Dataset Information

Compositional and Functional Comparisons of the Microbiota in the Colostrum and Mature Milk of Dairy Goats.

ABSTRACT: Goat milk is essential for the initial development of kids by providing a great source of commensal bacteria. In this study, we analyzed the microbiota of the milk of 30 healthy Saanen dairy goats. The 30 samples comprised 15 colostrum and 15 mature milk samples, collected from three different farms of Shaanxi Province. Colostrum samples were collected daily for five days post-delivery and mature milk was collected on the 7th, 10th, 20th, 30th, and 40th days. The result showed that microbial alpha diversity was higher in the mature milk compared with that in the colostrum. Linear discriminant analysis effect size (LEfSe) was performed to detect differentially abundant taxa in colostrum and goat milk. According to taxonomy results, Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the predominant bacteria phyla in both colostrum and mature milk. In addition, lactation stage noticeably influenced the composition of milk microbiota. Specifically, Novosphingobium, Brachybacterium, Psychrobacter, Lactobacillus, Yersinia, Roseateles, Rothia, Sanguibacter, Cloacibacterium, Variovorax, Sphingobacterium, and Coxiella were enriched in the colostrum, while Georgenia, Peptostreptococcus, Bacteroidales, Yaniella, Planomicrobium, Cloacibacterium, Azospirillum, Turicibacter, Cupriavidus, Herbaspirillum, Rhodobacteraceae, and Aeromonadales were the dominant genera in the mature milk. The enriched metabolic functions of the goat milk microbiota were predicted by PICRUSt and classified by KEGG pathway. Moreover, the abundances of environmental information processing, cellular processes pathway, genetic information processing pathway, organismal systems pathway, and metabolism pathway were significantly different between microbiota of colostrum and mature milk. Altogether, our study disclosed the significant difference between the microbial communities of colostrum and mature milk and provided grounds for further research in dairy microbiology.

SUBMITTER: Niyazbekova Z

PROVIDER: S-EPMC7690780 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Compositional and Functional Comparisons of the Microbiota in the Colostrum and Mature Milk of Dairy Goats.

Niyazbekova Zhannur Z Yao Xiao-Ting XT Liu Ming-Jie MJ Bold Nomin N Tong Juan-Zhen JZ Chang Jian-Jun JJ Wen Ying Y Li Li L Wang Yong Y Chen De-Kun DK Ma Wen-Tao WT

Animals : an open access journal from MDPI 20201023 11

Goat milk is essential for the initial development of kids by providing a great source of commensal bacteria. In this study, we analyzed the microbiota of the milk of 30 healthy Saanen dairy goats. The 30 samples comprised 15 colostrum and 15 mature milk samples, collected from three different farms of Shaanxi Province. Colostrum samples were collected daily for five days post-delivery and mature milk was collected on the 7th, 10th, 20th, 30th, and 40th days. The result showed that microbial alp ...[more]

PMID: 33114109

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Project description:In this work we aimed at sequencing and assembling the goat milk transcriptome corresponding at colostrum and 120 days of lactation. To reconstruct transcripts we used both the genome as reference, and a de novo assembly approach. Additionally, we aimed at identifying the differentially expressed genes (DEGs) between the two lactation stages and at analyzing the expression of genes involved in oligosaccharides metabolism.A total of 44,635 different transcripts, organized in 33,757 tentative genes, were obtained using the goat genome as reference. A significant sequence similarity match was found for 40,353 transcripts (90%) against the NCBI NT and for 35,701 (80%) against the NR databases. 68% and 69% of the de novo assembled transcripts, in colostrum and 120 days of lactation samples respectively, have a significant match with the merged transcriptome obtained using Cufflinks/Cuffmerge. CSN2, PAEP, CSN1S2, CSN3, LALBA, TPT1, FTH1, M-SAA3, SPP1, GLYCAM1, EEF1A1, CTSD, FASN, RPS29, CSN1S1, KRT19 and CHEK1 were found between the top fifteen highly expressed genes. 418 loci were differentially expressed between lactation stages, among which 207 and 122 were significantly up- and down-regulated in colostrum, respectively. Functional annotation and pathway enrichment analysis showed that in goat colostrum somatic cells predominate biological processes involved in glycolysis, carbohydrate metabolism, defense response, cytokine activity, regulation of cell proliferation and cell death, vasculature development, while in mature milk, biological process associated with positive regulation of lymphocyte activation and anatomical structure morphogenesis are enriched. The analysis of 144 different oligosaccharide metabolism-related genes showed that most of these (64%) were more expressed in colostrum than in mature milk, with eight expressed at very high levels (SLCA3, GMSD, NME2, SLC2A1, B4GALT1, B3GNT2, NANS, HEXB).To our knowledge, this is the first study comparing goat transcriptome of two lactation stages: colostrum and 120 days. Our findings suggest putative differences of expression between stages and can be envisioned as a base for further research in the topic. Moreover because a higher expression of genes involved in immune defense response, carbohydrate metabolism and related to oligosaccharide metabolism was identified in colostrum we here corroborate the potential of goat milk as a natural source of lactose-derived oligosaccharides and for the development of functional foods.

Project description:BackgroundDiets rich in starch have been shown to increase a risk of reducing milk fat content in dairy goats. While bile acids (BAs) have been used as a lipid emulsifier in monogastric and aquatic animals, their effect on ruminants is not well understood. This study aimed to investigate the impact of BAs supplementation on various aspects of dairy goat physiology, including milk composition, rumen fermentation, gut microbiota, and BA metabolism.ResultsWe randomly divided eighteen healthy primiparity lactating dairy goats (days in milk = 100 ± 6 d) into two groups and supplemented them with 0 or 4 g/d of BAs undergoing 5 weeks of feeding on a starch-rich diet. The results showed that BAs supplementation positively influenced milk yield and improved the quality of fatty acids in goat milk. BAs supplementation led to a reduction in saturated fatty acids (C16:0) and an increase in monounsaturated fatty acids (cis-9 C18:1), resulting in a healthier milk fatty acid profile. We observed a significant increase in plasma total bile acid concentration while the proportion of rumen short-chain fatty acids was not affected. Furthermore, BAs supplementation induced significant changes in the composition of the gut microbiota, favoring the enrichment of specific bacterial groups and altering the balance of microbial populations. Correlation analysis revealed associations between specific bacterial groups (Bacillus and Christensenellaceae R-7 group) and BA types, suggesting a role for the gut microbiota in BA metabolism. Functional prediction analysis revealed notable changes in pathways associated with lipid metabolism, suggesting that BAs supplementation has the potential to modulate lipid-related processes.ConclusionThese findings highlight the potential benefits of BAs supplementation in enhancing milk production, improving milk quality, and influencing metabolic pathways in dairy goats. Further research is warranted to elucidate the underlying mechanisms and explore the broader implications of these findings.

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Project description:As one of the pioneer bacterial sources of intestinal microbiota, the information of bacterial composition in colostrum might provide a reference for developing specific probiotics for newborn calves, especially calves fed with pasteurized milk. The present study aimed to detect the core bacteria at different taxonomic levels and the common beneficial ones in colostrum by analyzing the bacterial composition in 34 colostrum samples of healthy cows selected from two dairy farms. The results of the further analysis showed that the bacterial composition in the colostrum of the two dairy farms was different, but their four most dominant phyla were the same including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. The microbiome of all colostrum samples shared ten core operational taxonomic units (OTUs), 21 core genera, and 34 core families, and most of them had no difference in relative abundance between the two farms. The ten core OTUs did not belong to the identified commensal bacteria and have not been detected by previous study. However, several core genera found in our study were also identified as core genus in a previous study. Some well-known beneficial and pathogenic bacteria including Lactobacillus plantarum, Bacillus subtilis, Acinetobacter lwoffii, and Streptococcus pneumoniae were present in the colostrum of healthy cows. However, none had a correlation with the number of somatic cell count (SCC), but the core genera Nubella and Brevundinimas and the core families Methylobacteriaceae and Caulobacteraceae positively correlated with the number of SCC. The genus Staphylococcus, Pseudomonas, and Chryseobacterium in colostrum had a positive correlation with each other, while the probiotics unidentified-Bacteroidales-S24-7-group had a negative correlation with Pseudomonas and Chryseobacterium. In addition, more than 50% bacterial OTUs in colostrum were detected in the rectal content including some strictly anaerobic bacteria that are generally present in the intestine and rumen. However, of the top 30 commonly shared bacterial genera in the colostrum and rectal feces, no genus in colostrum was positively correlated with that same genus in rectal feces. In conclusion, the bacterial composition of colostrum microbiota is greatly influenced by external factors and individuals. There were several core OTUs, and some core genus and families in the colostrum samples. Colostrum from healthy cows contained both beneficial and pathogenic bacteria and shared many common bacteria with rectal content including some gastrointestinal anaerobes.

Dataset Information

Compositional and Functional Comparisons of the Microbiota in the Colostrum and Mature Milk of Dairy Goats.

Publications

Compositional and Functional Comparisons of the Microbiota in the Colostrum and Mature Milk of Dairy Goats.

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