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. 2017 Jul 14;7:5439. doi: 10.1038/s41598-017-05376-z

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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The flow scheme of this study. Calves were fed colostrum within 2 h after birth. At 22 d of age, whole milk was gradually replaced with milk replacer, which was then fed twice daily until d 64. At d 28, 56, and 64 of age, body weight of each calf was recorded. From d 28 to 64 of age, feed intake and fecal scores were recorded. At 28 d of age, calves were randomly assigned to 5 treatments and treated with alternatives to antibiotics. At 57 d of age, E. coli K99 challenge were carried out. At 64 d of age, calves were euthanized and jejunum digesta samples were collected and sequenced.