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

Ilma Tapio, Daniel Fischer, Lucia Blasco, Miika Tapio, R. John Wallace, Ali R. Bayat, Laura Ventto, Minna Kahala, Enyew Negussie, Kevin J. Shingfield, Johanna Vilkki

Research output: Contribution to journalArticle

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Abstract

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.

Original languageEnglish
Article numbere0180260
Pages (from-to)1-21
Number of pages21
JournalPloS ONE
Volume12
Issue number7
DOIs
Publication statusPublished - 13 Jul 2017

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Dairies
Microbiota
Nutrition
Electric network analysis
dairy cows
Diet
diet
Microbial Interactions
Rumen
digesta
sunflower oil
Fungi
rumen
Methanobrevibacter
Protozoa
microbiome
fungi
Archaea
Ruminants
cannulas

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows. / Tapio, Ilma; Fischer, Daniel; Blasco, Lucia; Tapio, Miika; Wallace, R. John; Bayat, Ali R.; Ventto, Laura; Kahala, Minna; Negussie, Enyew; Shingfield, Kevin J.; Vilkki, Johanna.

In: PloS ONE, Vol. 12, No. 7, e0180260, 13.07.2017, p. 1-21.

Research output: Contribution to journalArticle

Tapio, I, Fischer, D, Blasco, L, Tapio, M, Wallace, RJ, Bayat, AR, Ventto, L, Kahala, M, Negussie, E, Shingfield, KJ & Vilkki, J 2017, 'Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows', PloS ONE, vol. 12, no. 7, e0180260, pp. 1-21. https://doi.org/10.1371/journal.pone.0180260
Tapio, Ilma ; Fischer, Daniel ; Blasco, Lucia ; Tapio, Miika ; Wallace, R. John ; Bayat, Ali R. ; Ventto, Laura ; Kahala, Minna ; Negussie, Enyew ; Shingfield, Kevin J. ; Vilkki, Johanna. / Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows. In: PloS ONE. 2017 ; Vol. 12, No. 7. pp. 1-21.
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abstract = "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.",
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