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.

Bacteria fasta files: File containing demultiplexed bacteria 16S rRNA gene (107f-530r) fasta files for individual animals. Barcodes, forward and reverse primer sequences are trimmed. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.
bacteria.tar.gz

Archaea fasta files: File containing demultiplexed archaea 16S rRNA gene (V9) fasta files for individual animals. Barcodes, forward and reverse primer sequences are trimmed. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.
archaea.tar.gz

Ciliate protozoa fasta files: File containing demultiplexed ciliate protozoa 18S rRNA gene (316f-539r) fasta files for individual animals. Barcodes, forward and reverse primer sequences are trimmed. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.
ciliate.tar.gz

Fungi fasta files: File containing demultiplexed anaerobic fungi ITS1 region fasta files for individual animals. Barcodes, forward and reverse primer sequences are trimmed. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.
fungi.tar.gz

Sequence metadata

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