Microbiome

Rumen fluid metagenomics revealed parity-driven changes in microbiome diversity, activity, and abundance in Holstein-Friesian dairy cows

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Abstract

Parity is known to influence energy metabolism and rumen function in dairy cows. Primiparous cows often experience negative energy balance (NEB) during early lactation, requiring metabolic adaptations that may be reflected in the rumen microbiome. This study aimed to investigate the effects of parity on rumen microbiome diversity, activity, and abundance in lactating Holstein Friesian cows under commercial farm conditions. Twenty pregnant lactating Holstein Friesian cows were selected and grouped by parity: first parity (P1; n = 10) and third parity (P3; n = 10). Rumen fluid samples were collected two hours post-feeding. Targeted sequencing of the 16S rRNA gene was conducted using the PacBio long-read platform with universal 16S primers. Bioinformatic analyses were performed in R using standard pipelines for microbial community profiling. Alpha diversity was estimated using Chao1, Shannon, and Simpson indices. Differences between parities were assessed using t-tests, with significance set at P < 0.05. Species richness (Chao1 index) ranged from 25 to 59 across all samples, indicating moderate variability in microbial richness. The mean Chao1 index was numerically higher in P3 cows compared with P1, suggesting greater microbial richness with increasing parity. Shannon diversity ranged from 1.66 to 2.76, and was numerically higher in P3 than in P1, reflecting a more even and diverse microbial community. Simpson's index (0.59-0.87) also indicated reduced dominance of individual taxa in P3. Relative abundance analyses revealed notable differences between parities in key genera, with Ruminococcus being more abundant in P1 and Bifidobacterium in P3. We found that parity exerted a measurable influence on rumen microbiome structure and diversity in lactating dairy cows. Third-parity cows exhibited higher microbial richness and evenness compared with first-parity cows, indicating that age and repeated lactation cycles promote a more stable and functionally diverse rumen microbial community. These findings highlight the role of physiological maturity in shaping rumen microbial ecology and may have implications for dietary management strategies targeting energy balance and methane mitigation across parities. Hence, the result may highlight the importance of including parity in dairy cow nutrition and management, particularly to address NEB in primiparous cows, to maintain production and health.

Keywords: 2026

How to Cite:

Kolathingal-Thodika, N., Elayadeth-Meethal, M., Tunkala, B., Dunshea, F., Eckard, R., Flavel, M. & Chauhan, S., (2026) “Rumen fluid metagenomics revealed parity-driven changes in microbiome diversity, activity, and abundance in Holstein-Friesian dairy cows”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286116. doi: https://doi.org/10.31274/wcgalp.23855

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