A defined microbial community reproduces attributes of fine flavour chocolate fermentation

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Gopaulchan D., Moore C., Ali N., Sukha D., Florez González S.L., Herrera Rocha F.E., Yang N., Lim M., Dew T.P., González Barrios A.F., Umaharan P., Salt D.E., Castrillo G.
Journal
Nature microbiology
Year
2025
Cocoa (Theobroma cacao L.) bean fermentation is a spontaneous process involving interactions between abiotic and biotic factors that contribute to the final flavours of chocolate. Understanding these underlying interactions could enable desired flavour profiles to be reproduced under controlled conditions. Here, using bean fermentation samples from Colombian farms, we established that pH, temperature and microbiota composition, including both bacteria and fungi, influence key flavour attributes of premium chocolate. Genome-resolved metagenomics revealed that metabolic traits necessary for the development of the flavour profile of chocolate are redundantly present in the fermentation microbial community. Using a defined and metabolically competent microbial consortium, the feasibility of replicating fine flavour attributes of chocolate under controlled conditions was confirmed via omics, metabolic networks and a trained tasting panel. Our results provide the basis for the design of fermentation starters to robustly reproduce fine chocolate characteristics.

Experiment 1


Needs review

Curated date: 2025/09/30

Curator: YokoC

Revision editor(s): YokoC

Subjects

Location of subjects
Colombia
Host species Species from which microbiome was sampled. Contact us to have more species added.
Theobroma cacao
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Diet Dietary,Diets,Diet,diet
Group 0 name Corresponds to the control (unexposed) group for case-control studies
0 hrs fermentation
Group 1 name Corresponds to the case (exposed) group for case-control studies
24 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
DESeq2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes


Signature 1

Needs review

Curated date: 2025/09/30

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1b

Description: Heatmap showing bacterial enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.

Abundance in Group 1: increased abundance in 24 hrs fermentation

NCBI Quality ControlLinks
Aerococcus
Candidatus Kinetoplastidibacterium
Cohaesibacter
Ehrlichia
Enterococcus
Frateuria
Fusobacterium
Jeotgalibaca
Lactococcus
Leuconostoc
Listeria
Lysinibacillus
Oenococcus
Pediococcus
Polynucleobacter
Spiroplasma
Tatumella
Vagococcus
Weissella

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/09/30

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1b

Description: Heatmap showing bacterial enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.

Abundance in Group 1: decreased abundance in 24 hrs fermentation

NCBI Quality ControlLinks
Achromobacter
Acidovorax
Agrobacterium
Arthrospira
Brenneria
Brevundimonas
Candidatus Midichloria
Crinalium
Cupriavidus
Desulfohalobium
Dickeya
Erwinia
Geminocystis
Herbaspirillum
Hymenobacter
Leptolyngbya
Limnobaculum
Lonsdalea
Microcystis
Mixta
Nissabacter
Ornithobacterium
Oscillatoria
Pantoea
Pasteurella
Pectobacterium
Photorhabdus
Rhodococcus
Sodalis
Sphingomonas
Sphingopyxis
Stenotrophomonas
Synechococcus

Revision editor(s): YokoC

Experiment 2


Needs review

Curated date: 2025/10/02

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
48 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/02

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1b

Description: Heatmap showing bacterial enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.

Abundance in Group 1: increased abundance in 48 hrs fermentation

NCBI Quality ControlLinks
Acetobacter
Aerococcus
Asaia
Bacillus
Carnobacterium
Ehrlichia
Enterococcus
Frateuria
Fusobacterium
Gluconacetobacter
Gluconobacter
Granulibacter
Jeotgalibaca
Komagataeibacter
Kozakia
Lachnoclostridium
Lactobacillus
Lactococcus
Leuconostoc
Listeria
Lysinibacillus
Melissococcus
Neoasaia
Neokomagataea
Oceanobacillus
Oenococcus
Parasaccharibacter
Pediococcus
Polynucleobacter
Rhodobacter
Spiroplasma
Sporosarcina
Swingsia
Tetragenococcus
Vagococcus
Weissella
Zymomonas

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/02

Curator: YokoC

Revision editor(s): YokoC

Source:

Description: Heatmap showing bacterial enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.

Abundance in Group 1: decreased abundance in 48 hrs fermentation

NCBI Quality ControlLinks
Atlantibacter
Brenneria
Buttiauxella
Cedecea
Cellvibrio
Chania
Citrobacter
Crinalium
Cronobacter
Dickeya
Edwardsiella
Enterobacter
Erwinia
Escherichia
Geminocystis
Gibbsiella
Hafnia
Hydrogenophaga
Hymenobacter
Izhakiella
Klebsiella
Kluyvera
Kosakonia
Leclercia
Lelliottia
Leptolyngbya
Limnobaculum
Lonsdalea
Mixta
Moorena
Morganella
Neorhizobium
Nissabacter
Obesumbacterium
Oscillatoria
Pantoea
Pasteurella
Pectobacterium
Photorhabdus
Pluralibacter
Pragia
Proteus
Providencia
Pseudescherichia
Rahnella
Raoultella
Rhodococcus
Salmonella
Serratia
Shigella
Shimwellia
Sodalis
Spirosoma
Synechococcus
Xenorhabdus
Yersinia

Revision editor(s): YokoC

Experiment 3


Needs review

Curated date: 2025/10/02

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
72 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/07

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1b

Description: Heatmap showing bacterial enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.

Abundance in Group 1: increased abundance in 72 hrs fermentation

NCBI Quality ControlLinks
Acetobacter
Acidiphilium
Acidithiobacillus
Aerococcus
Alloyangia
Altererythrobacter
Asaia
Azorhizobium
Bacillus
Blautia
Brochothrix
Candidatus Izemoplasma
Carnobacterium
Castellaniella
Clostridioides
Crassaminicella
Enterococcus
Erysipelothrix
Filomicrobium
Fusobacterium
Gemella
Gluconacetobacter
Gluconobacter
Gracilibacillus
Granulibacter
Intestinibaculum
Jeotgalibaca
Komagataeibacter
Kozakia
Lachnoclostridium
Lactobacillus
Lactococcus
Leptotrichia
Leuconostoc
Listeria
Lutibacter
Lysinibacillus
Magnetospirillum
Marinilactibacillus
Melissococcus
Methyloceanibacter
Myroides
Neoasaia
Oceanobacillus
Oenococcus
Parasaccharibacter
Pediococcus
Psychrobacillus
Salicibibacter
Salinisphaera
Solibacillus
Spiroplasma
Sporosarcina
Swingsia
Tetragenococcus
Thermoanaerobacterium
Vagococcus
Virgibacillus
Zymomonas

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/07

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1b

Description: Heatmap showing bacterial enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.

Abundance in Group 1: decreased abundance in 72 hrs fermentation

NCBI Quality ControlLinks
Aeromonas
Arsenophonus
Arthrospira
Atlantibacter
Brenneria
Brevundimonas
Buttiauxella
Calothrix
Campylobacter
Candidatus Azobacteroides
Candidatus Bipolaricaulis
Candidatus Hodgkinia
Candidatus Midichloria
Candidatus Phytoplasma
Cedecea
Chania
Citrobacter
Crinalium
Cronobacter
Cylindrospermum
Desulfohalobium
Dickeya
Edwardsiella
Enterobacter
Erwinia
Escherichia
Fischerella
Frankia
Frateuria
Geminocystis
Gibbsiella
Hafnia
Halomonas
Hydrogenophaga
Hymenobacter
Izhakiella
Klebsiella
Kluyvera
Kosakonia
Leclercia
Lelliottia
Leminorella
Leptolyngbya
Limnobaculum
Lonsdalea
Microcoleaceae
Microcystis
Mixta
Moorena
Morganella
Neorhizobium
Nissabacter
Nodularia
Oceanicoccus
Ornithobacterium
Oscillatoria
Pantoea
Pasteurella
Pectobacterium
Pedobacter
Photorhabdus
Phytobacter
Plesiomonas
Pluralibacter
Pragia
Prochlorococcus
Proteus
Providencia
Pseudescherichia
Rahnella
Raoultella
Salmonella
Serratia
Shewanella
Shigella
Shimwellia
Sodalis
Stenotrophomonas
Synechococcus
Tatumella
Trichormus
Woeseia
Xenorhabdus
Yersinia

Revision editor(s): YokoC

Experiment 4


Needs review

Curated date: 2025/10/07

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
96 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/07

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1b

Description: Heatmap showing bacterial enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.

Abundance in Group 1: increased abundance in 96 hrs fermentation

NCBI Quality ControlLinks
Acetobacter
Acidiphilium
Acidipropionibacterium
Acidithiobacillus
Aerococcus
Arthrobacter
Azorhizobium
Bacillus
Blautia
Brachybacterium
Brevibacterium
Candidatus Pelagibacter
Carnobacterium
Castellaniella
Ehrlichia
Enterococcus
Erysipelothrix
Exiguobacterium
Faecalitalea
Filomicrobium
Fusobacterium
Geobacillus
Gluconacetobacter
Granulibacter
Helicobacter
Intestinibaculum
Komagataeibacter
Kozakia
Lachnoclostridium
Lactobacillus
Leptospira
Leuconostoc
Listeria
Lysinibacillus
Magnetospirillum
Melissococcus
Methyloceanibacter
Micromonospora
Neoasaia
Neokomagataea
Nitrobacter
Niveispirillum
Oenococcus
Parasaccharibacter
Pediococcus
Polaromonas
Rhodopseudomonas
Roseomonas
Salinisphaera
Sporosarcina
Swingsia
Syntrophus
Thermoanaerobacterium
Vagococcus
Virgibacillus
Zymomonas
Maribacter
Olleya
Kutzneria
Cystobacter
Phaeobacter
Alloyangia
Methylocystis
Shinella
Ketobacter

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/07

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1b

Description: Heatmap showing bacterial enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the Genus taxonomic level.

Abundance in Group 1: decreased abundance in 96 hrs fermentation

NCBI Quality ControlLinks
Arsenophonus
Arthrospira
Atlantibacter
Brenneria
Brevundimonas
Buttiauxella
Campylobacter
Candidatus Azobacteroides
Candidatus Bipolaricaulis
Candidatus Hodgkinia
Candidatus Midichloria
Candidatus Phytoplasma
Cedecea
Chania
Citrobacter
Clostridium
Crinalium
Cronobacter
Cylindrospermum
Desulfohalobium
Dickeya
Edwardsiella
Enterobacter
Erwinia
Escherichia
Fischerella
Geminocystis
Gibbsiella
Hafnia
Hydrogenophaga
Hymenobacter
Izhakiella
Klebsiella
Kluyvera
Kosakonia
Leclercia
Lelliottia
Leptolyngbya
Limnobaculum
Lonsdalea
Microcoleaceae
Microcystis
Mixta
Nissabacter
Nodularia
Ornithobacterium
Oscillatoria
Pantoea
Pasteurella
Pectobacterium
Pedobacter
Photorhabdus
Pluralibacter
Polaribacter
Pragia
Prochlorococcus
Providencia
Pseudescherichia
Rahnella
Raoultella
Salmonella
Shimwellia
Sodalis
Synechococcus
Tatumella
Xenorhabdus
Trichodesmium
Serratia
Yersinia
Morganella
Proteus
Phytobacter

Revision editor(s): YokoC

Experiment 5


Needs review

Curated date: 2025/10/07

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
24 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/07

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1c

Description: Heatmap showing bacterial enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.

Abundance in Group 1: increased abundance in 24 hrs fermentation

NCBI Quality ControlLinks
Aerococcaceae
Carnobacteriaceae
Enterococcaceae
Fusobacteriaceae
Listeriaceae
Rhodanobacteraceae
Streptococcaceae
Cohaesibacteraceae
Spiroplasmataceae
Lactobacillaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/07

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1c

Description: Heatmap showing bacterial enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.

Abundance in Group 1: decreased abundance in 24 hrs fermentation

NCBI Quality ControlLinks
Caulobacteraceae
Chromatiaceae
Hymenobacteraceae
Nocardiaceae
Pectobacteriaceae
Propionibacteriaceae
Gomontiellaceae
Microcystaceae

Revision editor(s): YokoC

Experiment 6


Needs review

Curated date: 2025/10/07

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
48 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/07

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1c

Description: Heatmap showing bacterial enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.

Abundance in Group 1: increased abundance in 48 hrs fermentation

NCBI Quality ControlLinks
Acetobacteraceae
Aerococcaceae
Bacillaceae
Carnobacteriaceae
Enterococcaceae
Fusobacteriaceae
Listeriaceae
Rhodanobacteraceae
Streptococcaceae
Spiroplasmataceae
Lactobacillaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1c

Description: Heatmap showing bacterial enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.

Abundance in Group 1: decreased abundance in 48 hrs fermentation

NCBI Quality ControlLinks
Enterobacteriaceae
Morganellaceae
Pectobacteriaceae
Propionibacteriaceae
Selenomonadaceae
Yersiniaceae
Hafniaceae

Revision editor(s): YokoC

Experiment 7


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
72 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1c

Description: Heatmap showing bacterial enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.

Abundance in Group 1: increased abundance in 72 hrs fermentation

NCBI Quality ControlLinks
Acetobacteraceae
Acidithiobacillaceae
Aerococcaceae
Bacillaceae
Carnobacteriaceae
Enterococcaceae
Entomoplasmataceae
Erysipelotrichaceae
Erythrobacteraceae
Fusobacteriaceae
Halanaerobiaceae
Hyphomicrobiaceae
Lachnospiraceae
Leptotrichiaceae
Listeriaceae
Peptoniphilaceae
Peptostreptococcaceae
Spiroplasmataceae
Staphylococcaceae
Streptococcaceae
Lactobacillaceae
Caryophanaceae
Candidatus Nanopelagicaceae
Salinisphaeraceae
Candidatus Pelagibacteraceae
Francisellaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1c

Description: Heatmap showing bacterial enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.

Abundance in Group 1: decreased abundance in 72 hrs fermentation

NCBI Quality ControlLinks
Aeromonadaceae
Comamonadaceae
Desulfohalobiaceae
Enterobacteriaceae
Erwiniaceae
Hymenobacteraceae
Microcoleaceae
Morganellaceae
Pasteurellaceae
Pectobacteriaceae
Propionibacteriaceae
Rhodobiaceae
Shewanellaceae
Spongiibacteraceae
Synechococcaceae
Yersiniaceae
Oscillatoriaceae
Chroococcaceae
Prochloraceae
Gomontiellaceae
Microcystaceae
Leptolyngbyaceae
Frankiaceae
Hafniaceae
Budviciaceae
Candidatus Midichloriaceae

Revision editor(s): YokoC

Experiment 8


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
96 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1c

Description: Heatmap showing bacterial enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.

Abundance in Group 1: increased abundance in 96 hrs fermentation

NCBI Quality ControlLinks
Acetobacteraceae
Acidithiobacillaceae
Aerococcaceae
Bacillaceae
Brevibacteriaceae
Carnobacteriaceae
Deinococcaceae
Dermabacteraceae
Eggerthellaceae
Enterococcaceae
Erysipelotrichaceae
Fusobacteriaceae
Helicobacteraceae
Hyphomicrobiaceae
Lachnospiraceae
Listeriaceae
Methylocystaceae
Mycobacteriaceae
Peptoniphilaceae
Pseudonocardiaceae
Rhodospirillaceae
Sphingomonadaceae
Spirochaetaceae
Streptococcaceae
Streptomycetaceae
Xanthobacteraceae
Lactobacillaceae
Salinisphaeraceae
Candidatus Pelagibacteraceae
Archangiaceae
Syntrophaceae
Leptospiraceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1c

Description: Heatmap showing bacterial enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the Family taxonomic level.

Abundance in Group 1: decreased abundance in 96 hrs fermentation

NCBI Quality ControlLinks
Desulfohalobiaceae
Enterobacteriaceae
Erwiniaceae
Microcoleaceae
Morganellaceae
Nostocaceae
Oscillatoriaceae
Pasteurellaceae
Pectobacteriaceae
Rhodobiaceae
Spongiibacteraceae
Synechococcaceae
Yersiniaceae
OscillatorialesOscillatoriales
Candidatus Midichloriaceae
Budviciaceae
Hafniaceae
Leptolyngbyaceae
Hapalosiphonaceae
Chroococcaceae
Prochloraceae
Microcystaceae
Gomontiellaceae

Revision editor(s): YokoC

Experiment 9


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
24 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1d

Description: Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.

Abundance in Group 1: increased abundance in 24 hrs fermentation

NCBI Quality ControlLinks
Candida albicans
Candida orthopsilosis
Debaryomyces hansenii
Kluyveromyces marxianus
Komagataella phaffii
Scheffersomyces stipitis
Sugiyamaella lignohabitans
Eremothecium cymbalariae
Huiozyma naganishii
Saccharomyces cerevisiae
Henningerozyma blattae
Zygosaccharomyces rouxii
Nakaseomyces glabratus
Lachancea thermotolerans
Naumovozyma castellii
Tetrapisispora phaffii
Naumovozyma dairenensis
Saccharomyces eubayanus
Eremothecium gossypii
Kazachstania africana
Eremothecium sinecaudum
Kluyveromyces lactis

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1d

Description: Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.

Abundance in Group 1: decreased abundance in 24 hrs fermentation

NCBI Quality ControlLinks
Aspergillus fumigatus
Colletotrichum higginsianum
Malassezia restricta
Zymoseptoria tritici
Mycosarcoma maydis
Cercospora beticola
Botrytis cinerea
Thermothielavioides terrestris

Revision editor(s): YokoC

Experiment 10


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
48 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1d

Description: Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.

Abundance in Group 1: increased abundance in 48 hrs fermentation

NCBI Quality ControlLinks
Candida albicans
Candida orthopsilosis
Eremothecium gossypii
Eremothecium sinecaudum
Henningerozyma blattae
Kazachstania africana
Kluyveromyces lactis
Komagataella phaffii
Lachancea thermotolerans
Nakaseomyces glabratus
Naumovozyma castellii
Naumovozyma dairenensis
Pichia kudriavzevii
Saccharomyces cerevisiae
Saccharomyces eubayanus
Scheffersomyces stipitis
Sugiyamaella lignohabitans
Tetrapisispora phaffii
Zygosaccharomyces rouxii

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1d

Description: Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.

Abundance in Group 1: decreased abundance in 48 hrs fermentation

NCBI Quality ControlLinks
Aspergillus fumigatus
Colletotrichum higginsianum
Fusarium fujikuroi
Malassezia restricta
Neurospora crassa
Zymoseptoria tritici
Mycosarcoma maydis
Cercospora beticola
Botrytis cinerea
Thermothielavioides terrestris
Fusarium oxysporum
Fusarium verticillioides
Fusarium graminearum
Fusarium pseudograminearum
Fusarium venenatum

Revision editor(s): YokoC

Experiment 11


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
72 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1d

Description: Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.

Abundance in Group 1: increased abundance in 72 hrs fermentation

NCBI Quality ControlLinks
Aspergillus fumigatus
Cryptococcus neoformans
Sugiyamaella lignohabitans
Yarrowia lipolytica
Pichia kudriavzevii
Saccharomyces cerevisiae
Eremothecium gossypii

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1d

Description: Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.

Abundance in Group 1: decreased abundance in 72 hrs fermentation

NCBI Quality ControlLinks
Debaryomyces hansenii
Cercospora beticola
Fusarium fujikuroi
Fusarium verticillioides
Fusarium pseudograminearum

Revision editor(s): YokoC

Experiment 12


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
96 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1d

Description: Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.

Abundance in Group 1: increased abundance in 96 hrs fermentation

NCBI Quality ControlLinks
Aspergillus fumigatus
Cryptococcus neoformans
Sugiyamaella lignohabitans
Yarrowia lipolytica
Saccharomyces cerevisiae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1d

Description: Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the species taxonomic level.

Abundance in Group 1: decreased abundance in 96 hrs fermentation

NCBI Quality ControlLinks
Scheffersomyces stipitis
Fusarium pseudograminearum
Fusarium verticillioides
Fusarium venenatum

Revision editor(s): YokoC

Experiment 13


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
24 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1e

Description: Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.

Abundance in Group 1: increased abundance in 24 hrs fermentation

NCBI Quality ControlLinks
Kluyveromyces
Saccharomyces
Scheffersomyces
Sugiyamaella
Tetrapisispora
Candida NakaseomycesCandida Nakaseomyces
Naumovozyma
Zygosaccharomyces
Eremothecium
Lachancea

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1e

Description: Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.

Abundance in Group 1: decreased abundance in 24 hrs fermentation

NCBI Quality ControlLinks
Colletotrichum
Malassezia
Neurospora
Zymoseptoria
Ustilago
Cercospora
Botrytis
Thermothielavioides

Revision editor(s): YokoC

Experiment 14


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
48 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1e

Description: Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.

Abundance in Group 1: increased abundance in 48 hrs fermentation

NCBI Quality ControlLinks
Saccharomyces
Sugiyamaella
Candida NakaseomycesCandida Nakaseomyces
Pichia

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1e

Description: Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.

Abundance in Group 1: decreased abundance in 48 hrs fermentation

NCBI Quality ControlLinks
Aspergillus
Botrytis
Cercospora
Colletotrichum
Fusarium
Malassezia
Neurospora
Pochonia
Pyricularia
Thermothielavioides
Ustilago
Zymoseptoria

Revision editor(s): YokoC

Experiment 15


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
72 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1e

Description: Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.

Abundance in Group 1: increased abundance in 72 hrs fermentation

NCBI Quality ControlLinks
Saccharomyces
Sugiyamaella
Yarrowia
Pichia

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1e

Description: Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.

Abundance in Group 1: increased abundance in 72 hrs fermentation

NCBI Quality ControlLinks
Zymoseptoria
Cercospora
Botrytis
Fusarium
Debaryomyces

Revision editor(s): YokoC

Experiment 16


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
96 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1e

Description: Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.

Abundance in Group 1: increased abundance in 96 hrs fermentation

NCBI Quality ControlLinks
Aspergillus
Saccharomyces
Sugiyamaella
Yarrowia

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1e

Description: Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.

Abundance in Group 1: decreased abundance in 96 hrs fermentation

NCBI Quality ControlLinks
Debaryomyces
Fusarium
Scheffersomyces
Zymoseptoria
Cercospora
Botrytis

Revision editor(s): YokoC

Experiment 17


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
24 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 24 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1f

Description: Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.

Abundance in Group 1: increased abundance in 24 hrs fermentation

NCBI Quality ControlLinks
Debaryomycetaceae
Saccharomycetaceae
Trichomonascaceae
Pichiaceae
Phaffomycetaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1f

Description: Heatmap showing fungal enrichment profiles at 24 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.

Abundance in Group 1: decreased abundance in 24 hrs fermentation

NCBI Quality ControlLinks
Malasseziaceae
Mycosphaerellaceae

Revision editor(s): YokoC

Experiment 18


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
48 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 48 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1f

Description: Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.

Abundance in Group 1: increased abundance in 48 hrs fermentation

NCBI Quality ControlLinks
Debaryomycetaceae
Saccharomycetaceae
Trichomonascaceae
Pichiaceae
Phaffomycetaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1f

Description: Heatmap showing fungal enrichment profiles at 48 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.

Abundance in Group 1: decreased abundance in 48 hrs fermentation

NCBI Quality ControlLinks
Malasseziaceae
Mycosphaerellaceae
Nectriaceae

Revision editor(s): YokoC

Experiment 19


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
72 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 72 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1f

Description: Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the genus taxonomic level.

Abundance in Group 1: increased abundance in 72 hrs fermentation

NCBI Quality ControlLinks
Saccharomycetaceae
Trichomonascaceae
Dipodascaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1f

Description: Heatmap showing fungal enrichment profiles at 72 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.

Abundance in Group 1: decreased abundance in 72 hrs fermentation

NCBI Quality ControlLinks
Chaetomiaceae
Mycosphaerellaceae
Nectriaceae
Sclerotiniaceae

Revision editor(s): YokoC

Experiment 20


Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
96 hrs fermentation
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
200-400 kg of cocoa beans undergoing fermentation for 96 hours in wooden boxes at ambient temperature.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1f

Description: Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.

Abundance in Group 1: increased abundance in 96 hrs fermentation

NCBI Quality ControlLinks
Aspergillaceae
Saccharomycetaceae
Trichomonascaceae
Dipodascaceae

Revision editor(s): YokoC

Signature 2

Needs review

Curated date: 2025/10/08

Curator: YokoC

Revision editor(s): YokoC

Source: Supplementary Figure 1f

Description: Heatmap showing fungal enrichment profiles at 96 hours fermentation time point compared to the start of fermentation (0 hours) for the family taxonomic level.

Abundance in Group 1: decreased abundance in 96 hrs fermentation

NCBI Quality ControlLinks
Mycosphaerellaceae
Nectriaceae
Sclerotiniaceae

Revision editor(s): YokoC