Data from: Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows

The effects of sunflower oil (SO) (0 or 50 g/kg diet dry matter),
supplemented to diets contrasting in the proportion of forage and
concentrate (FC) (65:35 vs 35:65), were evaluated for their influence on
rumen microbiome. Four multiparous Nordic Red dairy cows fitted with rumen
cannulae were used in a 4 × 4 Latin square with a 2 × 2 factorial
arrangement of treatments and four 35-d periods. Ruminal digesta samples
were collected on d 22 and d 24 of each experimental period and DNA was
extracted from a combined sample. Diet effect on rumen microbial community
was explored by qPCR, T-RFLP and metabarcoding sequencing. QPCR analysis
showed that the total amounts of bacteria, archaea or ciliate protozoa
were not significantly altered either by FC ratio or addition of SO. Only
fungi were reduced by half in high concentrate (H) compared to high forage
(L) diets (P=0.03). Further significant reduction of fungi was observed
due to SO in both HSO and LSO diets but the effect was stronger in HSO (H
vs HSO by 10.5x, P=0.03; L vs LSO by 1.9x, P=0.04). Metabarcoding
sequencing analysis showed that SO affected bacterial, archaeal, ciliate
protozoa and fungal community structure and diversity and the effect was
FC ratio dependent. As expected, Simpson’s index of diversity was higher
in diets containing higher proportion of forage. These diets were
dominated by Firmicutes, while Bacteroidetes and Proteobacteria were more
abundant in H diets. Methanobrevibacter ruminantium and Methanobrevibacter
gottschalkii dominated archaea community but they were in negative
relation to each other. Methanobrevibacter gottschalkii was more abundant
in L, while Methanobrevibacter ruminantium in H diet. The strongest diet
effect was observed on fungal community, represented by both well
classified and novel fungal groups. Both, increase in concentrate and
supplementation of SO significantly reduced fungal diversity. We explored
microbial interactions by building taxa co-occurrence networks. Our
results suggest that studying entire rumen microbiome simultaneously is
needed aiming to better understand how diet induced changes within
microbial community are associated with microbial function, subsequently
leading to better understanding of rumen fermentation and methanogenesis.