Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF

SIMPLE SUMMARY: The present study aimed to characterize and understand how the gastrointestinal microbiome (in rumen and feces) of pre-weaning dairy calves is affected by feeding a starter concentrate with two levels of fiber and the inclusion of hay in the diet. Another study objective was to verify if the effects on the microbiome remained after weaning. The ruminal bacteriome was not affected by levels or sources of fiber. The fecal bacteriome was affected by age and diet. The inclusion of hay affected the fecal microbial diversity. ABSTRACT: A starter concentrate containing different levels and sources of NDF can modify the gastrointestinal bacteriome. This study evaluated 18 Holstein calves housed in un-bedded suspended individual cages, fed one of three treatments: 22NDF: a conventional starter containing 22% NDF (n = 7); 31NDF: a starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22Hay: diet 22NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily, weaned at 8th week of age, and housed in wood shelters until week 10. To evaluate the bacteriome, the bacterial community of ruminal fluid and fecal samples was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene. Bacterial diversity in rumen was not affected by diet or age. The phyla Firmicutes and Bacteroidota, and Prevotella’ genus were the most abundant in ruminal fluid and fecal samples. In feces, the α-diversity indices were higher for 22Hay. All indices were significantly affected by age. We believe that the ruminal bacteriome was affected by basal diet components, but not affected by NDF levels or sources. The supply of hay was effective in modifying the fecal bacteriome of dairy calves due to hind gut fermentation.