Single Molecule Real-Time Sequencing and Traditional Cultivation Techniques Reveal Complex Community Structures and Regional Variations of Psychrotrophic Bacteria in Raw Milk

Du, Bingyao; Meng, Lu; Liu, Huimin; Zheng, Nan; Zhang, Yangdong; Zhao, Shengguo; Wang, Jiaqi

doi:10.3389/fmicb.2022.853263

Cited by 3 publications

(2 citation statements)

References 34 publications

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“…Moreover, the dominant fungal species in soybean kefir grains was Kazachstania unispora (>97%). Clustering heat map analysis was performed for a further exploration of the differences in the bacterial and fungal community structures of the two groups ( Figure 3 C,B) [ 25 , 26 ]. The results reflected that the dominant strains and community structures of bacteria and fungi in kefir grains obviously varied depending on the growing culture.…”

Section: Resultsmentioning

confidence: 99%

Microbial Community Variations and Bioconversion Improvements during Soybean-Based Fermentation by Kefir Grains

Luo

Liu

et al. 2023

Foods

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Soybeans possess unexpected flavors and are difficult to be absorbed by the gastrointestinal tract. Kefir grain fermentation provides diverse strains and bioactive compounds, which may enhance flavor and bioaccessibility. Third-generation sequencing was applied to analyze the microbial diversity in milk and soybean kefir grains in this study. In both types of kefir grains, the most common bacterial genus was Lactobacillus, and their fungal communities were dominated by Kazachstania. Lactobacillus kefiranofaciens was the most abundant species in kefir grains, while Lactobacillus kefiri showed a higher proportion in soybean kefir grains. In addition, the quantification of free amino acids and volatile flavor compounds in soybean solution and soybean kefir have shown the increased content of glutamic acid and a decreased amount of unpleasant beany flavor compounds, demonstrating that the nutritive value and sensory properties of soybean can be improved by kefir grain fermentation. Finally, the bioconversion of isoflavones during fermentation and in vitro digestion was evaluated, suggesting that fermentation is beneficial for aglycone formation and absorption. To conclude, kefir fermentation is proposed to change the microbial structure of kefir grains, promote the nutritional value of soybean-based fermented products, and provide possible solutions for the development of soybean products.

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Section: Resultsmentioning

confidence: 99%

Microbial Community Variations and Bioconversion Improvements during Soybean-Based Fermentation by Kefir Grains

Luo

Liu

et al. 2023

Foods

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“…The development of high-throughput sequencing technology for 16S rRNA high-variability regions has provided relatively comprehensive community taxonomic information, which has been widely applied in the field of dairy microbial applied research. This includes correlations between specific dairy processing techniques and microbial community structures [ 11 ], an overview of the formation of microbial diversity in the production process of dairy enterprises [ 12 ], changes in microbial communities during the production process [ 13 , 14 , 15 ], and characteristic microbial communities in specific dairy products [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

Dynamic Interplay between Microbiota Shifts and Differential Metabolites during Dairy Processing and Storage

Zhang,

Yu,

Tao

2024

Molecules

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Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy quality using traditional methods is challenging. In this study, raw milk, pasteurized milk, and ultra-heat-treated (UHT) milk samples were collectively analyzed using metagenomic next-generation sequencing (mNGS), high-throughput liquid chromatography-mass spectrometry (LC-MS), and gas chromatography–mass spectrometry (GC-MS). The results revealed that raw milk and its corresponding heated dairy products exhibited different trends in terms of microbiota shifts and metabolite changes during storage. Via the analysis of differences in microbiota and correlation analysis of the microorganisms present in differential metabolites in refrigerated pasteurized milk, the top three differential microorganisms with increased abundance, Microbacterium (p < 0.01), unclassified Actinomycetia class (p < 0.05), and Micrococcus (p < 0.01), were detected; these were highly correlated with certain metabolites in pasteurized milk (r > 0.8). This indicated that these genera were the main proliferating microorganisms and were the primary genera involved in the metabolism of pasteurized milk during refrigeration-based storage. Microorganisms with decreased abundance were classified into two categories based on correlation analysis with certain metabolites. It was speculated that the heat-resistant enzyme system of a group of microorganisms with high correlation (r > 0.8), such as Pseudomonas and Acinetobacter, was the main factor causing milk spoilage and that the group with lower correlation (r < 0.3) had a lower impact on the storage process of pasteurized dairy products. By comparing the metabolic pathway results based on metagenomic and metabolite annotation, it was proposed that protein degradation may be associated with microbial growth, whereas lipid degradation may be linked to raw milk’s initial heat-resistant enzymes. By leveraging the synergy of metagenomics and metabolomics, the interacting factors determining the quality evolution of dairy products were systematically investigated, providing a novel perspective for controlling dairy processing and storage effectively.

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Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods

Li,

Miao,

et al. 2024

Genes

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Milking methods have significant impacts on the microbiological composition, which could affect the quality of raw buffalo milk. Hence, the current study was conducted on the impact of milking methods on microorganisms in buffalo tank raw milk from 15 farms in Guangxi, China. The farms were divided into two groups based on the milking method: mechanical milking (MM, n = 6) and hand milking (HM, n = 9). Somatic cell counts, bacterial cell counts and nutrients of the raw buffalo milk samples were analyzed. The comparison of raw buffalo milk samples was analyzed using metagenomic sequencing to detect any differences between the two groups. There was no significant difference in the basic nutritional compositions and somatic cell count of raw buffalo milk between the two milking methods. However, the HM samples had significantly higher bacterial counts and diversity compared to the MM samples. The results showed that Staphylococcus spp., Klebsiella spp., Streptococcus spp., and Pseudomonas spp. were the major microbes present in canned raw buffalo milk. However, the differences between the two milking methods were the relative abundance of core microorganisms and their potential mastitis-causing genera, including the content of antibiotic-resistance genes and virulence genes. Our study revealed that Staphylococcus spp. and Streptococcus spp. were significantly more abundant in the MM group, while Klebsiella spp. was more abundant in the HM group. Regardless of the milking method used, Pseudomonas spp. was identified as the primary genus contributing to antibiotic resistance and virulence genes in canned raw buffalo milk. These findings affirm that there are differences in the microbial and genomic levels in canned raw milk. To prove the functional roles of the discovered genes and how these genes affect milk quality, further research and experimental validation are necessary.

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Single Molecule Real-Time Sequencing and Traditional Cultivation Techniques Reveal Complex Community Structures and Regional Variations of Psychrotrophic Bacteria in Raw Milk

Cited by 3 publications

References 34 publications

Microbial Community Variations and Bioconversion Improvements during Soybean-Based Fermentation by Kefir Grains

Microbial Community Variations and Bioconversion Improvements during Soybean-Based Fermentation by Kefir Grains

Dynamic Interplay between Microbiota Shifts and Differential Metabolites during Dairy Processing and Storage

Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods

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