Metagenomic analysis revealed the individualized shift in ileal microbiome of neonatal calves in response to delaying the first colostrum feeding

摘要

The aim of this study was to explore the effect ofcolostrum feeding time on the ileal microbiome of neonatalcalves. In this study, 22 male Holstein calves wererandomly assigned to different colostrum feeding timetreatments: after birth (at 45 min, n = 7); at 6 h afterbirth (n = 8); and at 12 h after birth (TRT12h; n = 7).At 51 h after birth, calves were killed and ileum digestawas collected for microbiome analysis using shotgunmetagenomic sequencing. Bacteria, archaea, eukaryotes,and viruses were identified from the ileum microbiome.For the bacteriome, Firmicutes and Proteobacteria werethe predominant phyla, and Escherichia, Streptococcus,Lactobacillus were the 3 most abundant genera. For thearchaeal community, Euryarchaeota and Crenarchaeotawere the 2 major phyla, and Methanosarcina, Methanobrevibacter,and Methanocorpusculum were the 3 mostabundant genera. In total, 116 Kyoto Encyclopedia ofGenes and Genomes (KEGG) pathways were identifiedfrom the ileal microbiome, with “biosynthesis ofvancomycin group antibiotics,” “biosynthesis of ansamycins,”“valine, leucine, and isoleucine biosynthesis,”“ribosome,” and “d-alanine metabolism” as the top 5functions. When the ileal microbiomes were comparedamong the 3 treatments, the relative abundance ofEnterococcus was higher in TRT12h calves, suggestingthat calves may have a higher abundance of opportunisticpathogens when the feeding of colostrum is delayedfor 12 h. Moreover, among all KEGG pathways,the enriched “taurine and hypotaurine metabolism”(KO00430) pathway was identified in the ileal microbiomeof TRT12h calves; however, future studies areneeded to understand the effect on the host. Additionally,2 distinct ileal microbial profiles were identifiedacross all samples, indicating that that host factorsmay play a significant role in driving varied microbiomechanges in response to colostrum feeding time.Whether such microbiome shifts affect long-term gutfunction and calf performance warrants future studies.