Identification of bacterial genetic diversity in the rumen of goat using 16S rRNA sequencing

Genetic diversity of rumen bacterial population in goats was identified using a modern molecular culture independent method. It is probable that structure of bacterial colonies of goats show special characters and some differences, in comparison to the other ruminants because of their distinct diet and habitat. So that obtaining enough knowledge about bacterial diversity in various breeds of goats and their variations in response to diverse diets and also determination of bacterial diversity in various environments is essential. Therefore a mixture sample of whole rumen content of 12 native goats from the north of Iran was collected. PCR amplification was done by universal primers of bacteria and 16S rRNA gene clone library was sequenced. Samples were collected from herds that fed by a mixture of forage and concentrate. Totally fifteen sequences of 16S rRNA were analyzed. From these 15 sequences, 4 sequences showed similarity (94%) to Streptococcus bovis and 3 sequences were similar (90%) to Selenomonas ruminantium. Also 2 sequences were similar (89%) to Megasphera elsdenii and two others resembled (96%) to Prevotella ruminicola. Two sequences had similarity (89%) to uncultured bacteria from the rumen of cow. One sequence from these 15 sequences showed similarity (90%) to Lactobacillus plantarum and one last sequence was similar (92%) to Prevotella multiformis. This study is the first identification of rumen bacterial population diversity from the goats in Iran. The results of this study showed that bacterial population diversity in the rumen of goats is similar to other ruminants in other parts of the world. Although we isolated some sequences which are not clustered to common bacteria in digestive tract. It may as results of individual differences during sample collection, types of rations, methods of DNA extraction or used primers.