as Shannon-Weaver index were calculated at family-, genus-, and species -levels in control and infected animals, respectively. These indices were not significantly different between two groups, suggesting that infection and ensuing abomasal pH elevation did not induce any which accounted for approximately 50% of all 16S rDNA sequences in control animals. Among them, 2 OTU were annotated to the genus Prevotella while the rest 2 OTU belonged to Bacteroidales and Succinivibrio. Ostertagi “2987739 ostertagi infection significantly impacted only 2 OTU in immune animals. The relative abundance of OTU#32 was increased from 0.4% in control to 1.0% in infected animals while the relative abundance of OTU#25 decreased from 0.3% in control to 0.1% in infected animals. Hierarchical clustering failed to group immune animals together in terms of their infection status based on relative abundances of the microorganisms making up the microbial community. Principal Coordinate Analysis provided further evidence that the separation between control and infected animals in their abomasal microbial composition derived from 16S rDNA sequences was not distinct. September 2011 | Volume 6 | Issue 9 | e24417 The Bovine Abomasal Microbiota notable change in biodiversity in the abomasal microbiota of immune cattle. Functional MX 69 changes in the abomasal microbiota induced by infection Functional and metabolic potentials of the bovine abomasal microbiota and possible alteration by parasitic infection were evaluated using WGS sequence reads. A total of 3,381 COG protein families were collectively identified in the bovine abomasal microbiota. The most abundant COG families in the microbiota of control animals included signal transduction histidine kinase, ABC-type multidrug transport system, “2987731 Na+-driven multidrug pump, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog, and b-galactosidase/b-glucuronidas