Identification of a Novel Rumen Bacteria Using Starch As a Selective Nutrient in Batch Cultures

Venkata Bandarupalli and Benoit St-Pierre

 

The bovine rumen is a complex and diverse microbial ecosystem composed of bacteria, protozoa, fungi, and bacteriophages. Among these diverse and complex microbes, bacteria are the predominant community with a range of 10¹⁰-10¹³ cells per gram of ruminal contents that play a vital role in the fermentation process. However, the knowledge about the role of most bacteria in digestion of feedstuff is still in its infancy. The primary objective of this research was to identify uncharacterized bacteria that are involved in metabolizing starch. Our general approach involved collecting rumen fluid from cannulated cattle to culture under anaerobic conditions at a constant temperature in laboratory-scale bioreactors. More specifically, for this experiment, 3 treatment replicate cultures were supplemented with starch (ADM Corn processing Clinton, Iowa) as substrate and 2 replicate cultures received no supplementation. To determine bacterial composition, microbial DNA was extracted from bioreactor samples collected on day’s 0, 7, and 14, followed by PCR amplification of the 16S rRNA gene (V1-V3 region), and amplicons were sequenced using the illumina Miseq 2×300 platform. A combined total of 309,715 high quality sequence reads were used to determine the bacterial composition in control and treatment groups. The number of reads per sample ranged between 49,517 and 131,704. Our results showed that one species-level Operational Taxonomic Unit (OTU), corresponding to an uncultured species of Prevotella, was enriched on day 7 (15.6±3.22) and 14 (17.7±5.02) in treatment groups when compared to control cultures (0.17±0.08). Difference between starch and control were found to be statistically significant (ANOVA, p<0.05). A better understanding of the role of novel bacteria in feed digestion will provide new avenues for developing supplements or feed additives that support animal health and increase production efficiency of the livestock industry.