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

ELife
Nicholas A BokulichDavid A Mills

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.

References

Apr 1, 1992·The Journal of Applied Bacteriology·W J Simpson, A R Smith
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 16, 2006·Journal of Applied Microbiology·K IijimaH Yamashita
Jun 26, 2007·Applied and Environmental Microbiology·Qiong WangJames R Cole
Apr 5, 2008·Canadian Journal of Microbiology·Monique Haakensen, Barry Ziola
Nov 3, 2009·Applied and Environmental Microbiology·Jürgen Behr, Rudi F Vogel
Nov 17, 2009·Bioinformatics·J Gregory CaporasoRob Knight
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Apr 23, 2010·The New Phytologist·Kessy AbarenkovUrmas Kõljalg
Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·J Gregory CaporasoRob Knight
Aug 17, 2010·Bioinformatics·Robert C Edgar
Jul 19, 2011·Nature Methods·Dan KnightsScott T Kelley
Dec 16, 2011·Bioinformatics·Antonio GonzalezRob Knight
Jul 27, 2012·BMB Reports·Nicholas A Bokulich, David A Mills
Dec 4, 2012·Nature Methods·Nicholas A BokulichJ Gregory Caporaso
Mar 22, 2013·Genome Biology·Scott T Kelley, Jack A Gilbert
May 24, 2013·Microbiology and Molecular Biology Reviews : MMBR·Nicholas A Bokulich, Charles W Bamforth
Jun 7, 2013·Journal of Clinical Microbiology·Nicholas A BokulichMark A Underwood
Jun 25, 2013·Applied and Environmental Microbiology·Nicholas A Bokulich, David A Mills
Jul 11, 2013·PloS One·Nicholas A BokulichDavid A Mills
Oct 3, 2013·Environmental Science & Technology·Robert M BowersNoah Fierer
Nov 30, 2013·Nucleic Acids Research·James R ColeJames M Tiedje
Feb 4, 2014·PloS One·Steven W KembelJessica L Green
Apr 22, 2014·PloS One·Freek SpitaelsPeter Vandamme
Jun 29, 2014·Applied and Environmental Microbiology·Nicholas A BokulichDavid A Mills
Dec 17, 2014·Applied and Environmental Microbiology·Jordyn BergsveinsonBarry Ziola

❮ Previous
Next ❯

Citations

Jan 17, 2016·Current Opinion in Biotechnology·Nicholas A BokulichDavid A Mills
Sep 5, 2015·Current Opinion in Genetics & Development·John G Gibbons, David C Rinker
Oct 7, 2016·Microbial Biotechnology·Francesca De FilippisDanilo Ercolini
Jan 27, 2017·Annual Review of Food Science and Technology·Aaron M WalshPaul D Cotter
Jan 20, 2018·Annual Review of Food Science and Technology·Francesca De FilippisDanilo Ercolini
Nov 14, 2017·F1000Research·Jonathan SobelGianpaolo Rando
Nov 7, 2016·Applied and Environmental Microbiology·Conor J DoylePaul D Cotter
Feb 3, 2019·Applied and Environmental Microbiology·Sophia Jiyuan ZhangLuc De Vuyst
Sep 15, 2017·Critical Reviews in Food Science and Nutrition·Lindsey Rodhouse, Franck Carbonero
Sep 2, 2018·Applied and Environmental Microbiology·Jonah E EinsonDavid A Sela
Jul 12, 2020·NPJ Biofilms and Microbiomes·Benjamin ZwirzitzEvelyne Selberherr
Dec 10, 2020·Food Research International·Magaly Rodríguez-SaavedraM Victoria Moreno-Arribas

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
electrophoresis

Software Mentioned

BLAST
ChimeraSlayer
ref
UCLUST
R
MiCA
Peak Scanner
SitePainter
PyNAST
Quantasoft

Related Concepts

Related Feeds

Biofilm & Infectious Disease

Biofilm formation is a key virulence factor for a wide range of microorganisms that cause chronic infections.Here is the latest research on biofilm and infectious diseases.

© 2022 Meta ULC. All rights reserved