DOI: 10.5281/zenodo.7033893
title: 16S Phyloseq R object accompanying the paper: Effects of storage methods on total bacterial count and microbial composition of bovine colostrum

description: This ready to load <strong>phyloseq</strong> R S4 object contains the ASV table, taxonomy table and sample metadata (16S V3-V4). This data was build using the DaDa2 (version 1.12.1) and phyloseq (version 1.32) R packages using our raw Illumina MiSeq PE300 sequencing data deposited at NCBI-SRA under BioProject: PRJNA872909. The accompanying (peer-reviewed) scientific article can be found here: https://www.todo DOI: todo <strong>Study/draft abstract:</strong> Lisa Robbers, Hannes Bijkerk, Lars Ravesloot, Alex Bossers, Mirjam Nielen, Ruurd Jorritsma, Ad Koets, Lindert Benedictus Neonatal calves need to acquire passive immunity through maternal colostrum, as they are immunologically naïve and the structure of the bovine placenta does not allow passage of maternal antibodies during pregnancy. Milked colostrum is not initially sterile and may even contain high bacterial counts. Minimizing total bacterial counts in colostrum is generally advised, however bacterial quality of colostrum comprises more than just bacterial quantities, but also depends on the specific bacteria present. While duration and temperature of colostrum storage are known to affect total plate counts (TPC), less is known about the effects of storage on the actual bacterial composition of the TPC. We speculated that, depending on the storage conditions, colostrum is a substrate in which certain bacterial species can thrive affecting the quality of colostrum. We therefore aimed to characterize the effects of different colostrum storage methods on the composition of the viable, aerobic, microbial community. Colostrum samples were stored at different temperatures and for different durations. Next, bacterial growth was assessed using the aerobe plate count culture method, followed by 16S rRNA gene amplicon sequencing. Differences in the TPC bacterial compositions of the stored colostrum samples, as determined by 16S rRNA gene amplicon sequencing, were mostly explained by the variation in bacterial composition of the colostrum sample directly after milking. In line with earlier studies, the results from our study show that the TPC increased when colostrum was stored for 24 hours at room temperature, but not when stored in a refrigerator for the same duration. Community structure of the TPC of colostrum stored at room temperature for 24 hours and stored in a refrigerator for a week was significantly different from the baseline samples. The 16S rRNA sequencing results indicate this is because of increased numbers of <em>Enterobacteriaceae.</em> <em>Enterobacteriaceae</em> abundance in refrigerated samples seemed to remain stable for the first 24 hours, but increased drastically after one week. The results indicate that microbial composition of stored colostrum is mostly influenced by the composition of the colostrum sample directly after milking, which is most probably the result of contamination or other environmental influences during the milking process. This study provides a deeper insight in the changes in the microbial composition of colostrum TPC during practical storage conditions and provides a primer for more detailed research into the determinants of bacterial composition of colostrum and the linked health effects.
description: This ready to load phyloseq R S4 object contains the ASV table, taxonomy table and sample metadata. This data was build using the DaDa2 (version 1.12.1) and phyloseq (version 1.32) R packages using our raw Illumina MiSeq PE300 sequencing data deposited at NCBI-SRA under BioProject: PRJNA872909.