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Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance.

Bokulich NA, Bergsveinson J, Ziola B, Mills DA - Elife (2015)

Bottom Line: Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment.Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk.Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Science and Technology, University of California, Davis, Davis, United States.

ABSTRACT
Distinct microbial ecosystems have evolved to meet the challenges of indoor environments, shaping the microbial communities that interact most with modern human activities. Microbial transmission in food-processing facilities has an enormous impact on the qualities and healthfulness of foods, beneficially or detrimentally interacting with food products. To explore modes of microbial transmission and spoilage-gene frequency in a commercial food-production scenario, we profiled hop-resistance gene frequencies and bacterial and fungal communities in a brewery. We employed a Bayesian approach for predicting routes of contamination, revealing critical control points for microbial management. Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment. Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk. Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments.

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Related in: MedlinePlus

Lactic acid bacterial community composition on brewery surfaces, beers, and ingredients.LAB-TRFLP profiles of samples exhibiting high Lactobacillales relative abundance by 16S rRNA gene sequencing.DOI:http://dx.doi.org/10.7554/eLife.04634.010
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fig8: Lactic acid bacterial community composition on brewery surfaces, beers, and ingredients.LAB-TRFLP profiles of samples exhibiting high Lactobacillales relative abundance by 16S rRNA gene sequencing.DOI:http://dx.doi.org/10.7554/eLife.04634.010

Mentions: Results indicate that different surface and sample types exhibit distinct lactic acid bacterial patterns, corresponding to the substrates encountered at that site or contained in that sample (Figure 8). Wort samples contained a mixture of Lactobacillus delbrueckii, Lactobacillus sakei, Lactobacillus hilgardii, Leuconostoc mesenteroides, Lactococcus lactis, Streptococcus sp., and Bacillus sp. A, most of which were only rarely detected in other fermenting and bottled beer samples. Many of these species are also rarely found in beers (Bokulich and Bamforth, 2013), but instead appear associated with grain, hence their detection in wort. Coolship and fermenting sour beers (in this case coolship beers produced from different wort types) were dominated by Pediococcus and/or L. lindneri, corroborating previous studies of coolship beers in this brewery (Bokulich et al., 2012b). Fermenters and barrel surfaces that contacted these fermentations near the time of sampling exhibited similar communities, though Lactobacillus brevis and Lactobacillus sp. A were more common on these surfaces than in the beers or on other surfaces. Other sour and barrel-aged beers contained unique profiles, with involvement of other Lactobacillus species only weakly detected in coolship beers. Floor and packaging area surfaces contained a more diverse mixture of LAB, but primarily the L. lindneri, L. brevis, and L. delbrueckii detected in the wort and beer samples. Interestingly, only Pediococcus was detected on grain samples, though only weak amplification could be had from these samples, suggesting low LAB populations or inhibition of PCR by grain polyphenols, possibly suppressing the detection of less abundant populations. Hop pellet samples also contained a mixture of different LAB populations, including Pediococcus, L. lindneri, and L. brevis.10.7554/eLife.04634.010Figure 8.Lactic acid bacterial community composition on brewery surfaces, beers, and ingredients.


Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance.

Bokulich NA, Bergsveinson J, Ziola B, Mills DA - Elife (2015)

Lactic acid bacterial community composition on brewery surfaces, beers, and ingredients.LAB-TRFLP profiles of samples exhibiting high Lactobacillales relative abundance by 16S rRNA gene sequencing.DOI:http://dx.doi.org/10.7554/eLife.04634.010
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4352708&req=5

fig8: Lactic acid bacterial community composition on brewery surfaces, beers, and ingredients.LAB-TRFLP profiles of samples exhibiting high Lactobacillales relative abundance by 16S rRNA gene sequencing.DOI:http://dx.doi.org/10.7554/eLife.04634.010
Mentions: Results indicate that different surface and sample types exhibit distinct lactic acid bacterial patterns, corresponding to the substrates encountered at that site or contained in that sample (Figure 8). Wort samples contained a mixture of Lactobacillus delbrueckii, Lactobacillus sakei, Lactobacillus hilgardii, Leuconostoc mesenteroides, Lactococcus lactis, Streptococcus sp., and Bacillus sp. A, most of which were only rarely detected in other fermenting and bottled beer samples. Many of these species are also rarely found in beers (Bokulich and Bamforth, 2013), but instead appear associated with grain, hence their detection in wort. Coolship and fermenting sour beers (in this case coolship beers produced from different wort types) were dominated by Pediococcus and/or L. lindneri, corroborating previous studies of coolship beers in this brewery (Bokulich et al., 2012b). Fermenters and barrel surfaces that contacted these fermentations near the time of sampling exhibited similar communities, though Lactobacillus brevis and Lactobacillus sp. A were more common on these surfaces than in the beers or on other surfaces. Other sour and barrel-aged beers contained unique profiles, with involvement of other Lactobacillus species only weakly detected in coolship beers. Floor and packaging area surfaces contained a more diverse mixture of LAB, but primarily the L. lindneri, L. brevis, and L. delbrueckii detected in the wort and beer samples. Interestingly, only Pediococcus was detected on grain samples, though only weak amplification could be had from these samples, suggesting low LAB populations or inhibition of PCR by grain polyphenols, possibly suppressing the detection of less abundant populations. Hop pellet samples also contained a mixture of different LAB populations, including Pediococcus, L. lindneri, and L. brevis.10.7554/eLife.04634.010Figure 8.Lactic acid bacterial community composition on brewery surfaces, beers, and ingredients.

Bottom Line: Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment.Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk.Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Science and Technology, University of California, Davis, Davis, United States.

ABSTRACT
Distinct microbial ecosystems have evolved to meet the challenges of indoor environments, shaping the microbial communities that interact most with modern human activities. Microbial transmission in food-processing facilities has an enormous impact on the qualities and healthfulness of foods, beneficially or detrimentally interacting with food products. To explore modes of microbial transmission and spoilage-gene frequency in a commercial food-production scenario, we profiled hop-resistance gene frequencies and bacterial and fungal communities in a brewery. We employed a Bayesian approach for predicting routes of contamination, revealing critical control points for microbial management. Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment. Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk. Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments.

Show MeSH
Related in: MedlinePlus