High Throughput Approaches to Evaluate Between-Animal Variation in Digestion of Cattle

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Student thesis: Doctoral ThesisDoctor of Philosophy

Original languageEnglish
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Award date2016
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Abstract

Existing techniques to explore between-animal variation in digestion processes and their potential contribution to feed efficiency (FE) are laborious, expensive or invasive. The aim of this thesis was to refine and apply rapid techniques to assess the chemical (near infrared reflectance spectroscopy; NIRS) and physical (laser diffraction; LD) attributes of faeces, and characterise the rumen microbiome (16S next generation sequencing) associated with between-animal variation in FE. Preliminary work developed methods for LD, NIRS and 16S analysis. Differences in microbial communities were found between liquid and solid phases of rumen digesta. Nominal stem and leaf fractions of fresh grasses were incubated in vitro to assess the time course of rumen digestion using NIRS. Spectral regions associated with protein, starch, glucose and cellulose were highly degradable whilst those associated with lipids and lignin were less degradable. Principal component analysis (i.e. without the use of calibrations) of faecal NIR spectra from a compensatory growth study showed differences in digestion processes between restricted and ad libitum fed bulls. However, these differences were not apparent during a subsequent period of compensatory growth (when feed was offered ad libitum), confirming that differences in FE (feed conversion ratio; FCR) were not related to effects on digestion processes. A further study assessed relationships between all three techniques and FE; steers were offered one of 4 dietary treatments designed to alter methane emissions. A 56 day FE measurement provided residual feed intake (RFI) and FCR values for each steer. There were significant effects of the dietary treatments on measurements made using each of the techniques, but no consistent relationships with FCR or RFI within each dietary treatment group. Whilst the techniques used in these studies provided rapid and low-cost characterisation of between-animal variation in digestion processes, these differences made little contribution to between-animal variation in feed efficiency.