The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility

Kable, Mary E.; Srisengfa, Yanin; Laird, Miles; Zaragoza, José J.; McLeod, J. W.; Heidenreich, J.; Marco, Maria L.

doi:10.1128/mbio.00836-16

Cited by 129 publications

(141 citation statements)

References 85 publications

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“…Streptococcus was the most abundant bacterial genus in the milk on both sampling dates, as was previously observed for raw milk in tanker trucks delivered to the same facility (20). Because this genus was consistently found in milk from all pieces of equipment, including among the viable cells measured after pasteurization, our findings support the work of others showing the persistence of this genus in milk during the manufacture of cheese and other dairy products (13,23).…”

Section: Discussionsupporting

confidence: 89%

“…We previously reported that milk produced and transported in tanker trucks in central California contains a highly diverse assemblage of bacteria that is subject to modification over relatively short periods of time in storage silos at dairy processing facilities (20). Here, we characterized the bacterial diversity in milk as it passes through different processing stages at a large-scale dairy facility prior to the final pasteurization step used in cheese manufacture.…”

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confidence: 99%

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Viable and Total Bacterial Populations Undergo Equipment- and Time-Dependent Shifts during Milk Processing

Kable

Srisengfa

Xue

et al. 2019

Appl Environ Microbiol

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We set out to identify the viable and total bacterial content in milk as it passes through a large-scale, dairy product manufacturing plant for pasteurization, concentration, separation, blending, and storage prior to cheese manufacture. A total of 142 milk samples were collected from up to 10 pieces of equipment for a period spanning 21 h on two collection dates in the spring and late summer of 2014. Bacterial composition in the milk was determined by 16S rRNA marker gene, highthroughput DNA sequencing. Milk samples from the late summer were paired such that half were treated with propidium monoazide (PMA) to enrich for viable cells prior to quantification by PCR and identification by DNA sequence analysis. Streptococcus had the highest median relative abundance across all sampling sites within the facility on both sampling dates. The proportions of Anoxybacillus, Thermus, Lactococcus, Lactobacillus, Micrococcaceae, and Pseudomonas were also elevated in some samples. Viable cells detected by PMA treatment showed that Turicibacter was enriched after high-temperature short-time pasteurization, whereas proportions of Staphylococcus were significantly reduced. Using clean-in-place (CIP) times as a reference point, Bacillus, Pseudomonas, and Anoxybacillus were found in high relative proportions in several recently cleaned silos (Ͻ19 h since CIP). At later times (Ͼ19 h after CIP), 10 of 11 silos containing elevated viable cell numbers were enriched in Acinetobacter and/or Lactococcus. These results show the tremendous point-to-point and sample-dependent variations in bacterial composition in milk during processing. IMPORTANCE Milk undergoes sustained contact with the built environment during processing into finished dairy products. This contact has the potential to influence the introduction, viability, and growth of microorganisms within the milk. Currently, the population dynamics of bacteria in milk undergoing processing are not well understood. Therefore, we measured for total and viable bacterial composition and cell numbers in milk over time and at different processing points in a cheese manufacturing facility in California. Our results provide new perspectives on the dramatic variations in microbial populations in milk during processing even over short amounts of time. Although some of the changes in the milk microbiota were predictable (e.g., reduced viable cell numbers after pasteurization), other findings could not be easily foreseen based on knowledge of bacteria contained in raw milk or when the equipment was last cleaned. This information is important for predicting and controlling microbial spoilage contaminants in dairy products.

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Section: Discussionsupporting

confidence: 89%

mentioning

confidence: 99%

Viable and Total Bacterial Populations Undergo Equipment- and Time-Dependent Shifts during Milk Processing

Kable

Srisengfa

Xue

et al. 2019

Appl Environ Microbiol

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“…In this study, the less prevalent genera in goat milk constituted a significant proportion of the total bacterial population; this result is similar to results published in other reports (Kable et al, 2016; Quigley et al, 2013).…”

Section: Discussionsupporting

confidence: 92%

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

Huang

Liu

Zhou

et al. 2019

Preprint

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The 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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“…The 16S rRNA V4 region was amplified as previously described [31] using primers F515 and R806 [32]. A unique eight nucleotide Hamming code sequence was included on the 5’ end of F515 [33, 34] for amplification of each sample.…”

Section: Methodsmentioning

confidence: 99%

Impact of sequence variant detection and bacterial DNA extraction methods on the measurement of microbial community composition in human stool

Hughes

Alkan

Keim

et al. 2017

Preprint

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BackgroundThe human gut microbiome has been widely studied in the context of human health and metabolism, however the question of how to analyze this community remains contentious. This study compares new and previously well established methods aimed at reducing bias in bioinformatics analysis (QIIME 1 and DADA2) and bacterial DNA extraction of human fecal samples in 16S rRNA marker gene surveys.ResultsAnalysis of a mock DNA community using DADA2 identified more chimeras (QIIME 1: 0.70% of total reads vs DADA2: 1.96%), fewer sequence variants, (QIIME 1: 1297.4 + 98.88 vs. DADA2: 136.27 + 11.35, mean + SD) and correct taxa at a higher resolution of classification (i.e. genus-level) than open reference OTU picking in QIIME 1. Additionally, the extraction of whole cell mock community bacterial DNA using four commercially available kits resulted in varying DNA yield, quality and bacterial community composition. Of the four kits compared, ZymoBIOMICS DNA Miniprep Kit provided the greatest yield, with a slight enrichment of Enterococcus. However, QIAamp Fast DNA Stool Mini Kit resulted in the highest DNA quality. Mo Bio PowerFecal DNA Kit had the most dramatic effect on the mock community composition, resulting in an increased proportion of members of the family Enterobacteriaceae and genus Eshcerichia as well as members of genera Lactobacillus and Pseudomonas. The presence of a sterile fecal matrix had a slight, but inconsistent effect on the yield, quality and taxa identified after extraction with all four DNA extraction kits. Extraction of bacterial DNA from native stool samples revealed a distinct effect of the DNA stabilization reagent DNA/RNA Shield on community composition, causing an increase in the detected abundance of members of orders Bifidobacteriales, Bacteroidales, Turicibacterales, Clostridiales and Enterobacteriales.ConclusionThese results confirm that the DADA2 algorithm is superior to sequence clustering by similarity to determine microbial community structure. Additionally, commercially available kits used for bacterial DNA extraction from fecal samples have some effect on the proportion of high abundance members detected in a microbial community, but it is less significant than the effect of using DNA stabilization reagent, DNA/RNA Shield.

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The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility

Cited by 129 publications

References 85 publications

Viable and Total Bacterial Populations Undergo Equipment- and Time-Dependent Shifts during Milk Processing

Viable and Total Bacterial Populations Undergo Equipment- and Time-Dependent Shifts during Milk Processing

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

Impact of sequence variant detection and bacterial DNA extraction methods on the measurement of microbial community composition in human stool

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