Monitoring Seasonal Changes in Winery-Resident Microbiota

Bokulich, Nicholas A.; Ohta, Moe; Richardson, Paul M.; Mills, David A.

doi:10.1371/journal.pone.0066437

Cited by 166 publications

(132 citation statements)

References 51 publications

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“…Amplification and sequencing were performed as described previously for analysis of bacterial (26) and fungal communities (53). Briefly, the V4 domain of bacterial 16S rRNA genes was amplified using primers F515 (5′-NNNNNNNNGTGTGCCAGCMGCCGCGG-TAA-3′) and R806 (5′-GGACTACHVGGGTWTCTAAT-3′) (54), with the forward primer modified to contain a unique 8-nt barcode (italicized poly-N section of primer above) and a 2-nt linker sequence (bold portion) at the 5′ terminus.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Bokulich

Thorngate²,

Richardson³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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795

758

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Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grapevariety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.viticulture | agriculture | metagenomics | next-generation sequencing

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Section: Methodsmentioning

confidence: 99%

“…However, recent advances in massively parallel, short-amplicon sequencing technologies have launched a breakthrough in microbial ecology studies of wine-and foodfermentation systems (14,(21)(22)(23)(24)(25)(26)(27), putting hitherto untenable ecological questions within reach.…”

Section: Significancementioning

confidence: 99%

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Bokulich

Thorngate²,

Richardson³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

795

758

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show abstract

“…Moreover, the interplay between the wine microbiota and the microbiota of the fermentation facilities has been verified but not completely understood [6]. Due to this complexity of interactions between microorganisms in the wine itself, during fermentation, but also between wine microbiota and environment, the wine industry has adopted the use of starter cultures as a mean of control and quality improvement [7].…”

Section: Introductionmentioning

confidence: 99%

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

et al. 2018

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Abstract:In wine industry, there is a prevalent use of starter cultures to promote a controlled and efficient alcoholic fermentation preventing the growth of spoilage microbes. However, current trends in enology aim to combine the guaranteed success of monitored process and the complexity of fermentations either by inoculating autochthonous starters or by performing spontaneously to produce distinctive wines. To understand the complex roles of microorganisms on wine fermentation, we must understand their population dynamics and their relationships with wine quality and metabolome. Current metagenomics techniques based on massive sequencing are gaining relevance to study the diversity and evolution of microbial population on every stage of the wine making process. This new tool and technique increases the throughput and sensitivity to study microbial communities. This review focuses on the current knowledge about wine alcoholic fermentation, the contribution of massive sequencing techniques and the possibility of using this tool for microbial control.

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“…Using these culture-based techniques, Vacheyrou previously examined possible routes of microbial transfer in farms supplying raw milk for Comte style cheese, revealing that the extent to which milk was contaminated varied depending on the type of barns used to house animals (2). However, recent advances in molecular microbiology, and in high-throughput DNA sequencing (HTS) in particular, have allowed for a more in-depth analysis of the flow of microbes through environments (7)(8)(9)(10)(11)(12).…”

mentioning

confidence: 99%

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

Doyle

Gleeson

O’Toole

et al. 2017

Appl Environ Microbiol

134

121

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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. IMPORTANCEThe 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.KEYWORDS farm practices, food chain, food safety, metagenomics, microbial source tracking, raw milk microbiota T he impact of the dairy farm environment on the microbial composition of raw milk and raw milk products has been appreciated for some time (1). There are numerous niches that collectively constitute the dairy farm environment, and these harbor a vast array of microbes. The transfer of microbes from the farm environment to raw milk can be influenced be a number of factors, including farmer hygiene, husbandry practices,

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Monitoring Seasonal Changes in Winery-Resident Microbiota

Cited by 166 publications

References 51 publications

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

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