High-throughput sequencing reveals bacterial diversity in raw milk production environment and production chain in Tangshan city of China

ABSTRACT In pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. High-throughput sequencing on a variety of microbial niches on farms was used to study the patterns of microbial movement through the dairy production chain and, in the process, to investigate the impact of seasonal housing and the inclusion/exclusion of a teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor. Beta diversity and network analyses showed that environmental and milk microbiotas separated depending on whether they were sourced from an indoor or outdoor environment. Within these respective habitats, similarities between the milk microbiota and that of teat swab samples and, to a lesser extent, fecal samples were apparent. Indeed, SourceTracker identified the teat surface as the most significant source of contamination, with herd feces being the next most prevalent source of contamination. In milk from cows grazing outdoors, teat prep significantly increased the numbers of total bacteria present. In summary, sequence-based microbiota analysis identified possible sources of raw milk contamination and highlighted the influence of environment and farm management practices on the raw milk microbiota. IMPORTANCE The composition of the raw milk microbiota is an important consideration from both a spoilage perspective and a food safety perspective and has implications for milk targeted for direct consumption and for downstream processing. Factors that influence contamination have been examined previously, primarily through the use of culture-based techniques. We describe here the extensive application of high-throughput DNA sequencing technologies to study the relationship between the milk production environment and the raw milk microbiota. The results show that the environment in which the herd was kept was the primary driver of the composition of the milk microbiota composition.

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Snapshot of Cyprus Raw Goat Milk Bacterial Diversity via 16S rDNA High-Throughput Sequencing; Impact of Cold Storage Conditions

Fermentation ◽

10.3390/fermentation6040100 ◽

2020 ◽

Vol 6 (4) ◽

pp. 100

Author(s):

Eleni Kamilari ◽

Dimitrios A. Anagnostopoulos ◽

Photis Papademas ◽

Marina Efthymiou ◽

Svitlana Tretiak ◽

...

Keyword(s):

Bacterial Diversity ◽

High Throughput ◽

Cold Storage ◽

High Throughput Sequencing ◽

Goat Milk ◽

Raw Milk ◽

Storage Conditions ◽

Gram Negative ◽

Milk Samples ◽

The Impact

In general, it is a common practice among dairy producers to store the milk in the refrigerator directly after milking, in order to preserve it and prevent the development of spoilage microbes. However, the impact of keeping the milk in the refrigerator overnight on milk microbial diversity has been poorly investigated. This study aimed to provide a snapshot of the bacterial composition of goat milk after direct storage at −80 °C and after being kept overnight at 4 °C and then in storage at −80 °, using high-throughput sequencing (HTS). Goat milk samples from four different farms were analyzed, to reveal that milk bacterial diversity differed between the two different storage conditions. Goat milk directly stored at −80 °C was characterized by the presence of the Gram-negative contaminants Pseudomonas and Acinetobacter, in addition to the genera Corynebacterium, Chryseobacterium, Bacteroides and Clostridium. Milk samples that were kept overnight at 4 °C were characterized by a reduction in their bacterial biodiversity and the predominance of the Gram-negative, aerobic Phyllobacterium. Overall, HTS methodologies provide an in-depth identification and characterization of the goat raw milk microbiome. Further, they offer a better understanding of the contribution of cold storage conditions to milk microbiota formation. This study may assist dairy producers in improving raw milk and raw milk cheeses quality and guaranteeing consumers’ safety.

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High-throughput sequencing analysis of bacterial diversity in raw and pasteurized goat milk

10.1101/751149 ◽

2019 ◽

Cited By ~ 1

Author(s):

Feng Huang ◽

Siqi Liu ◽

Xiaokang Zhou ◽

Pengfei Wang ◽

Rengchun He ◽

...

Keyword(s):

Bacterial Diversity ◽

High Throughput ◽

High Throughput Sequencing ◽

Bacterial Species ◽

Goat Milk ◽

Raw Milk ◽

Sequencing Analysis ◽

Quality And Safety ◽

Microbial Composition ◽

High Throughput Dna Sequencing

AbstractThe aim of this study was to evaluate the microbial composition of both raw and pasteurized goat milk using high-throughput DNA sequencing. This analysis revealed that the dominant phylum found in the raw milk was Proteobacteria, and the dominant genus was Kluyvera; Proteobacteria and Kluyvera constituted up to 67.66% and 28.85% of the total bacteria population, respectively. The microorganisms in goat milk predominantly consist of Gram-negative bacteria. Notably, Akkermansia and Faecalibacterium were identified in goat milk for the first time. In addition, the results also indicate that some bacteria in pasteurized goat milk may exist in a viable but nonculturable (VBNC) state. This study provides a theoretical basis that may aid the community in better understanding bacterial diversity in goat milk. The results of this study will help us to improve the quality and safety of goat milk.ImportanceThe microbial diversity in goat milk and pasteurized goat milk at different refrigeration stages was described. Several bacterial species that have not previously been reported in goat milk were identified, including many VBNC bacteria. The findings provided the necessary microbial information for quality and safety of goat milk and dairy products.

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Characterization of oral bacterial diversity of irradiated patients by high-throughput sequencing

International Journal of Oral Science ◽

10.1038/ijos.2013.15 ◽

2013 ◽

Vol 5 (1) ◽

pp. 21-25 ◽

Cited By ~ 15

Author(s):

Yue-Jian Hu ◽

Qian Wang ◽

Yun-Tao Jiang ◽

Rui Ma ◽

Wen-Wei Xia ◽

...

Keyword(s):

Bacterial Diversity ◽

High Throughput ◽

High Throughput Sequencing

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Microbial diversity in raw milk and Sayram Ketteki from southern of Xinjiang, China

10.1101/2021.03.15.435442 ◽

2021 ◽

Author(s):

Dongla Gao ◽

Weihua Wang ◽

Zhanjiang Han ◽

Qian Xi ◽

Ruicheng Guo ◽

...

Keyword(s):

High Throughput ◽

Fungal Community ◽

High Throughput Sequencing ◽

Principal Component ◽

Raw Milk ◽

Fermented Milk ◽

Community Diversity ◽

Sampling Location ◽

Fungal Community Structure ◽

Microbial Resources

Raw milk and fermented milk are rich in microbial resources, which are essential for the formation of texture, flavor and taste. In order to gain a deeper knowledge of the bacterial and fungal community diversity in local raw milk and home-made yogurts from Sayram town, Baicheng county, Akesu area, southern of Xinjiang, China,30 raw milk and 30 home-made yogurt samples were collected and experiment of high-throughput sequencing was implemented.The results of experiments revealed the species of fungi in raw milk was the most, and the species of bacteria in fermented milk was the least.Based on principal component analysis (PCA), it was found that the bacterial and fungal community structure differed in samples from two types of dairy products.And the presence of 15 bacterial and 12 fungal phyla, comprising 218 bacterial and 495 fungal genera respectively, among all samples. Firmicutes and Ascomycota,Lactobacillus and Candida were the predominant phyla and genera of bacteria and fungi, respectively. The results indicated that the microbial community of raw milk differs from home-made yogurts due to sampling location and manufacturing process. The study suggested that high-throughput sequencing could provide a better understanding of microbiological diversity as well as lay a theoretical foundation for selecting beneficial microbial resources from this natural yogurt.

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Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities

Scientific Reports ◽

10.1038/s41598-019-56690-7 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

S. Le Guillou ◽

A. Leduc ◽

J. Laubier ◽

S. Barbey ◽

M.-N. Rossignol ◽

...

Keyword(s):

Lipid Metabolism ◽

Milk Production ◽

High Throughput ◽

Genetic Background ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

Whole Milk ◽

Mammary Morphogenesis ◽

Regulatory Properties

AbstractThe concept of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, molecules with broad regulatory properties present in large quantities in milk. Characterization of these components has been performed in several species, such as humans and bovine, depending on the stages of lactation. Here, we have studied the variation in milk microRNA composition according to genetic background. Using high throughput sequencing, we have characterized and compared the milk miRNomes of Holstein and Normande cattle, dairy breeds with distinct milk production features, in order to highlight microRNAs that are essential for regulation of the lactation process. In Holstein and Normande milk, 2,038 and 2,030 microRNAs were identified, respectively, with 1,771 common microRNAs, of which 1,049 were annotated and 722 were predicted. The comparison of the milk miRNomes of two breeds allowed to highlight 182 microRNAs displaying significant differences in the abundance. They are involved in the regulation of lipid metabolism and mammary morphogenesis and development, which affects lactation. Our results provide new insights into the regulation of molecular mechanisms involved in milk production.

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