Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AEM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Applied and Environmental Microbiology
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AEM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
Food Microbiology

Dynamics and Biodiversity of Bacterial and Yeast Communities during Fermentation of Cocoa Beans

Jatziri Mota-Gutierrez, Cristian Botta, Ilario Ferrocino, Manuela Giordano, Marta Bertolino, Paola Dolci, Marcella Cannoni, Luca Cocolin
Johanna Björkroth, Editor
Jatziri Mota-Gutierrez
aDepartment of Agricultural, Forest, and Food Science, University of Turin, Grugliasco, Turin, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Cristian Botta
aDepartment of Agricultural, Forest, and Food Science, University of Turin, Grugliasco, Turin, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ilario Ferrocino
aDepartment of Agricultural, Forest, and Food Science, University of Turin, Grugliasco, Turin, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Manuela Giordano
aDepartment of Agricultural, Forest, and Food Science, University of Turin, Grugliasco, Turin, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marta Bertolino
aDepartment of Agricultural, Forest, and Food Science, University of Turin, Grugliasco, Turin, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paola Dolci
aDepartment of Agricultural, Forest, and Food Science, University of Turin, Grugliasco, Turin, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marcella Cannoni
bSoremartec Italia S.r.l., Alba, Cuneo, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luca Cocolin
aDepartment of Agricultural, Forest, and Food Science, University of Turin, Grugliasco, Turin, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Johanna Björkroth
University of Helsinki
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/AEM.01164-18
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Additional Files
  • FIG 1
    • Open in new tab
    • Download powerpoint
    FIG 1

    Dynamics of the sugar and organic acid compounds in the cocoa bean pulp inoculated and noninoculated during box and heap fermentations, expressed as milligrams per gram. Data are expressed as mean ± standard deviation (SD) values from triplicate determinations. (A) Sucrose; (B) glucose; (C) fructose; (D) citric acid; (E) succinic acid; (F) malic acid; (G) acetic acid; (H) gluconic acid; and (I) lactic acid.

  • FIG 2
    • Open in new tab
    • Download powerpoint
    FIG 2

    Spearman's correlation between the microbial OTUs observed with an incidence >1% in at least 2 samples. The samples are labeled according to the box (A) and heap (B) fermentation methods. Rows and columns are clustered by means of Ward's linkage hierarchical clustering. The intensity of the colors represents the degree of correlation between the fungal and bacterial OTUs, as measured by Spearman's correlation. The intensity of the colors represents the degree of correlation between the yeast and bacteria, where blue represents a negative degree of correlation and red a positive degree of correlation.

  • FIG 3
    • Open in new tab
    • Download powerpoint
    FIG 3

    Correlation plot showing Spearman's correlation between the microbial OTUs and metabolites observed with an incidence >1% in at least 2 samples. The samples are labeled according to the box (A) and heap (B) fermentation methods. Only significant associations between the OTUs and metabolites are shown (P < 0.05). The intensity of the colors represents the degree of correlation between the fungal and bacterial OTUs, as measured by Spearman's correlation, where the blue color represents a positive degree of correlation and red a negative correlation between the sugars, organic acids, and OTUs.

Tables

  • Figures
  • Additional Files
  • TABLE 1

    Average changes in the physical and microbiological parameters during the inoculated and noninoculated box and heap fermentations of cocoa bean pulp turned after 48 and 96 h

    Parameter by fermentationInoculationaData by fermentation time (h)b
    04896120
    Box
        °CS26.73 ± 0.6036.20 ± 1.5341.88 ± 1.7843.70 ± 2.94
    ST26.48 ± 0.3435.10 ± 2.4641.73 ± 2.0642.78 ± 3.68
    C26.73 ± 0.6236.20 ± 1.5341.88 ± 1.7843.70 ± 2.94
    Avg26.58 ± 0.08 C35.80 ± 1.22 B42.09 ± 0.50 A43.33 ± 0.70 A
        pHS3.55 ± 0.033.88 ± 0.164.15 ± 0.113.96 ± 0.18
    ST3.54 ± 0.014.00 ± 0.164.20 ± 0.154.18 ± 0.26
    C3.55 ± 0.033.88 ± 0.174.27 ± 0.113.96 ± 0.18
    Avg3.57 ± 0.03 C4.08 ± 0.11 B4.31 ± 0.09 A4.15 ± 0.17 AB
        Log CFU
            YeastS7.08 ± 0.057.19 ± 0.15NCNC
    ST7.14 ± 0.017.05 ± 0.06NCNC
    C7.19 ± 0.177.55 ± 0.27NCNC
    Avg7.14 ± 0.11 A7.26 ± 0.29 ANCNC
            LABS5.38 ± 0.307.18 ± 0.025.11 ± 1.286.75 ± 0.17
    ST6.13 ± 0.226.85 ± 0.274.33 ± 0.387.35 ± 0.25
    C6.21 ± 0.746.88 ± 0.404.00 ± 0.005.49 ± 0.59
    Avg5.91 ± 0.61 B6.97 ± 0.31 A5.44 ± 2.85 C6.55 ± 0.94 A
            AABS6.41 ± 0.117.01 ± 0.125.54 ± 1.785.63 ± 1.88
    ST6.28 ± 0.216.96 ± 0.065.60 ± 1.847.34 ± 0.09
    C6.28 ± 0.257.31 ± 0.264.00 ± 0.005.76 ± 0.49
    Avg6.32 ± 0.20 A7.09 ± 0.23 A5.05 ± 2.01 B6.69 ± 2.85 A
    Heap
        °CS28.20 ± 1.1538.17 ± 0.7536.57 ± 1.8040.07 ± 0.12
    ST27.37 ± 0.3239.00 ± 2.2136.57 ± 0.9039.38 ± 0.32
    C26.27 ± 0.0638.97 ± 0.3239.37 ± 2.5740.30 ± 0.56
    Avg27.28 ± 0.97 C38.71 ± 0.47 B38.40 ± 1.59 B40.07 ± 0.23 A
        pHS3.55 ± 0.014.24 ± 0.174.48 ± 0.794.90 ± 0.97
    ST3.53 ± 0.014.32 ± 0.234.05 ± 0.404.52 ± 0.74
    C3.50 ± 0.053.87 ± 0.084.24 ± 0.293.99 ± 0.33
    Avg3.54 ± 0.02 B4.28 ± 0.24 A4.26 ± 0.21 A4.71 ± 0.90 A
        Log CFU
            YeastS7.16 ± 0.927.80 ± 0.157.13 ± 0.168.03 ± 0.29
    ST6.76 ± 0.857.72 ± 0.157.24 ± 1.417.43 ± 0.07
    C7.02 ± 0.716.62 ± 0.026.34 ± 0.047.24 ± 0.28
    Avg6.98 ± 0.20 C7.38 ± 0.66 B6.90 ± 0.48 D7.57 ± 0.41 A
            LABS5.67 ± 0.257.28 ± 0.197.36 ± 0.047.69 ± 0.28
    ST5.95 ± 0.297.07 ± 0.097.00 ± 0.017.50 ± 0.04
    C5.72 ± 0.036.17 ± 0.217.40 ± 0.048.10 ± 0.13
    Avg5.78 ± 0.15 D6.84 ± 0.59 C7.25 ± 0.22 B7.76 ± 0.30 A
            AABS6.20 ± 0.236.81 ± 0.148.33 ± 0.027.80 ± 0.18
    ST5.70 ± 0.047.15 ± 0.288.08 ± 0.117.66 ± 0.01
    C6.60 ± 0.045.65 ± 0.158.42 ± 0.028.56 ± 0.04
    Avg6.17 ± 0.45 D6.54 ± 0.79 C8.28 ± 0.18 A8.00 ± 0.49 B
    • ↵a S, S. cerevisiae; ST, S. cerevisiae and T. delbrueckii; C, noninoculated.

    • ↵b Values are expressed as the mean ± SD from triplicate determinations. Different letters indicate statistical differences related to the fermentation period using the least significant difference test (P < 0.05). P values were adjusted using Bonferroni's method. NC, below the detection limit.

  • TABLE 2

    Incidence of the fungal taxonomic groups, achieved by means of amplicon sequencing, expressed as relative abundancesa

    Taxonomic groupRelative abundance
    S. cerevisiaeS. cerevisiae + T. delbrueckiiNoninoculated
    BoxHeapBoxHeapBoxHeap
    T0T48T96T120T0T48T96T120T0T48T96T120T0T48T120T0T48T96T120T0T48T96T120
    Botryosphaeria1.330.430.460.210.591.550.130.130.530.440.913.510.560.320.590.660.201.080.1611.070.000.470.12
    Candida3.331.351.211.271.030.460.310.741.890.970.775.560.530.340.722.831.482.590.490.890.241.391.73
    Candida butyri2.230.270.420.500.160.030.070.090.770.690.340.400.150.040.070.700.211.160.090.070.000.070.03
    Candida diversa0.000.000.000.000.010.000.000.000.000.000.005.500.000.000.000.001.000.960.000.000.000.000.00
    Candida inconspicua0.000.582.637.820.060.030.250.320.000.741.5112.970.000.040.940.032.610.9613.470.000.871.621.43
    Candida jaroonii13.074.403.631.244.011.650.591.008.063.802.291.243.411.551.964.342.183.040.861.890.241.270.80
    Candida quercitrusa2.271.030.780.321.310.940.320.811.400.721.170.491.270.991.342.431.081.040.160.470.091.460.89
    Ceratocystis3.085.982.931.421.430.990.500.502.462.912.913.411.271.562.324.192.459.324.812.070.871.530.80
    Hanseniaspora opuntiae38.3340.9839.7228.2149.7639.1048.6764.3736.7837.2515.620.3843.7329.5111.7054.2148.1129.1321.7869.2272.3535.0544.81
    Issatchenkia0.090.000.000.000.000.000.000.000.000.000.001.270.250.000.370.000.410.370.000.000.002.461.18
    Kluyveromyces marxianus0.000.280.188.910.060.1311.181.790.000.420.3815.760.000.132.800.014.611.0343.540.097.767.231.98
    Lasiodiplodia theobromae0.830.612.071.330.490.490.090.073.300.911.220.900.800.090.254.940.610.920.270.100.160.070.16
    Penicillium0.620.391.090.160.190.130.000.060.120.160.310.250.100.190.270.550.120.240.100.150.020.520.21
    Pichia0.560.090.050.160.120.120.010.780.060.090.150.600.070.010.490.370.410.550.190.190.001.211.28
    Pichia pijperi10.9010.2312.7515.3610.2114.556.798.427.679.579.0518.0113.6218.3517.1311.3210.9114.248.3810.376.2929.4224.14
    Saccharomyces cerevisiae12.9528.6228.3030.2226.0837.6730.2919.117.7321.5031.9715.987.6721.5733.960.2819.9527.123.350.3710.2811.9217.96
    Saccharomycopsis0.720.350.320.150.130.150.070.131.120.300.320.030.270.100.320.820.491.210.220.520.130.320.34
    Torulaspora delbrueckii0.060.010.040.010.030.000.010.0425.3516.3228.188.4823.0220.4522.500.020.070.270.030.120.090.130.09
    • ↵a Only OTUs with an incidence above 1% in at least 2 samples are shown. Values are expressed as the mean of duplicate determinations. The abundances of OTUs in the 2 biological replicates of each sampling time were averaged. Samples are labeled according to the fermentation period (0 h [T0], 48 h [T48], 96 h [T96], and 120 h [T120]), fermentation method (box and heap), and condition (inoculated with S, inoculated with ST, and noninoculated).

  • TABLE 3

    Classification at the family/genus level of the occurrence of the bacterial taxonomic groups, achieved by means of amplicon sequencing, expressed as relative abundancesa

    Taxonomic groupRelative abundance
    S. cerevisiaeS. cerevisiae + T. delbrueckiiNoninoculated
    BoxHeapBoxHeapBoxHeap
    T0T48T96T120T0T48T96T120T0T48T96T120T0T48T96T120T0T48T96T120T0T48T96T120
    Acetobacter pasteurianus3.1613.8162.9052.831.0540.2776.9969.223.0242.6763.4286.960.9657.2479.1924.742.4018.2242.6764.244.7028.5236.6745.93
    Acetobacteraceae0.191.731.011.290.0016.876.235.080.294.700.861.050.1011.794.410.860.100.583.452.400.385.421.440.10
    Acinetobacter0.000.000.000.000.000.000.000.290.000.000.050.000.000.000.004.990.000.000.000.000.000.000.050.00
    Acinetobacter guillouiae0.240.000.000.000.000.000.000.860.100.000.100.000.000.000.001.250.000.000.000.000.050.000.000.14
    Acinetobacter rhizosphaerae0.000.000.000.000.000.000.191.440.000.000.000.000.000.000.001.250.000.000.000.000.050.000.190.24
    Bacillus0.000.000.0016.350.000.000.000.770.000.0011.940.290.000.000.003.360.000.100.004.410.050.000.968.96
    Dyella1.680.580.100.140.770.100.000.000.430.380.100.000.190.190.000.001.250.290.580.190.961.100.530.14
    Enterobacteriaceae3.261.341.200.290.000.000.000.100.960.580.100.000.190.000.000.101.821.530.580.192.211.530.620.34
    Erwinia4.941.681.100.530.190.190.000.001.630.720.190.000.290.100.000.003.451.530.770.582.301.821.050.34
    Gluconobacter3.361.250.380.051.631.340.380.194.071.150.050.102.971.250.380.102.400.670.580.002.881.340.100.10
    Klebsiella0.340.430.190.240.000.000.190.191.100.190.100.000.000.000.100.481.251.150.480.100.380.340.343.93
    Lactobacillaceae0.052.063.881.200.000.380.000.100.051.680.960.000.000.100.190.100.105.372.211.250.190.621.100.34
    Lactobacillus plantarum group1.4415.5812.274.310.002.110.380.190.9110.741.920.670.001.150.191.630.5828.5714.095.470.293.746.621.49
    Lactobacillus fermentum0.1931.593.408.630.0010.077.195.750.146.1410.121.440.009.206.9012.180.103.550.587.000.0530.8713.7116.73
    Lysinibacillus0.000.000.000.580.000.000.000.670.000.001.630.000.000.000.000.960.000.000.000.670.000.000.190.05
    Trabulsiella5.133.122.491.530.380.290.000.002.640.810.530.190.580.100.000.105.751.731.530.862.974.120.960.38
    • ↵a Only OTUs with an incidence above 1% in at least 2 samples are shown. Values are expressed as the mean of duplicate determinations. The abundances of OTUs in the 2 biological replicates of each sampling time were averaged. Samples are labeled according to the fermentation period (0 h [T0], 48 h [T48], 96 h [T96], and 120 h [T120]), fermentation method (box and heap), and condition (inoculated with S, inoculated with ST, and noninoculated).

Additional Files

  • Figures
  • Tables
  • Supplemental material

    • Supplemental file 1 -

      Relative percentages of volatile compounds (Table S1); yeast community of fermented cocoa beans (Table S2); bacterial community of fermented cocoa beans (Table S3).

      PDF, 622K

PreviousNext
Back to top
Download PDF
Citation Tools
Dynamics and Biodiversity of Bacterial and Yeast Communities during Fermentation of Cocoa Beans
Jatziri Mota-Gutierrez, Cristian Botta, Ilario Ferrocino, Manuela Giordano, Marta Bertolino, Paola Dolci, Marcella Cannoni, Luca Cocolin
Applied and Environmental Microbiology Sep 2018, 84 (19) e01164-18; DOI: 10.1128/AEM.01164-18

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print

Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Applied and Environmental Microbiology article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Dynamics and Biodiversity of Bacterial and Yeast Communities during Fermentation of Cocoa Beans
(Your Name) has forwarded a page to you from Applied and Environmental Microbiology
(Your Name) thought you would be interested in this article in Applied and Environmental Microbiology.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Dynamics and Biodiversity of Bacterial and Yeast Communities during Fermentation of Cocoa Beans
Jatziri Mota-Gutierrez, Cristian Botta, Ilario Ferrocino, Manuela Giordano, Marta Bertolino, Paola Dolci, Marcella Cannoni, Luca Cocolin
Applied and Environmental Microbiology Sep 2018, 84 (19) e01164-18; DOI: 10.1128/AEM.01164-18
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • INTRODUCTION
    • RESULTS
    • DISCUSSION
    • MATERIALS AND METHODS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

KEYWORDS

cocoa beans
HTS
bacteria
fermentation
nonvolatile organic compounds
volatile organic compounds
yeast

Related Articles

Cited By...

About

  • About AEM
  • Editor in Chief
  • Editorial Board
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Ethics
  • Contact Us

Follow #AppEnvMicro

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

 

Print ISSN: 0099-2240; Online ISSN: 1098-5336