Microbiota comparison of individual and pooled cow fecal samples from PEI dairy farms

The aim of this study was to compare the microbiota diversity captured in individual versus pooled fecal samples from dairy cattle and evaluate the feasibility of using pooled sampling to assess the microbiota of dairy cattle at the herd level. A cross-sectional study utilized animals from 28 dairy farms in Prince Edward Island (PEI), Canada. The farms were visited between July and December 2020. Both free-stall and tie-stall housing systems were eligible. Manure samples were obtained from dry and lactating cows. Then, approximately 20g of fecal samples from each group were pooled. DNA extractions were performed on all subsamples using the Qiagen PowerMax Soil Kit and then submitted for 16S rRNA gene amplification and sequencing. Operational taxonomic units were determined, and four alpha diversity indices were computed. A total of 128 and 132 manure samples from pos and prepartum cows, respectively, were analyzed. Mixed-effects random slope models were employed, incorporating herd-level random effects to estimate the correlation among individual samples and between individual and pooled samples. The estimated Shannon observed features, Pielou evenness, and Faith PD were 5.9, 580, 0.93, and 44.1 for the individual samples, and 5.93, 587, 0.93, and 45.5 for the pooled samples, respectively. All alpha diversity metrics were not significantly different between individual and pooled samples. Overall, pooled sampling does not significantly affect diversity and yields comparable results to individual samples, although it tends to show slightly higher diversity in some indices. This sampling strategy could be used in microbiota studies of dairy herds.