Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder

Abstract

Microorganisms from the environment can enter the dairy supply chain at multiple stages, including production, milk collection, and processing, with potential implications for quality and safety. The ability to track these microorganisms can be greatly enhanced by the use of high-throughput DNA sequencing (HTS). Here HTS, both 16S rRNA gene amplicon and shotgun metagenomic sequencing were applied to investigate the microbiomes of fresh mid- and late-lactation milk collected from farm bulk tanks, collection tankers, milk silos, skimmed milk silos, a cream silo, and powder samples to investigate the microbial changes throughout a skim milk powder manufacturing process. 16S rRNA gene analysis established that the microbiota of raw milks from farm bulk tanks and in collection tankers were very diverse but that psychrotrophic genera associated with spoilage, Pseudomonas and Acinetobacter, were present in all samples. Upon storage within the whole-milk silo at the processing facility, the species Pseudomonas fluorescens and Acinetobacter baumannii became dominant. The skimmed milk powder generated during the mid-lactation period had a microbial composition that was very different from that of raw milk; specifically, two thermophilic genera, Thermus and Geobacillus, were enriched. In contrast, the microbiota of skimmed milk powder generated from late-lactation milk more closely resembled that of the raw milk and was dominated by spoilage-associated psychrotrophic bacteria. This study demonstrates that the dairy microbiota can differ significantly across different sampling days. More specifically, HTS can be used to trace microbial species from raw milks through processing to final powdered products. IMPORTANCE Microorganisms can enter and persist in dairy at several stages of the processing chain. Detection of microorganisms within dairy food processing is currently a time-consuming and often inaccurate process. This study provides evidence that high-throughput sequencing can be used as an effective tool to accurately identify microorganisms along the processing chain. In addition, it demonstrates that the populations of microbes change from raw milk to the end product. Routine implementation of high-throughput sequencing would elucidate the factors that influence population dynamics. This will enable a manufacturer to adopt control measures specific to each stage of processing and respond in an effective manner, which would ultimately lead to increased food safety and quality.

Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome

“…These MAGs provide essentially-complete genome information for key taxa present in the sample, revealing their functional and safety related properties 27 . However, shotgun sequencing, as an untargeted approach, sequences all the DNA in the sample, including that from the human or animal host, which in the case of milk represents a considerable majority (up to 95%) of the DNA present 28 . To address this challenge, previous shotgun metagenomic-based studies of the human milk microbiome 1 , 29 carried out sequencing at great depth, followed by post-processing of data to remove non-microbial reads using bioinformatic approaches.…”

Impacts of Milking and Housing Environment on Milk Microbiota

“…may cause mild to severe illnesses [ 5 ]. Microorganisms may contaminate raw milk during milking, transportation, storage and processing, which pose a serious threat to the quality and safety of milk and milk products [ 6 , 7 , 8 , 9 , 10 ].…”

Gaps in the assortment of rapid assays for microorganisms of interest to the dairy industry

“…flavithermus ), Geobacillus (of particular relevance to the dairy industry is G . stearothermophilis ) and Paenibacillus ( Doyle et al, 2015 ; McHugh et al, 2020 ). The vegetative cells of sporeformers, once they germinate and begin to grow, display preferences for growth at certain temperatures, leading to the sub-classification of sporeformers into groups based on this ( Boor et al, 2017 ).…”

“…cereus and C . perfringens ) in milk powders (which can regularly contain up to 100 endospores/g, Eijlander et al, 2019 ), especially those destined for infant formula will also assume greater importance ( McHugh et al, 2020 ).…”