title: Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves.
abstract: The community structure of colonised bacteria in the gastrointestinal tracts (GITs) of pre-weaned calves is affected by extrinsic factors, such as the genetics and diet of the calves; however, the dietary impact is not fully understood and warrants further research. Our study revealed that a total of 6, 5, 2 and 10 bacterial genera showed biologically significant differences in the GITs of pre-weaned calves fed four waste-milk diets: acidified waste milk, pasteurised waste milk, untreated bulk milk, and untreated waste milk, respectively. Specifically, generic biomarkers were observed in the rumen (e.g., Bifidobacterium, Parabacteroides, Fibrobacter, Clostridium, etc.), caecum (e.g., Faecalibacterium, Oxalobacter, Odoribacter, etc.) and colon (e.g., Megamonas, Comamonas, Stenotrophomonas, etc.) but not in the faeces. In addition, the predicted metabolic pathways showed that the expression of genes related to metabolic diseases was increased in the calves fed untreated waste milk, which indicated that untreated waste milk is not a suitable liquid diet for pre-weaned calves. This is the first study to demonstrate how different types of waste milk fed to pre-weaned calves affect the community structure of colonised bacteria, and the results may provide insights for the intentional adjustment of diets and gastrointestinal bacterial communities.
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: Y F
authors.initials: YF
authors.lastname: Deng
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: Y J
authors.initials: YJ
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: Y
authors.initials: Y
authors.lastname: Zou
authors.affiliation: Department of Animal Science, Faculty of Agriculture, Lorestan University, PO Box 465, Khorramabad, Iran.
authors.forename: A
authors.initials: A
authors.lastname: Azarfar
authors.affiliation: Sichuan Animal Science Academy, Animal Breeding and Genetics key Laboratory of Sichuan Province, Chengdu 610066, P. R. China.
authors.forename: X L
authors.initials: XL
authors.lastname: Wei
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: S K
authors.initials: SK
authors.lastname: Ji
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: J
authors.initials: J
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: Z H
authors.initials: ZH
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: S X
authors.initials: SX
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: S Z
authors.initials: SZ
authors.lastname: Dong
authors.affiliation: Beijing Computing Center, Beijing 100094, P. R. China.
authors.forename: Y
authors.initials: Y
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: D F
authors.initials: DF
authors.lastname: Shao
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: J X
authors.initials: JX
authors.lastname: Xiao
authors.affiliation: College of Animal Science, Xinjiang Agricultural University, Wulumuqi 830052, P. R. China.
authors.forename: K L
authors.initials: KL
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: Z J
authors.initials: ZJ
authors.lastname: Cao
authors.affiliation: State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China.
authors.forename: S L
authors.initials: SL
authors.lastname: Li
mesh_terms: D000821:Animal Feed; D000818:Animals; D001419:Bacteria / Q000145:classification; D044822:Biodiversity; D002417:Cattle; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000378:metabolism / Q000382:microbiology; D053858:Metabolic Networks and Pathways; D008892:Milk; D014866:Waste Products; D014886:Weaning
chemical_list: D014866:Waste Products