DOI: 10.5061/dryad.t6t0q
title: Data from: Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows

description: 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.
description: Bacteria fasta
 filesFile 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.gzArchaea fasta filesFile 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.gzCiliate protozoa fasta filesFile 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.gzFungi fasta filesFile 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.gzSequence metadata