Short communication: Signs of host genetic regulation in the microbiome composition in 2 dairy breeds: Holstein and Brown Swiss

Gonzalez-Recio, O., Zubiria, I., García-Rodríguez, A., Hurtado, A., & Atxaerandio, R. (2018). Short communication: Signs of host genetic regulation in the microbiome composition in 2 dairy breeds: Holstein and Brown Swiss. Journal of Dairy Science, 101(3), 2285–2292.

This study aimed to evaluate whether the host genotype exerts any genetic control on the microbiome composition of the rumen in cattle. Microbial DNA was extracted from 18 samples of ruminal content from 2 breeds (Holstein and Brown Swiss). Reads were processed using mothur ( in 16S and 18S rRNA gene-based analyses. Then, reads were classified at the genus clade, resulting in 3,579 operational taxonomic units (OTU) aligned against the 16S database and 184 OTU aligned against the 18S database. After filtering on relative abundance (>0.1%) and penetrance (95%), 25 OTU were selected for the analyses (17 bacteria, 1 archaea, and 7 ciliates). Association with the genetic background of the host animal based on the principal components of a genomic relationship matrix based on single nucleotide polymorphism markers was analyzed using Bayesian methods. Fifty percent of the bacteria and archaea genera were associated with the host genetic background, including Butyrivibrio, Prevotella, Paraprevotella, and Methanobrevibacter as main genera. Forty-three percent of the ciliates analyzed were also associated with the genetic background of the host. In total, 48% of microbes were associated with the host genetic background. The results in this study support the hypothesis and provide some evidence that there exists a host genetic component in cattle that can partially regulate the composition of the microbiome.

Comparison Between Non-Invasive Methane Measurement Techniques in Cattle

Rey, J., Atxaerandio, R., Ruiz, R., Ugarte, E., González-Recio, O., Garcia-Rodriguez, A., & Goiri, I. (2019). Comparison Between Non-Invasive Methane Measurement Techniques in Cattle. Animals : an open access journal from MDPI9(8), 563. doi:10.3390/ani9080563

Enteric methane emissions pose a serious issue to ruminant production and environmental sustainability. To mitigate methane emissions, combined research efforts have been put into animal handling, feeding and genetic improvement strategies. For all research efforts, it is necessary to record methane emissions from individual cows on a large scale under farming conditions. The objective of this trial was to compare two large-scale, non-invasive methods of measuring methane (non-dispersive infrared methane analyzer (NDIR) and laser), in order to see if they can be used interchangeably. For this, paired measurements were taken with both devices on a herd of dairy cows and compared. Significant sources of disagreement were identified between the methods, such that it would not be possible to use both methods interchangeably without first correcting the sources of disagreement.

Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study

Saborío‐Montero, A, Gutiérrez‐Rivas, M, García‐Rodríguez, A, et al. Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study. J Anim Breed Genet. 2020; 137: 3648.

The advent of metagenomics in animal breeding poses the challenge of statistically modelling the relationship between the microbiome, the host genetics and relevant complex traits. A set of structural equation models (SEMs) of a recursive type within a Markov chain Monte Carlo (MCMC) framework was proposed here to jointly analyse the host–metagenome–phenotype relationship. A non‐recursive bivariate model was set as benchmark to compare the recursive model. The relative abundance of rumen microbes (RA), methane concentration (CH4) and the host genetics was used as a case of study. Data were from 337 Holstein cows from 12 herds in the north and north‐west of Spain. Microbial composition from each cow was obtained from whole metagenome sequencing of ruminal content samples using a MinION device from Oxford Nanopore Technologies. Methane concentration was measured with Guardian® NG infrared gas monitor from Edinburgh Sensors during cow’s visits to the milking automated system. A quarterly average from the methane eructation peaks for each cow was computed and used as phenotype for CH4. Heritability of CH4 was estimated at 0.12 ± 0.01 in both the recursive and bivariate models. Likewise, heritability estimates for the relative abundance of the taxa overlapped between models and ranged between 0.08 and 0.48. Genetic correlations between the microbial composition and CH4 ranged from −0.76 to 0.65 in the non‐recursive bivariate model and from −0.68 to 0.69 in the recursive model. Regardless of the statistical model used, positive genetic correlations with methane were estimated consistently for the seven genera pertaining to the Ciliophora phylum, as well as for those genera belonging to the Euryarchaeota (Methanobrevibacter sp.), Chytridiomycota (Neocallimastix sp.) and Fibrobacteres (Fibrobacter sp.) phyla. These results suggest that rumen’s whole metagenome recursively regulates methane emissions in dairy cows and that both CH4 and the microbiota compositions are partially controlled by the host genotype.

Mitigation of greenhouse gases in dairy cattle via genetic selection: 2. Incorporating methane emissions into the breeding goal

González-Recio, O., López-Paredes, J., Ouatahar, L., Charfeddine, N., Ugarte, E., Alenda, R., & Jiménez-Montero, J. A. (2020). Mitigation of greenhouse gases in dairy cattle via genetic selection: 2. Incorporating methane emissions into the breeding goal. Journal of Dairy Science103(8), 7210-7221.

The objective of this study was to analyze the impact of incorporating enteric methane into the breeding objective of dairy cattle in Spain, and to evaluate both genetic and economic response of traits in the selection index under 4 scenarios: (1) the current ICO (Spanish total merit index), used as benchmark; (2) a hypothetical penalization of methane emissions through a carbon tax; (3) considering methane as a net energy loss for the animal; and (4) desired genetic response to reduce methane production by 20% in 10 yr. A bio-economic model was developed to derive the economic values for production and methane traits in each scenario. The estimated economic values for methane were estimated at −€1.21/kg and −€0.32/kg for scenarios 2 and 3, respectively. When merged with other traits in the selection index, methane had less economic importance (1–5%) than milk protein yield (39–42%) or milk fat yield (27–28%). Under these scenarios, selection resulted in an unfavorable response in methane emissions when it was included with an economic weight, with an increase in methane estimated from 0.52 to 0.60 kg/cow per year. Small differences in total profit per cow per year were observed between indices. The incorporation of methane production into the breeding objective had a negligible effect on production, with minor reductions in the expected genetic gain for fat and protein yields and in total economic benefits. However, total methane emissions in the dairy industry in Spain were estimated to decrease between 2 and 5% in the next 10 yr due to positive genetic trends for milk yield and an expected decrease in the total number of dairy cows. Additionally, methane intensity per 1 billion liters of milk would decrease in all scenarios. The uncertainty in the genetic parameters of methane and in carbon prices were tested in a sensitivity analysis, resulting in small deviations from the benchmark scenario. A major effect was observed only under the desired genetic response scenario. In this case, it was possible to achieve a 20% reduction of methane production in 10 yr via selective breeding but at the expense of a larger ad hoc weight (33%) of methane in the selection index and decelerating the genetic gain for production traits from 6 to 18%. This study shows the potential of including environmental traits in the selection indices while retaining populations profitable for producers.

Mitigation of greenhouse gases in dairy cattle via genetic selection: 1. Genetic parameters of direct methane using noninvasive methods and proxies of methane

López-Paredes, J., Goiri, I., Atxaerandio, R., García-Rodríguez, A., Ugarte, E., Jiménez-Montero, J. A., … & González-Recio, O. (2020). Mitigation of greenhouse gases in dairy cattle via genetic selection: 1. Genetic parameters of direct methane using noninvasive methods and proxies of methane. Journal of Dairy Science103(8), 7199-7209.

Records of methane emissions from 1,501 cows on 14 commercial farms in 4 regions of Spain were collected from May 2018 to June 2019. Methane concentrations (MeC) were measured using a nondispersive infrared methane detector installed within the feed bin of the automatic milking system during 14- to 21-d periods. Rumination time (RT; min/d) was collected using collars with a tag that registered time (minutes) spent eating and ruminating. The means of MeC and methane production (MeP) were 1,254.28 ppm and 182.49 g/d, respectively; mean RT was 473.38 min/d. Variance components for MeC, MeP, and RT were estimated with REML using pedigree and genomic information in a single-step model. Heritabilities for MeC and MeP were 0.11 and 0.12, respectively. Rumination time showed a slightly larger heritability estimate (0.17). The genetic correlation between MeP and MeC was high (>0.95), suggesting that selection on either trait would lead to a positive correlated response on the other. Negative correlations were estimated between RT and MeC (−0.24 ± 0.38) and MeP (−0.43 ± 0.35). Methane concentration and MeP had slightly positive correlations with milk yield (0.17 ± 0.39 and 0.21 ± 0.36), protein percentage (0.08 ± 0.32 and 0.30 ± 0.45), protein yield (0.22 ± 0.41 and 0.31 ± 0.35), fat percentage (0.02 ± 0.40 and 0.27 ± 0.36), and fat yield (0.27 ± 0.28 and 0.29 ± 0.28) from bivariate analyses. Rumination time had positive correlations with milk yield (0.41 ± 0.75) and protein yield (0.26 ± 0.57) and negative correlations with fat yield (−0.45 ± 0.32), protein percentage (−0.15 ± 0.38), and fat percentage (−0.40 ± 0.47). A positive approximated genetic correlation was estimated between fertility and MeC (0.10 ± 0.05) and MeP (0.18 ± 0.05), resulting in slightly higher CH 4 production when selecting for better fertility [days open estimated breeding values (EBV) are expressed with mean 100 and SD 10, inversely related to days from calving to conception; that is, greater days open EBV implies better fertility]. Positive correlations were also estimated for stature with MeC and MeP (0.30 ± 0.04 and 0.43 ± 0.04, respectively). Other type traits (chest width, udder depth, angularity, and capacity) were positively correlated with methane traits, possibly because of higher milk yield and higher feed intake from these animals. Rumination time showed positive EBV correlations with production traits and type traits, and negative correlations with somatic cell count and body condition score. Based on the genetic correlations and heritabilities estimated in this study, methane is measurable and heritable, and estimates of genetic correlations suggest no strong opposition to current breeding objectives in Spanish Holsteins.