Abstract
Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR). Metagenomic Rapid Annotation using Subsystem Technology (MG-RAST) taxonomical analysis of shotgun metagenomic sequences showed that the genera Butyrivibrio, Clostridium, Eubacterium, Prevotella, and Selenomonas dominated the attached microbiome irrespective of time. MG-RAST also showed that Acidaminococcus, Bacillus, Butyrivibrio, and Prevotella rDNA increased in read abundance during secondary colonization, whilst Blautia decreased in read abundance. MG-RAST Clusters of Orthologous Groups (COG) functional analysis also showed that the primary function of the attached microbiome was categorized broadly within “metabolism;” predominantly amino acid, carbohydrate, and lipid metabolism and transport. Most sequence read abundances (51.6, 43.8, and 50.0% of COG families pertaining to amino acid, carbohydrate and lipid metabolism, respectively) within these categories were higher in abundance during secondary colonization. Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis confirmed that the PRG-attached microbiota present at 1 and 4 h of rumen incubation possess a similar functional capacity, with only a few pathways being uniquely found in only one incubation time point only. FT-IR data for the plant residues also showed that the main changes in plant chemistry between primary and secondary colonization was due to increased carbohydrate, amino acid, and lipid metabolism. This study confirmed primary and secondary colonization events and supported the hypothesis that functional changes occurred as a consequence of taxonomical changes. Sequences within the carbohydrate metabolism COG families contained only 3.2% of cellulose activities, on average across both incubation times (1 and 4 h), suggesting that degradation of the plant cell walls may be a key rate-limiting factor in ensuring the bioavailability of intra-plant nutrients in a timely manner to the microbes and ultimately the animal. This suggests that a future focus for improving ruminant nutrient use efficiency should be altering the recalcitrant plant cell wall components and/or improving the cellulolytic capacity of the rumen microbiota.
Highlights
Due to a growing population and increased demand for livestock products by developing countries, current projections estimate that global demand for meat and milk will have doubled by 2050 compared to the start of the twenty-first century (Foresight, 2011)
Post incubation of perennial ryegrass (PRG) under rumen-like in vitro conditions, rumen bacteria attached quickly to the plant material, and bacterial 16S rDNA abundance increased rapidly and continued to rise for the duration of the experiment; by 4 h attached bacterial 16S rDNA concentration had increased by 1.9X, and by 24 h by 2.6X compared with 0 h concentrations (Table 1)
We demonstrate that colonization of PRG by rumen bacteria is biphasic with primary and secondary events observed based on changes seen in attached bacterial diversity
Summary
Due to a growing population and increased demand for livestock products by developing countries, current projections estimate that global demand for meat and milk will have doubled by 2050 compared to the start of the twenty-first century (Foresight, 2011). As little as 30% of the ingested nitrogen is utilized by ruminants for milk or meat production, and the non-incorporated nitrogen is excreted to the environment as urea or ammonia (MacRae and Ulyatt, 1974; Dewhurst et al, 1996; Kingston-Smith et al, 2008, 2010). The rumen, via it’s complex microbiome is responsible for the breakdown of plant material and the functional capacity of the microbiome defines the amount, quality, and composition of meat and milk produced, whilst defining the release of nitrogen and greenhouse gases to the environment (Edwards et al, 2008a; Kim et al, 2009; Kingston-Smith et al, 2010; Brown Kav et al, 2012; Huws et al, 2014a). The functionality of the primary and secondary colonizers in terms of plant degradation and availability of nutrients to the host remains unclear
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