Sniffer position in an automated milking system affects the variability, repeatability, and consistent ranking of enteric methane emission measurements of dairy cows

Methane (CH 4 ) sniffers integrated into automated milking systems (AMS) are increasingly deployed to collect high-resolution, large-scale CH 4 emission data from dairy cows. The objective of this study was to assess how sniffer nozzle placement in AMS affects enteric CH 4 measurements in dairy cows. Nine CH 4 sniffer units (SimpleScan; C-Lock Inc.) were installed inside the AMS (DeLaval VMS) to measure enteric CH 4 concentration (ppm), with intake nozzles arranged in a 3 × 3, 15-cm grid above the feed bin. They were labeled from the top left to the bottom right position: upper left (UL), upper center (UC), upper right (UR), middle left (ML), middle center (MC), middle right (MR), lower left (LL), lower center (LC), and lower right (LR). Concurrently, a GreenFeed system (GF; C-Lock Inc.) was placed inside the freestall barn to measure enteric CH 4 production (g/d) from the same animals. Data from 107 cows were collected for 154 d. Visit-level data were aggregated by calculating mean values for each cow at the daily, weekly, and biweekly levels. Considerable variation in sniffer-based CH 4 concentration measurements was observed at the visit level, with mean (±SD) values ranging from 214 ± 102.5 ppm to 673 ± 239.9 ppm. The CV among sniffers ranged from 35.7% (LC) to 53.1% (MR) at the visit level and from 24.0% (UR) to 35.5% (LR) at the biweekly level. The Pearson correlation between each sniffer and the GF were moderate ( r p ranged from 0.25 [MR] to 0.49 [MC and LC]), with the central positions showing the strongest correlation. Stronger correlations ( r p >0.80) among sniffers were predominantly observed between sniffers positioned vertically. Visit-level CH 4 emission data were analyzed using generalized additive mixed-effects models. Aggregated data at daily, weekly, and biweekly levels of each cow were analyzed using a linear mixed-effects model. The variance components from these models were extracted to calculate repeatability. Repeatability estimates based on visit-level data were 0.19 for GF, with the values for individual sniffers ranging from 0.16 (UR) to 0.40 (LC). For both GF and sniffers, repeatability improved substantially when averaging weekly, with LC and MC achieving high repeatability (>0.70). To assess the potential of sniffers to rank cows as high or low emitters, estimated random cow effects of each sniffer position and the GF were used to calculate Spearman's rank correlation coefficients. Low to moderate correlations were observed ( r s ranged from 0.31 [MR] to 0.56 [MC]). The MC location showed the greatest potential to rank animals. Finally, the model-estimated systematic effects on CH 4 emission varied by sniffer locations, with LC and MC being able to consistently capture similar diurnal variations, as well as breed- and parity-specific effects on CH 4 emissions, comparable to those detected by the GF. In summary, the reliability, between-animal variability, and ranking correlations of CH 4 measurements vary between sniffer locations in AMS, with the sniffer positioned near the cow's muzzle being the most repeatable. Benchmarking on GreenFeed, sniffers exhibited differential uncertainty in ranking lactating dairy cows based on their CH 4 emissions, and require further investigations.