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

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.

Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants

“…The common rumen bacteria Prevotella ruminicola, P. brevis, P. bryantii and P. albensis tended to be more abundant in high-concentrate diets, and Fibrobacter abundance was higher in forage-fed cattle (Henderson et al, 2015). In addition, higher microbial diversity is also observed in forage diets as compared to highconcentrate diets (Tapio et al, 2017), a finding that likely reflects the greater complexity of carbohydrates and possibly functional conditions (i.e., pH, rate of passage, osmolality) in ruminants fed forage-based diets.…”

“…Recent metatranscriptomic analysis of the rumen contents of cattle fed a 50:50 forage:concentrate TMR supports the pivotal role of these well-characterized fibrolytic bacteria (Prevotella, Ruminoccocus and Fibrobacter) in fibre degradation (Comtet-Marre et al, 2017). Several studies have also found low levels of these well-known cellulolytic bacteria in cattle fed a high-forage diet (Creevey et al, 2014;Tapio et al, 2017). Interestingly, Tapio et al (2017) observed that increased forage content resulted in an increase the abundance of many uncharacterized bacteria within the Clostridiaceae and Lachnospiraceae families.…”

“…Several studies have also found low levels of these well-known cellulolytic bacteria in cattle fed a high-forage diet (Creevey et al, 2014;Tapio et al, 2017). Interestingly, Tapio et al (2017) observed that increased forage content resulted in an increase the abundance of many uncharacterized bacteria within the Clostridiaceae and Lachnospiraceae families. Similar results were also observed by Henderson et al (2015) and Noel et al (2017), which suggests that there are largely undescribed bacteria in the rumen that may have an important role in fibre degradation.…”

“…The anaerobic fungi play a key role in the initial colonization and degradation of the plant cell wall through the concerted action of carbohydrate-active enzymes and physical penetration of the plant cell wall by hyphae (Edwards et al, 2007). There are currently 11 cultured anaerobic fungi; however, metagenomic studies targeting the Internal transcribed spacer 1 (ITS-1) amplicon have revealed much greater taxonomic diversity in the rumen fungi with at least seven more phylogenetically distinct clades that are not represented by cultured isolates (Liggenstoffer et al, 2010;Koetschan et al, 2014;Tapio et al, 2017). Rumen fungi are associated with forage-based diets, and their abundance decreases rapidly upon the addition of concentrate to the diet (Belanche et al, 2012).…”

Bio-Hydrogen Production From Buffalo Waste With Rumen Inoculum and Metagenomic Characterization of Bacterial and Archaeal Community

“…Metagenomic studies have explored a number of environments, including cow rumen (Li et al, 2017;Tapio et al, 2017), human intestinal tract (Qin et al, 2010) and oral cavity (Dewhirst et al, 2010), marine (Venter et al, 2004), freshwater (Roux et al, 2012), soil (De Angelis et al, 2010), and air . The sequencing of 16S rRNA gene is the most efficient approach to assess the phylogeny and diversity of a community, especially if the studied environment contains a large fraction of uncharacterized microorganisms.…”