Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host

BACKGROUND

Producing animal protein while reducing the animal's impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible.

RESULTS

Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets.

CONCLUSIONS

Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual's future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.

Quantification of cytosol and membrane proteins in rumen epithelium of sheep with low or high CH4 emission phenotype

BACKGROUND

Ruminant livestock are a major contributor to Australian agricultural sector carbon emissions. Variation in methane (CH4) produced from enteric microbial fermentation of feed in the reticulo-rumen of sheep differs with different digestive functions.

METHOD

We isolated rumen epithelium enzymatically to extract membrane and cytosol proteins from sheep with high (H) and low (L) CH4 emission. Protein abundance was quantified using SWATH-mass spectrometry.

RESULTS

The research found differences related to the metabolism of glucose, lactate and processes of cell defence against microbes in sheep from each phenotype. Enzymes in the methylglyoxal pathway, a side path of glycolysis, resulting in D-lactate production, differed in abundance. In the H CH4 rumen epithelium the enzyme hydroxyacylglutathione hydrolase (HAGH) was 2.56 fold higher in abundance, whereas in the L CH4 epithelium lactate dehydrogenase D (LDHD) was 1.93 fold higher. Malic enzyme 1 which converts D-lactate to pyruvate via the tricarboxylic cycle was 1.57 fold higher in the L CH4 phenotype. Other proteins that are known to regulate cell defence against microbes had differential abundance in the epithelium of each phenotype.

CONCLUSION

Differences in the abundance of enzymes involved in the metabolism of glucose were associated with H and L CH4 phenotype sheep. Potentially this represents an opportunity to use protein markers in the rumen epithelium to select low CH4 emitting sheep.

Can we have our steak and eat it: The impact of breeding for lowered environmental impact on yield and meat quality in sheep

Global agreements in place to reduce methane emissions in livestock are a potential threat to food security. Successful but independent breeding strategies for improved production and lower methane are in place. The unanswered questions are whether these strategies can be combined and how they impact one another, physically and economically. The New Zealand economy is largely dependent on pastoral agriculture from grazing ruminants. The sheep industry produces ∼20 million lamb carcasses for export each year primarily from grass. Methane emitted from the fermentation of forage by grazing ruminants accounts for one-third of all New Zealand’s greenhouse gas emissions. Here, we use sheep selection lines bred for divergent methane production and large numbers of their relatives to determine the genetic and phenotypic correlations between enteric methane emissions, carcass yield, and meat quality. The primary objectives were to determine whether previously shown physiological differences between methane selection lines (differing by ∼12% in methane) result in a negative impact on meat production and quality by measuring close relatives. The results show no negative effects of breeding for lowered methane on meat and carcass quality. Gross methane emissions were highly correlated with liveweight and measures of carcass weight and negatively correlated with dressing-out percentage and fat yield (GR). Trends were similar but not significant for methane yield (g CH₄/kg DMI). Preliminary evidence, to date, shows that breeding for low methane may result in animals with higher lean yields that are economically favorable even before carbon costs and environmental benefits are taken into account. These benefits were seen in animals measured for methane on fixed intakes and require validation on intakes that are allowed to vary.

Genetic parameters for residual feed intake, methane emissions, and body composition in New Zealand maternal sheep

There is simultaneous interest in improving the feed efficiency of ruminant livestock and reducing methane (CH₄) emissions. The relationship (genetic and phenotypic) between feed efficiency (characterized as residual feed intake: RFI) and greenhouse gases [methane (CH₄) and carbon dioxide (CO₂)] traits in New Zealand (NZ) maternal sheep has not previously been investigated, nor has their relationship with detailed estimates of body composition. To investigate these relationships in NZ maternal sheep, a feed intake facility was established at AgResearch Invermay, Mosgiel, NZ in 2015, comprising automated feeders that record individual feeding events. Individual measures of feed intake, feeding behavior (length and duration of eating events), and gas emissions (estimated using portable accumulation chambers) were generated on 986 growing maternal ewe lambs sourced from three pedigree recorded flocks registered in the Sheep Improvement Limited database (www.sil.co.nz). Additional data were generated from a subset of 591 animals for body composition (estimated using ultrasound and computed tomography scanning). The heritability estimates for RFI, CH₄, and CH₄/(CH₄+CO₂) were 0.42 ± 0.09, 0.32 ± 0.08, and 0.29 ± 0.06, respectively. The heritability estimates for the body composition traits were high for carcass lean and fat traits; for example, the heritability for visceral fat (adjusted for body weight) was 0.93 ± 0.19. The relationship between RFI and CH₄ emissions was complex, and although less feed eaten will lead to a lowered absolute amount of CH₄ emitted, there was a negative phenotypic and genetic correlation between RFI and CH₄/(CH₄+CO₂) _of −0.13 ± 0.03 and −0.41 ± 0.15, respectively. There were also genetic correlations, that were different from zero, between both RFI and CH₄ traits with body composition including a negative correlation between the proportion of visceral fat in the body and RFI (−0.52 ± 0.16) and a positive correlation between the proportion of lean in the body and CH₄ (0.54 ± 0.12). Together the results provide the first accurate estimates of the genetic correlations between RFI, CH₄ emissions, and the body composition (lean and fat) in sheep. These correlations will need to be accounted for in genetic improvement programs.