Cited by 296Probiotics and Fermented FoodsFermentation and Sensory AnalysisMicrobial Community Ecology and Physiology

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Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants

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Bokulich, Nicholas A., Mills, David A.·2013·Applied and Environmental Microbiology

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Abstract

Cheese fermentations involve the growth of complex microbial consortia, which often originate in the processing environment and drive the development of regional product qualities. However, the microbial milieus of cheesemaking facilities are largely unexplored and the true nature of the fermentation-facility relationship remains nebulous. Thus, a high-throughput sequencing approach was employed to investigate the microbial ecosystems of two artisanal cheesemaking plants, with the goal of elucidating how the processing environment influences microbial community assemblages. Results demonstrate that fermentation-associated microbes dominated most surfaces, primarily Debaryomyces and Lactococcus, indicating that establishment of these organisms on processing surfaces may play an important role in microbial transfer, beneficially directing the course of sequential fermentations. Environmental organisms detected in processing environments dominated the surface microbiota of washed-rind cheeses maturing in both facilities, demonstrating the importance of the processing environment for populating cheese microbial communities, even in inoculated cheeses. Spatial diversification within both facilities reflects the functional adaptations of microbial communities inhabiting different surfaces and the existence of facility-specific "house" microbiota, which may play a role in shaping site-specific product characteristics.

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Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
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Search and clustering orders of magnitude faster than BLAST
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Anderson, M. J. (2001) · Austral Ecology · doi:10.1111/j.1442-9993.2001.01070.pp.x · Cited by 13,828
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,944
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Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S. K., Sodergren, E. J., et al. (2011) · Genome Research · doi:10.1101/gr.112730.110 · Cited by 3,527

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Additional file 2 of Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity
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Authors: Bokulich, N. A., & Mills, D. A.
Affiliations: University of California, Davis (US)
ORCID: Bokulich, Nicholas A.
Mills, David A.
Venue: Applied and Environmental Microbiology
Publisher: American Society for Microbiology
Published: 2013-09
Volume: 79
Issue: 17
Pages: 5214-5223
ISSN: 0099-2240 (ISSN-L)
1098-5336
DOI: 10.1128/aem.00934-13
PMC: PMC3753952
OpenAlex: W2134123776
Cited by: 295
References: 68
Citations by year: 2026: 16 · 2025: 25 · 2024: 23 · 2023: 25 · 2022: 28 · 2021: 32 · 2020: 27 · 2019: 19 · 2018: 30 · 2017: 25 · 2016: 13 · 2015: 19 · 2014: 11 · 2013: 1
FWCI: 21.85
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Applied and Environmental Microbiology (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
Life Sciences › Agricultural and Biological Sciences › Food Science › Fermentation and Sensory Analysis
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords: cheese fermentation, surface microbiota, Debaryomyces, Lactococcus, microbial transmission, spatial diversification, traditional cheese production
MeSH terms: Bacteria, Cheese, Environmental Microbiology, Fermentation, Fungi, Industrial Microbiology, Biota

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