Viral and bacterial dynamics in response to drastic and short dietary shifts in creole Colombian cattle

Abstract

<title>Abstract</title> The inclusion of grains in cattle diets aims to boost milk and meat production but can reduce ruminal pH and disrupt normal rumen function, mainly affecting fiber-degrading microbes. While bacterial responses to pH shifts are well documented, the effects on rumen bacteriophage (phage) communities remain unclear. This study aimed at characterizing the viral and bacterial dynamics upon a short-term acidotic challenge induced by adding corn to the diets of three Colombian BON (Blanco Orejinegro) cows, ( <italic>Bos Taurus</italic> ), usually fed on pasture. Ruminal fluid samples were analyzed to monitor viral and bacterial diversity, pH, and short-chain fatty acids (SCFAs). Viral alpha diversity indices declined significantly with pH reduction, possibly due to lysogeny or phages with broad host ranges. In contrast, bacterial diversity stayed relatively stable, suggesting higher resilience to short-term pH shifts. Beta diversity analysis indicated that individual animal variation, rather than diet, was the main driver shaping both viral and bacterial communities. Moreover, distinct viral abundance patterns were strongly associated with pH fluctuations, highlighting the potential of phages as sensitive early indicators of ruminal acidification. These findings emphasize the important ecological role of the rumen virome and suggest that monitoring phage dynamics could improve understanding of ruminal pH-related disturbances in cattle.