Journal Article

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

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Luke / Uudet liiketoimintamahdollisuudet / Kiertotalouden ratkaisut / Energiaratkaisut, Tapio, Miika, Fischer, Daniel, Rowett Institute of Nutrition and Health, University of Aberdeen, 4100200213, Shingfield, Kevin J, Tapio, Ilma, Luke / Vihreä teknologia / Kotieläinteknologia / Maidontuotantoratkaisut, Vilkki, Johanna, 4100200515, Luke / Vihreä teknologia / Geneettinen tutkimus / Biometrinen genetiikka, Luke / Vihreä teknologia / Geneettinen tutkimus / Eläingenomiikka, 4100200214, Kahala, Minna, Wallace, R. John, 4100300412, Bayat, Ali R, Blasco, Lucia, Ventto, Laura, Negussie, Enyew

2017

Overview

The ruminal microbiome, comprising large numbers of bacteria, ciliate protozoa, archaea and fungi, responds to diet and dietary additives in a complex way. The aim of this study was to investigate the benefits of increasing the depth of the community analysis in describing and explaining responses to dietary changes. Quantitative PCR, ssu rRNA amplicon based taxa composition, diversity and co-occurrence network analyses were applied to ruminal digesta samples obtained from four multiparous Nordic Red dairy cows fitted with rumen cannulae. The cows received diets with forage:concentrate ratio either 35:65 (diet H) or 65:35 (L), supplemented or not with sunflower oil (SO) (0 or 50 g/kg diet dry matter), supplied in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and four 35-day periods. Digesta samples were collected on days 22 and 24 and combined. QPCR provided a broad picture in which a large fall in the abundance of fungi was seen with SO in the H but not the L diet. Amplicon sequencing showed higher community diversity indices in L as compared to H diets and revealed diet specific taxa abundance changes, highlighting large differences in protozoal and fungal composition. Methanobrevibacter ruminantium and Mbb. gottschalkii dominated archaeal communities, and their abundance correlated negatively with each other. Co-occurrence network analysis provided evidence that no microbial domain played a more central role in network formation, that some minor-abundance taxa were at nodes of highest centrality, and that microbial interactions were diet specific. Networks added new dimensions to our understanding of the diet effect on rumen microbial community interactions.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Abundance / Additives / Animal feeding behavior / Animal lactation / Animal Nutritional Physiological Phenomena / Animals / Archaea / Archaea - classification / Archaea - genetics / Archaea - isolation & purification / Bacteria / Bacteria - classification / Bacteria - genetics / Bacteria - isolation & purification / Biodiversity / Biology and Life Sciences / Cannulae / Cattle / Ciliophora - classification / Ciliophora - genetics / Ciliophora - isolation & purification / Clean technology / Communities / Composition / Computer and Information Sciences / Concentration (composition) / Dairy cattle / Deoxyribonucleic acid / Diet / Diet - veterinary / Diversity indices / DNA / Dry matter / Drying oils / Fatty acids / Female / Forage / Fungi / Fungi - classification / Fungi - genetics / Fungi - isolation & purification / Genes, rRNA / Latin square design / Medicine and Health Sciences / Microbiota / Microbiota (Symbiotic organisms) / Microorganisms / Natural resources / Network analysis / Network formation / Nodes / Oils & fats / Polymerase chain reaction / Protozoa / rRNA / Rumen / Rumen - microbiology / Sequence Analysis, DNA - methods / Studies / Sunflower oil / Taxa / Vegetable oils