Dataset Information

Microbiota in Dung and Milk Differ Between Organic and Conventional Dairy Farms.

ABSTRACT: Organic farming is increasingly promoted as a means to reduce the environmental impact of artificial fertilizers, pesticides, herbicides, and antibiotics in conventional dairy systems. These factors potentially affect the microbial communities of the production stages (soil, silage, dung, and milk) of the entire farm cycle. However, understanding whether the microbiota representative of different production stages reflects different agricultural practices - such as conventional versus organic farming - is unknown. Furthermore, the translocation of the microbial community across production stages is scarcely studied. We sequenced the microbial communities of soil, silage, dung, and milk samples from organic and conventional dairy farms in the Netherlands. We found that community structure of soil fungi and bacteria significantly differed among soil types, but not between organic versus conventional farming systems. The microbial communities of silage also did not differ among conventional and organic systems. Nevertheless, the dung microbiota of cows and the fungal communities in the milk were significantly structured by agricultural practice. We conclude that, while the production stages of dairy farms seem to be disconnected in terms of microbial transfer, certain practices specific for each agricultural system, such as the content of diet and the use of antibiotics, are potential drivers of shifts in the cow's microbiota, including the milk produced. This may reflect differences in farm animal health and quality of dairy products depending on farming practices.

SUBMITTER: Gomes SIF

PROVIDER: S-EPMC7399162 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Biases of antimicrobial use (AMU) reporting systems pose a challenge to monitoring of AMU. Our study aimed to cross-compare three data sources of AMU in Swedish dairy herds to provide an account of the validity of AMU reports. We studied AMU differences between two production systems, to investigate how the reporting system affected this comparison. On-farm quantification of AMU via a manual collection of empty drug containers (BIN) took place in organic (n = 30) and conventional (n = 30) dairy herds during two periods between February 2016 and March 2017. A data extract mirroring these periods was obtained from two linked datasets that contain AMU data as reported by the prescribing veterinarians. These included data from the Swedish Board of Agriculture system (SBA) and Växa milk recording system (VXA). Using the European Medicines Agency technical units, the total number of defined daily doses (DDDvet), and defined course doses (DCDvet) per animal/year were calculated for each herd/period/dataset. Descriptive statistics and Bland-Altman plots were used to evaluate the agreement and systematic bias between the datasets. Mixed models for repeated measures were used to assess AMU differences between production systems. We found consistent numerical differences for the calculated AMU metrics, with BIN presenting higher usage compared to the SBA and VXA. This was driven by a disparity in intramammary tubes (IMt) which appear to be underreported in the national datasets. A statistically significant interaction (BIN dataset) between the production system and drug administration form was found, where AMU for injectable and lactating cow IMt drug forms differed by the production system, but no difference was found for dry-cow IMt. We conclude that calculating AMU using DDDvet and DCDvet metrics at a herd level based on Swedish national datasets is useful, with the caveat of IMt potentially being misrepresented. The BIN method offers an alternative to monitoring AMU, but scaling up requires considerations. The lower disease caseload in organic herds partly explains the lower AMU in particular drug forms. The fact that organic and conventional herds' had equally low AMU for dry-cow IMt, coupled with mismatches in IMt report across herds indicated an area of further research.

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

Microbiota in Dung and Milk Differ Between Organic and Conventional Dairy Farms.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets