The inclusion of feed additives and the implementation of various nutritional strategies are studied to modify the rumen microbiome and consequently its function. Nevertheless, rumen enzymatic activity and its intermediate products are not always matched with the microbiome structure. To further elucidate such differences a two-phase trial using twenty-two dairy goats was carried out. During the first phase, both groups (20HF n = 11; high forage and 20HG n = 11; high grain) were supplemented with 20 g Schizochytrium spp./goat/day. The 20HF group consumed a diet with a forage:concentrate (F:C) ratio of 60:40 and the 20HG-diet consisted of a F:C = 40:60. In the second phase, the supplementation level of Schizochytrium spp. was increased to 40 g/day/goat while the F:C ratio between the two groups were remained identical (40HF n = 11; high forage and 40HG n = 11; high grain). By utilizing a next-generation sequencing technology, we monitored that the high microalgae inclusion level and foremost in combination with a high grains diet increased the unmapped bacteria within the rumen. Bacteroidetes and Prevotella brevis were increased in the 40HG -fed goats as observed by using a qPCR platform. Additionally, methanogens and Methanomassiliicoccales were increased in high microalgae-fed goats, while Methanobrevibacter and Methanobacteriales were decreased. Fibrolytic bacteria were decreased in high microalgae-fed goats, while cellulolytic activity was increased. Ammonia was decreased in high grains-fed goats, while docosapentaenoic and docosahexaenoic acids showed a lower degradation rate in the rumen of high forage-fed goats. The alteration of the F:C ratio in goats supplemented with Schizochytrium spp. levels modified both ruminal microbiota and enzymatic activity. However, there was no significant consistency in the relations between them.
Keywords: 16s rRNA; amylase; cellulase; goat; ion-torrent; microalgae; microbiome; qPCR; rumen.