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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #412812
Research Project: Developing Strategies to Improve Dairy Cow Performance and Nutrient Use Efficiency with Nutrition, Genetics, and Microbiology

Location: Cell Wall Biology and Utilization Research

Title: Meta-transcriptome analysis reveals temporal dynamics on the active rumen microbiome in transition Holstein cows

Author
item FREGULIA, PRISCILA - Oak Ridge Institute For Science And Education (ORISE)
item Zanton, Geoffrey
item Li, Wenli

Submitted to: American Dairy Science Association Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 3/18/2024
Publication Date: 6/16/2024
Citation: Fregulia, P., Zanton, G., Li, W. 2024. Meta-transcriptome analysis reveals temporal dynamics on the active rumen microbiome in transition Holstein cows [abstract]. Journal of Dairy Science. 107 (Supplement 1):28.

Interpretive Summary:

Technical Abstract: Dairy cows experience dramatic changes in metabolism in the transition period, during which the cows calve and switch from a high-forage prepartum to a high-concentrate postpartum diet. Understanding the changes in the active rumen microbiome (ARM) community structure over the transition period may provide insights for improving animal health and production. We evaluated the combined effects of calving and diet changes on the ARM from eight cannulated Holstein cows at three time points: 14 days before calving (-14), two days (+/- one day) postpartum (PP), and 14 days after calving (+14). The cows were fed with a high forage close-up diet before calving (containing 35.92% corn silage, 37.10% wheat straw, and 26.98% concentrate) and with a common lactating cow diet after calving (31.67% BMR corn silage, 28.00% alfalfa silage, and 40.33% concentrate). Rumen liquid (RL) was collected by filtering rumen content obtained via cannula through four layers of cheesecloth. Total RNAs extracted from RL were used for meta-transcriptomic analysis by whole transcriptome sequencing. We used Kraken2 for quantifying microbial taxa-level abundance, DESeq2 for identifying differentially abundant genera (DAG) between time points, and sPLS-DA for analyzing microbial community profiles. Correlation between microbial taxa and time points was done using clustered image maps (CIM). The biggest changes in microbial genus abundance were observed between -14 and +14, where 361 DAG were identified which agrees with the sPLS-DA analysis, where the microbial community profiles of +14 and -14 showed complete cluster separation and distinct microbial community structures. On a CIM plot, specific microbial taxa showed a strong correlation with the different time points. We found no difference in alpha-diversity among the three time points (Simpson’s index and Shannon’s diversity, p < 0.05). Our results indicate that the combined effects of calving and diet changes result in shifts in the ARM structure in the rumen of transition dairy cows, with distinct ruminal microbial profiles pre- and postpartum.