Analyzing the impact of an in vitro subacute rumen acidosis on the bacterial community and the recovery process applying amplicon Illumina MiSeq and PacBio sequencing. RUSITEC_2019

The impact of subacute rumen acidosis periods on the bacterial community has been frequently observed in in vivo trials. However, little is known about the bacterial recovery process from an acidosis challenge in a rumen simulation technique (RUSITEC) model. This present study observed the alterations during and after a subacute acidosis within the bacterial community using two next generation sequencing approaches. We combined the Illumina MiSeq sequencing approach of the 16S rRNA gene variable region V4 with the PacBio 16S rRNA gene full-length analysis in an in vitro RUSITEC experiment. With this hybrid approach, we gained an overview of the total bacterial diversity and received an increased taxonomic resolution of the most abundant bacterial groups. The experiment consisted of a first control period, an acidosis challenge, and ended after a second control period, of which each period lasted 5 days. The acidosis was induced by applying buffer solutions, which were reduced in their buffering capacity. Two control groups were constantly infused with the standard buffer solution. Furthermore, the two acidosis buffers were combined with three different feeding variations, which differed in their concentrate-to-hay ratio. Variations in the concentrate supply intended to reduce pH values. However, we were not able to observe a reduction of ruminal pH when a high concentrate ratio was supplied. The induction of acidosis led to a decreasing pH below pH 5.8, which then turned into a steady state acidosis. Accompanied with decreasing pH values, the bacterial diversity and richness were reduced. However, the diversity of high concentrate feeding groups in the solid fraction was lower throughout all experimental periods. During the whole experiment, Firmicutes and Bacteroidetes were the predominant phyla in the solid and the liquid fraction. During acidosis period, we observed a decrease in fibrolytic bacteria, while lactate producing and utilizing families increased in certain treatment groups. The families Prevotellaceae and Lactobacteriaceae dominated the solid fraction during acidosis period. With the induction of the regeneration period, most bacterial groups recovered and equaled the initial abundance. In conclusion, this study provides an in vitro model, which is capable of regeneration from acidotic bouts and therefore is able to mimic the rumen acidosis under laboratory conditions.