Predicting residual feed intake status using rumen microbial profiles in ewe lambs1

Predicting feed efficiency traits in growing lambs from their ruminal microbiota

Selecting feed-efficient sheep could improve the sustainability of this livestock production. However, most sheep breeding companies cannot afford to record feed intake to select feed-efficient animals. Past studies underlined the potential of omics data, including microbiota metabarcoding data, as proxies for feed efficiency. The study involved 277 Romane lambs from two lines divergently selected for residual feed intake (RFI). There were two objectives: check the consequences of selecting for feed efficiency over the rumen microbiota, and assess the predictive ability of the rumen microbiota for host traits. The study assessed two contrasting diets (concentrate diet and mixed diet) and two microbial groups (prokaryotes and eukaryotes). Discriminant analyses did not highlight any significant effect of sheep selection for residual feed intake on the rumen microbiota composition. Indeed, prokaryotic and eukaryotic microbiota compositions poorly discriminated the RFI lines, with averaged balanced error rates ranging from 45% to 55%. Correlations between host traits (feed efficiency and production traits) and their predictions from microbiota data varied between -0.07 and 0.56, depending on the trait, diet and sequencing. Feed intake was the most accurately predicted trait. However, predictions from fixed effects and BW were more accurate than or as accurate as predictions from the microbiota. Environmental effects can greatly affect the variability of microbiota compositions. Considering batch and environmental effects should be paramount when the predictive ability of the microbiota is assessed. This study argues why metabarcoding the rumen microbiota is not the best way to predict meat sheep production traits: fixed effects and BW were more cost-effective proxies and they led to similar or better predictive accuracies than microbiota metabarcoding (16S and 18S sequencing).

Histological and physical-mechanical characteristics of the skin of Dorper sheep related to residual feed intake and the confinement environment

The aim was to evaluate the effect of residual feed intake (RFI) on the histological, physical and mechanical characteristics of the sheep skin confined in full sun or shade. Dorper sheep (n = 64), male, with an initial bodyweight of 17.8 ± 2.43 kg was confined for 40 days to determine the RFI. After classification, 30 animals with positive RFI and 30 animals with negative RFI were selected, which were distributed in 2 confinement environments. This was a factorial arrangement of 2 (groups of animals-positive RFI and negative RFI) × 2 (environments-full sun and shade), with 15 animals for each combination of factors. The sheep remained in confinement for 60 days. After slaughter, skins were divided in half, and fragments were collected from the right portion for histological sections. The left part of each skin was subjected to tanning. Interaction effect RFI × environment was found in the evaluation of leather fragments in the horizontal direction on elongation at break, leather thickness and tear strength (p < 0.05). An isolated effect of the environment was found on elongation at break of leather fragments in the evaluation on the vertical direction (p = 0.01) and on the number of secondary follicles during the histological evaluation of the dorsal and lateral regions of the skin (p < 0.05). An effect of the interaction RFI × environment was observed for the thermostatic layer of the hip region (p = 0.03). Sheep with positive RFI and kept in confinement in full sun have a leather with greater elongation at break and tear strength, important aspects in determining the quality of the product by the leather industry.

Candidate serum metabolite biomarkers of residual feed intake and carcass merit in sheep

Mutton and lamb sales continue to grow globally at a rate of 5% per year. However, sheep farming struggles with low profit margins due to high feed costs and modest carcass yields. Selecting those sheep expected to convert feed efficiently and have high carcass merit, as early as possible in their life cycle, could significantly improve the profitability of sheep farming. Unfortunately, direct measurement of feed conversion efficiency (via residual feed intake [RFI]) and carcass merit is a labor-intensive and expensive procedure. Thus, indirect, marker-assisted evaluation of these traits has been explored as a means of reducing the cost of its direct measurement. One promising and potentially inexpensive route to discover biomarkers of RFI and/or carcass merit is metabolomics. Using quantitative metabolomics, we profiled the blood serum metabolome (i.e., the sum of all measurable metabolites) associated with sheep RFI and carcass merit and identified candidate biomarkers of these traits. The study included 165 crossbred ram-lambs that underwent direct measurement of feed consumption to determine their RFI classification (i.e., low vs. high) using the GrowSafe System over a period 40 d. Carcass merit was evaluated after slaughter using standardized methods. Prior to being sent to slaughter, one blood sample was drawn from each animal, and serum prepared and frozen at -80 °C to limit metabolite degradation. A subset of the serum samples was selected based on divergent RFI and carcass quality for further metabolomic analyses. The analyses were conducted using three analytical methods (nuclear magnetic resonance spectroscopy, liquid chromatography mass spectrometry, and inductively coupled mass spectrometry), which permitted the identification and quantification of 161 unique metabolites. Biomarker analyses identified three significant (P < 0.05) candidate biomarkers of sheep RFI (AUC = 0.80), seven candidate biomarkers of carcass yield grade (AUC = 0.77), and one candidate biomarker of carcass muscle-to-bone ratio (AUC = 0.74). The identified biomarkers appear to have roles in regulating energy metabolism and protein synthesis. These results suggest that serum metabolites could be used to categorize and predict sheep for their RFI and carcass merit. Further validation using a larger (3×) and more diverse cohort of sheep is required to confirm these findings.

Associations of feed efficiency with circulating IGF-1 and leptin, carcass traits and meat quality of lambs

The aim of this study was to investigate the effects of feed efficiency classifications on live animal measurements, circulating IGF-1 and leptin concentrations, and carcass, non-carcass and meat quality traits of lambs. One-hundred and two lambs approximately 70 days-old with initial live weight of 24.6 ± 3.71 kg (mean ± SD) were individually fed for 56 days to determine residual feed intake (RFI) and residual feed intake and gain (RIG). Lambs were then classified as phenotypically Low-, Medium- or High-RFI and Low-, Medium- or High-RIG phenotypes. Circulating leptin and IGF-1 concentrations were higher in more efficient lambs (Low-RFI or High-RIG). Variation in RFI and RIG did not affect meat redness or tenderness, but High-RIG lambs had darker meat. These findings show that the phenotypically more efficient Low-RFI and High-RIG lambs produced carcasses with similar characteristics and meat quality as the less efficient High-RFI and Low-RIG lambs but have a strategic advantage of lower feed intake to achieve similar production outcomes.

Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency

Rumen microbiome composition and functionality is linked to animal feed efficiency, particularly for bovine ruminants. To investigate this in sheep, we compared rumen bacterial and archaeal populations (and predicted metabolic processes) of sheep divergent for the feed efficiency trait feed conversion ratio (FCR). In our study 50 Texel cross Scottish Blackface (TXSB) ram lambs were selected from an original cohort of 200 lambs. From these, 26 were further selected for experimentation based on their extreme FCR (High Feed Efficiency, HFE = 13; Low Feed Efficiency, LFE = 13). Animals were fed a 95% concentrate diet ad libitum over 36 days. 16S rRNA amplicon sequencing was used to investigate the rumen bacterial and archaeal communities in the liquid and solid rumen fractions of sheep divergent for FCR. Weighted UniFrac distances separated HFE and LFE archaea communities from the liquid rumen fraction (Permanova, P < 0.05), with greater variation observed for the LFE cohort (Permdisp, P < 0.05). LFE animals exhibited greater Shannon and Simpson diversity indices, which was significant for the liquid rumen fraction (P < 0.05). Methanobrevibacter olleyae (in liquid and solid fractions) and Methanobrevibacter millerae (liquid fraction) were differentially abundant, and increased in the LFE cohort (P.adj < 0.05), while Methanobrevibacter wolinii (liquid fraction) was increased in the HFE cohort (P.adj < 0.05). This suggests that methanogenic archaea may be responsible for a potential loss of energy for the LFE cohort. Bacterial community composition (Permanova, P > 0.1) and diversity (P > 0.1) was not affected by the FCR phenotype. Only the genus Prevotella 1 was differentially abundant between HFE and LFE cohorts. Although no major compositional shifts of bacterial populations were identified amongst the feed efficient cohorts (FDR > 0.05), correlation analysis identified putative drivers of feed efficiency with Ruminococcaceae UCG-014 (liquid, rho = -0.53; solid, rho = -0.56) and Olsenella (solid, rho = -0.40) exhibiting significant negative association with FCR (P < 0.05). Bifidobacterium and Megasphaera showed significant positive correlations with ADG. Major cellulolytic bacteria Fibrobacter (liquid, rho = 0.43) and Ruminococcus 1 (liquid, rho = 0.41; solid, rho = 41) correlated positively with FCR (P < 0.05). Our study provides evidence that feed efficiency in sheep is likely influenced by compositional changes to the archaeal community, and abundance changes of specific bacteria, rather than major overall shifts within the rumen microbiome.