Data and Resources
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Additional Info
| Field | Value |
|---|---|
| Title | Bovine Colostrum Raw sequence reads |
| License | Licence Not Specified | Teagasc Department | Animal and Bioscience Research |
| Teagasc Programme | Animal and Grassland |
| Description | 16S rRNA gene (V4 region) amplicon sequencing data and associated colostrum quality data from 21 processed colostrum samples collected immediately before calf feeding on a single spring-calving Holstein-Friesian and Jersey dairy herd (Dairygold Research Farm, Kilworth, Co. Cork) during the spring 2022 calving season. Colostrum from 31 primiparous and multiparous donors was refrigerated at 4 C for up to 24 h, combined with a second donor's colostrum where needed (no more than two donors per sample), and reheated to 38 C in a water bath for 60 min before sampling. The dataset characterises the prokaryotic community of colostrum as it is commonly managed on commercial dairy farms, and complements an earlier dataset on fresh colostrum from the same herd and calving season. Colostral immunoglobulin (Ig A, Ig G, Ig M) concentrations were measured by single radial immunodiffusion. Breed and parity had no effect on alpha- or beta-diversity; the community was low in diversity, heterogeneous across samples, and dominated by Pseudomonas and Acinetobacter (bacteria) and Methanobrevibacter (archaea). |
| Language | English |
| Principal Investigator (PI) | Dr David Kenny |
| Principal Investigator (PI) email | david.kenny@teagasc.ie |
| Principal Investigator (PI) ORCID | https://orcid.org/0000-0001-9204-098X |
| Data creator(s) |
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| Geographic coverage | Dairygold Research Farm, Kilworth, Co. Cork, Ireland (Teagasc Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork). |
| Landing page | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1136803/ |
| Project funders | European Union Horizon 2020, "HoloRuminant" project (grant agreement no. 101000213) |
| Related resources |
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| Provenance information | Colostrum was collected from each quarter within 2-6 h of calving using a portable milking unit, following sterile microbiome sampling procedures (equipment cleaned with antimicrobial soap and boiling water, teats and clusters disinfected with 70% ethanol). Each donor's colostrum was stored separately in sterile buckets at 4 C for no more than 24 h, combined with a second donor where needed, and reheated to 38 C in a water bath for 60 min. Calves (n = 21) did not receive colostrum from their own dam and were fed 8.5% of birthweight within 2 h of birth. Immediately before feeding, 30 mL was collected aseptically into three sterile 10 mL tubes, snap frozen in liquid nitrogen and stored at -80 C. Samples were thawed stepwise (-20 C for 24 h, then 4 C for 24 h), treated with EDTA and centrifuged (4,500 x g, 20 min, 4 C). The fat layer was discarded, the supernatant kept for sRID assays, and the microbial pellet used for DNA extraction (Qiagen DNeasy PowerSoil Pro Kit, repeated bead beating). Bacterial DNA presence was confirmed by qPCR (Kittelmann et al. 2013 method). Library preparation and sequencing were performed by Macrogen (Seoul, South Korea): V4 region amplified with 515F/806R primers carrying Nextera overhang adapters, 25 PCR cycles, AMPure purification, sequenced on an Illumina MiSeq with the 500-cycle v2 reagent kit on one flow cell. Herd management: cows and heifers grazed perennial ryegrass/white clover until November, then were housed on grass silage ad libitum without concentrate. Dry-off treatments included parasite control and teat sealant for multiparous cows; 11 multiparous cows with SCC > 100,000 also received intramammary antibiotic. Full protocols: Scully et al. (2026) PLOS ONE 21(7), e0353693, and Scully et al. (2025) PLOS ONE 20(10), e0335718. |
| Time of data collection | January-March 2022 |