The Planktonic Core Microbiome and Core Functions in the Cattle Rumen by Next Generation Sequencing

Abstract

The cow rumen harbors a great variety of diverse microbes, which form a complex, organized community. Understanding the behavior of this multifarious network is crucial in improving ruminant nutrient use efficiency. The aim of this study was to expand our knowledge by examining 10 Holstein dairy cow rumen fluid fraction whole metagenome and transcriptome datasets. DNA and mRNA sequence data, generated by Ion Torrent, was subjected to quality control and filtering before analysis for core elements. The taxonomic core microbiome consisted of 48 genera belonging to Bacteria (47) and Archaea (1). The genus Prevotella predominated the planktonic core community. Core functional groups were identified using co-occurrence analysis and resulted in 587 genes, from which 62 could be assigned to metabolic functions. Although this was a minimal functional core, it revealed key enzymes participating in various metabolic processes. A diverse and rich collection of enzymes involved in carbohydrate metabolism and other functions were identified. Transcripts coding for enzymes active in methanogenesis made up 1% of the core functions. The genera associated with the core enzyme functions were also identified. Linking genera to functions showed that the main metabolic pathways are primarily provided by Bacteria and several genera may serve as a “back-up” team for the central functions. The key actors in most essential metabolic routes belong to the genus Prevotella. Confirming earlier studies, the genus Methanobrevibacter carries out the overwhelming majority of rumen methanogenesis and therefore methane emission mitigation seems conceivable via targeting the hydrogenotrophic methanogenesis.

Microbial Patterns in Rumen Are Associated with Gain of Weight in Beef Cattle

“…These reports indicated a high dominance of Bacteroidetes species inhabiting the ruminal fluid within various environments and conditions, followed by a smaller, but consistent, presence of Firmicutes. Our results are aligned with those findings (Figure 2), as well as with findings about fungal samples which were not correlated to any dominant phyla in rumen neither in the literature nor in our work (Figure 3) [2,17,34,37].…”

“…Once we established groups of animals with highly contrasting weight gain (Figure 1), kept for more than two years in the same conditions (Tables 1 and 2), we showed the overall community of heifers was similar in diversity of phyla (Figure 2 and 3) and in richness of microbial taxa (Figure 4), irrespective of the weigh gain. Several studies postulated the rumen microbiome presents a stable community [2,15,17,[34][35][36]. These reports indicated a high dominance of Bacteroidetes species inhabiting the ruminal fluid within various environments and conditions, followed by a smaller, but consistent, presence of Firmicutes.…”

“…Bacteria, Archaea and micro Eukaryotes are present across the entire gastrointestinal tract (GIT) of these animals. They digest complex molecules, such as cellulose and lignin, and help the absorption of water and nutrients [1,2]. Microbes from the rumen, in particular, are crucial for this process, once the rumen acts as a fermentation chamber hosting microbial fermentation of the food ingested by the cattle.…”

Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts

“…Prevotella spp. are key metabolisers of peptides and carbohydrates [52][53][54][55]; thus, the expansion of this genus of bacteria hadbeen hypothesized to serve as a compensatory mechanism to counteract the protein loss caused by abomasal helminth infections [42]. Nevertheless, the significant increase of Prevotella observed in the faeces of parasitized animals, together with the simultaneous expansion of other bacterial taxa, e.g.…”

Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage

“…This information was corroborated by the binning study, which helped to associate specific functions to taxa. Although the presence of a certain gene and the number of reads linked to it does not necessary mean that the gene is being transcribed and translated, it is safe to assume at least a limited correlation between these parameters (Wirth et al, 2018). The main functional profiles investigated were the carbohydrate-active enzymes (CAZy), protein degradation, syntrophic acetate oxidation, i.e., formate-tetrahydrofolate ligase, hydrogen metabolism and methanogenesis (Figure 7) (Hattori, 2008;Caspi et al, 2014;Lombard et al, 2014;Rawlings et al, 2018).…”