{ "id": "microorganisms", "url": "https://coffearium.org/entries/microorganisms/", "license": "CC-BY-4.0", "title": "Microorganisms in coffee processing", "summary": "The bacteria, yeasts and moulds that grow on coffee cherries and seeds after harvest, what each group does, and how processing method, place and starter cultures shape them.", "domain": "post-harvest-processing", "kind": "Concept", "stage": "process", "topics": [ "science" ], "topicSections": {}, "lang": "en", "status": "verified", "reviewer": "Coffearium verification pass", "lastVerified": "2026-10-08T00:00:00.000Z", "updated": "2026-10-08T00:00:00.000Z", "brief": [ "Wet processing is usually dominated by lactic acid bacteria, especially Leuconostoc, Lactococcus and Lactobacillus, together with enterobacteria and yeasts.1,6", "Dry processing favours acetic acid bacteria (Acetobacter, Gluconobacter) and yeasts such as Pichia and Candida.1", "Microbes break down mucilage, consume sugars and produce acids, alcohols and aroma compounds; some of these metabolites reach the seed.1,4", "Some Aspergillus species can produce ochratoxin A if coffee stays too long at a water activity of 0.80–0.95 during drying.5", "Selected yeasts and bacteria can be added as starter cultures; trials report distinct flavours, but score gains were not always statistically significant.8,9,10" ], "quickFacts": [ { "label": "Dominant in wet processing", "value": "Lactic acid bacteria (Leuconostoc, Lactococcus, Lactobacillus)" }, { "label": "Dominant in dry processing", "value": "Acetic acid bacteria and yeasts" }, { "label": "Frequent yeasts", "value": "Pichia, Candida, Hanseniaspora, Saccharomyces" }, { "label": "Mycotoxin risk", "value": "Aspergillus sections Circumdati and Nigri (ochratoxin A)" }, { "label": "Risk window during drying", "value": "Water activity 0.80–0.95" }, { "label": "Tested starter cultures", "value": "Saccharomyces cerevisiae, Pichia spp., Hanseniaspora uvarum, Lactiplantibacillus plantarum" } ], "aka": [ "Coffee microbiome", "Fermentation microbiota", "Coffee microbiota" ], "linkTerms": [ "microorganism", "microbial community", "microbial communities", "microbiota", "microbes" ], "related": [ "fermentation", "washed-process", "natural-process", "mucilage", "drying", "moisture-and-water-activity", "co-fermentation", "anaerobic-fermentation" ], "contested": [ "Do yeast starter cultures displace the resident bacteria? In one on-farm trial, inoculation with Pichia fermentans lowered lactic acid production9, while in another, strong growth of Hanseniaspora uvarum and Pichia kudriavzevii did not suppress lactic acid bacteria.10", "How long to ferment: the Codex code of practice against ochratoxin A advises fermentation as short as possible, 12 to 36 hours5, while a study following coffee from cherry to cup found that longer-fermented coffee had more notes preferred by consumers.3" ], "corrections": [], "sources": [ { "id": "s1", "title": "Exploring the impacts of postharvest processing on the microbiota and metabolite profiles during green coffee bean production", "authors": "De Bruyn, F.; Zhang, S. J.; Pothakos, V.; Torres, J.; Lambot, C.; Moroni, A. V.; Callanan, M.; Sybesma, W.; Weckx, S.; De Vuyst, L.", "year": 2017, "publisher": "Applied and Environmental Microbiology 83(1), e02398-16", "url": "https://journals.asm.org/doi/10.1128/aem.02398-16", "doi": "10.1128/AEM.02398-16", "tier": "A", "quote": "The concomitant increase in the mannitol concentration in the mucilage corroborated the activity of heterofermentative leuconostocs.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s2", "title": "Influence of various processing parameters on the microbial community dynamics, metabolomic profiles, and cup quality during wet coffee processing", "authors": "Zhang, S. J.; De Bruyn, F.; Pothakos, V.; Contreras, G. F.; Cai, Z.; Moccand, C.; Weckx, S.; De Vuyst, L.", "year": 2019, "publisher": "Frontiers in Microbiology 10, 2621", "url": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.02621/full", "doi": "10.3389/fmicb.2019.02621", "tier": "A", "quote": "The yeasts Candida humilis and Hanseniaspora uvarum were widely found in all fermentation variants.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s3", "title": "Following coffee production from cherries to cup: microbiological and metabolomic analysis of wet processing of Coffea arabica", "authors": "Zhang, S. J.; De Bruyn, F.; Pothakos, V.; Torres, J.; Falconi, C.; Moccand, C.; Weckx, S.; De Vuyst, L.", "year": 2019, "publisher": "Applied and Environmental Microbiology 85(6), e02635-18", "url": "https://journals.asm.org/doi/10.1128/aem.02635-18", "doi": "10.1128/AEM.02635-18", "tier": "A", "quote": "Hence, the initial occurrence of enterobacteria (and to a lesser degree, AAB) and the prevalence of Leuconostoc (accompanied by the transient occurrence of Lactococcus) characterized the standard fermentation.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s4", "title": "Coffee fermentation: Expedition from traditional to controlled process and perspectives for industrialization", "authors": "Elhalis, H.; Cox, J.; Zhao, J.", "year": 2023, "publisher": "Applied Food Research 3(1), 100253", "url": "https://www.sciencedirect.com/science/article/pii/S2772502222002086", "doi": "10.1016/j.afres.2022.100253", "tier": "A", "quote": "A wide range of endogenous isolates was detected with pectinolytic activities including bacteria such as Klebsiella, Erwinia, Bacillus and Lactobacillus and yeasts such as Pichia, Saccharomyces, and Candida.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s5", "title": "Code of Practice for the Prevention and Reduction of Ochratoxin A Contamination in Coffee (CAC/RCP 69-2009)", "authors": "Codex Alimentarius Commission (FAO/WHO)", "year": 2009, "publisher": "Codex Alimentarius", "url": "https://www.fao.org/input/download/standards/11250/CXP_069e.pdf", "tier": "A", "quote": "OTA is produced by a few species in the genera Aspergillus and Penicillium. In coffee, only Aspergillus species, specifically A. ochraceus and related species (A. westerdijkiae and A. steynii), A. niger and related species, and A. carbonarius are involved.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s6", "title": "First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing", "authors": "de Oliveira Junqueira, A. C.; de Melo Pereira, G. V.; Coral Medina, J. D.; Alvear, M. C. R.; Rosero, R.; de Carvalho Neto, D. P.; Enríquez, H. G.; Soccol, C. R.", "year": 2019, "publisher": "Scientific Reports 9, 8794", "url": "https://www.nature.com/articles/s41598-019-45002-8", "doi": "10.1038/s41598-019-45002-8", "tier": "A", "quote": "Lactic acid bacteria (LAB), mainly represented by the genera Leuconostoc and Lactobacillus, showed relative prevalence over 60% at all sampling times.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s7", "title": "The altitude of coffee cultivation causes shifts in the microbial community assembly and biochemical compounds in natural induced anaerobic fermentations", "authors": "Martinez, S. J.; Simão, J. B. P.; Pylro, V. S.; Schwan, R. F.", "year": 2021, "publisher": "Frontiers in Microbiology 12, 671395", "url": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.671395/full", "doi": "10.3389/fmicb.2021.671395", "tier": "A", "quote": "The altitude is an important variable that caused shifts in the microbial community and biochemical compounds content, even in coffees belonging to the same variety and cultivated in the same region under SIAF (self-induced anaerobic fermentation) conditions.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s8", "title": "Inoculation of starter cultures in a semi-dry coffee (Coffea arabica) fermentation process", "authors": "Evangelista, S. R.; Miguel, M. G. C. P.; Cordeiro, C. S.; Silva, C. F.; Pinheiro, A. C. M.; Schwan, R. F.", "year": 2014, "publisher": "Food Microbiology 44, 87–95", "url": "https://www.sciencedirect.com/science/article/pii/S0740002014001191", "doi": "10.1016/j.fm.2014.05.013", "tier": "A", "quote": "DGGE analysis showed that the inoculated yeasts were present throughout the fermentation.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s9", "title": "Conducting starter culture-controlled fermentations of coffee beans during on-farm wet processing: Growth, metabolic analyses and sensorial effects", "authors": "de Melo Pereira, G. V.; Neto, E.; Thomaz-Soccol, V.; Medeiros, A. B. P.; Woiciechowski, A. L.; Soccol, C. R.", "year": 2015, "publisher": "Food Research International 75, 348–356", "url": "https://www.sciencedirect.com/science/article/abs/pii/S0963996915300697", "doi": "10.1016/j.foodres.2015.06.027", "tier": "A", "quote": "The inoculation also increased the production of specific volatile aroma compounds (e.g., ethanol, acetaldehyde, ethyl acetate and isoamyl acetate) and decreased the production of lactic acid during the fermentation process.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s10", "title": "Microbiological and chemical characteristics of wet coffee fermentation inoculated with Hansinaspora uvarum and Pichia kudriavzevii and their impact on coffee sensory quality", "authors": "Elhalis, H.; Cox, J.; Frank, D.; Zhao, J.", "year": 2021, "publisher": "Frontiers in Microbiology 12, 713969", "url": "https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.713969/full", "doi": "10.3389/fmicb.2021.713969", "tier": "A", "quote": "H. uvarum and P. kudriavzevii dominated the fermentations, growing to maximum populations of about 10.0 log CFU/ml compared with 8.0 log CFU/ml in the spontaneous fermentation.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s11", "title": "Microbial ecology and fermentation of Coffea canephora", "authors": "Bernardes, P. C.; Coelho, J. M.; Martins, P. M. M.; Schwan, R. F.", "year": 2024, "publisher": "Frontiers in Food Science and Technology 4, 1377226", "url": "https://www.frontiersin.org/journals/food-science-and-technology/articles/10.3389/frfst.2024.1377226/full", "doi": "10.3389/frfst.2024.1377226", "tier": "A", "quote": "The presence of filamentous fungi is undesirable as it imparts negative sensory traits to the beverage and some species produce mycotoxins.", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s12", "title": "Probiotic potential of lactic acid bacteria and yeast isolated from cocoa and coffee bean fermentation: A review", "authors": "López-Palestino, A.; Gómez-Vargas, R.; Suárez-Quiroz, M. L.; González-Ríos, O.; Hernández-Estrada, Z. J.; Castellanos-Onorio, O. P.; Alonso-Villegas, R.; Estrada-Beltrán, A. E.; Figueroa-Hernández, C. Y.", "year": 2025, "publisher": "Fermentation 11(2), 95", "url": "https://www.mdpi.com/2311-5637/11/2/95", "doi": "10.3390/fermentation11020095", "tier": "A", "quote": "The role of yeasts during coffee fermentation is key to producing aroma precursors and pectinolytic activity", "accessed": "2026-09-30T00:00:00.000Z" }, { "id": "s13", "title": "Producers and Important Dietary Sources of Ochratoxin A and Citrinin", "authors": "Ostry, V.; Malir, F.; Ruprich, J.", "year": 2013, "publisher": "Toxins 5(9), 1574–1586", "url": "https://www.mdpi.com/2072-6651/5/9/1574", "doi": "10.3390/toxins5091574", "tier": "A", "quote": "OTA is produced worldwide in foodstuffs by microfungi of the genera, Aspergillus, mainly in subtropical and tropical areas, and Penicillium, especially in temperate and colder zones", "accessed": "2026-09-30T00:00:00.000Z" } ], "markdown": "## What lives on a coffee cherry\n\nA harvested cherry carries a mixed community of bacteria, yeasts and filamentous fungi. Once the fruit is pulped or left to dry, these microbes grow on the sugars and pectin of the pulp and mucilage.4 Six groups matter most:\n\n- **Lactic acid bacteria** – *Leuconostoc*, *Lactococcus*, *Lactobacillus* and *Weissella*. They dominate most wet fermentations.1,6\n- **Yeasts** – the yeast community often includes *Candida*, *Hanseniaspora*, *Pichia* and *Saccharomyces*.1 *Torulaspora delbrueckii* appears sporadically.2\n- **Acetic acid bacteria** – *Acetobacter* and *Gluconobacter*, most abundant in dry processing.1\n- **Enterobacteria** – genera such as *Pantoea*, *Erwinia* and *Klebsiella*.8 Their numbers rise at the start of wet fermentation and then fall.2\n- ***Bacillus*** – one of several bacterial genera with pectin-degrading activity.4\n- **Filamentous fungi** – moulds such as *Aspergillus*, *Penicillium*, *Fusarium*, *Mucor* and *Rhizopus*.4,11 Their presence is undesirable.11\n\n## What the microbes do\n\n**Break down mucilage.** Pectin-degrading (pectinolytic) activity has been found in the bacteria *Klebsiella*, *Erwinia*, *Bacillus* and *Lactobacillus*,4 and in yeasts: several *Pichia* strains produce the enzyme polygalacturonase.4 Yeasts are considered key both for pectinolysis and for aroma precursors.12\n\n**Consume sugars.** In wet fermentation, microbes use sucrose first, then glucose and fructose, then citric and malic acid.3\n\n**Make metabolites.** Lactic acid bacteria produce lactic acid; yeasts produce ethanol and aroma compounds.4 In a Colombian fermentation, lactic acid and acetaldehyde were the main end products of the lactic acid bacteria and of *Pichia*, respectively.6 Lactic acid, acetic acid and mannitol formed in the mucilage were later found inside the seed.1\n\n**Spoil.** Too much acetic acid, or propionic and butanoic acids, cause vinegary and onion-like defects.4 Some moulds give mouldy, earthy flavours, and some *Aspergillus* species produce ochratoxin A.4,5\n\n## Succession in wet and dry processing\n\n**Wet processing.** In Ecuador, lactic acid bacteria were the most common group during wet processing, with enterobacteria and the yeasts *Pichia* and *Starmerella*.1 A cherry-to-cup study there found lactic acid bacteria already prevalent before fermentation began; the pooled cherries and depulped beans carried high counts of lactic acid bacteria, acetic acid bacteria, enterobacteria and yeasts alike.3 The standard 16-hour fermentation was marked by an initial presence of enterobacteria (and, to a lesser degree, acetic acid bacteria), by *Leuconostoc* as the prevalent lactic acid bacterium, and by a transient peak of *Lactococcus lactis*.3 Enterobacteria and acetic acid bacteria then declined steadily.3 In the extended 64-hour fermentation, the lactic acid bacteria shifted from *L. pseudomesenteroides* to lactobacilli: *Lactobacillus vaccinostercus*, *L. brevis* and *L. plantarum*.3 *L. pseudomesenteroides* and the yeast *Pichia kluyveri* were important community members, whether or not the beans were soaked afterwards.3 In Colombia, *Leuconostoc* dominated the whole process and peaked at 84% of the bacterial community after 24 hours; the yeast *Pichia nakasei* dominated the fungi.6\n\n
\n
\n
    \n
  1. Enterobacteria. Present at the start of the standard 16-hour fermentation, then declining steadily.3
    2. \n
  2. Acetic acid bacteria. Present early to a lesser degree than enterobacteria, then declining steadily.3
    3. \n
  3. Leuconostoc. The prevalent lactic acid bacterium of the standard fermentation; lactic acid bacteria were already prevalent before fermentation began.3
    4. \n
  4. Lactococcus lactis. A transient peak during the standard fermentation.3
    5. \n
  5. Lactobacilli. In the extended 64-hour fermentation they take over from L. pseudomesenteroides: Lactobacillus vaccinostercus, L. brevis and L. plantarum.3
    6. \n
  6. Yeast Pichia kluyveri. An important community member, whether or not the beans were soaked afterwards.3
    7. \n
\n
How the main groups rise and fall in a washed fermentation in Ecuador, from cherry to an extended 64-hour fermentation; band width follows the study's description, not counts. Schematic, not to scale.
\n
\n\n**Dry processing.** On drying whole cherries, acetic acid bacteria (*Acetobacter*, *Gluconobacter*) were most abundant, with *Pichia*, *Candida*, *Starmerella* and *Saccharomycopsis* yeasts.1 Heaping the cherries favoured *Acetobacter*, *Gluconobacter* and the yeast *Saccharomycopsis crataegensis*.1\n\n## Place, altitude and method\n\nThe community is not the same everywhere. The Colombian study found more than 50 genera never before reported in coffee fermentation, associated with soil, seawater, plants, insects and human contact.6 The authors of a Chinese trial note that the effect of any processing parameter depends on variety and local geographical conditions.2\n\nAltitude alone can shift the community. In Brazil, natural-processed coffee of the same variety from one region, all given the same self-induced anaerobic fermentation, showed *Gluconobacter* and *Weissella* dominating at 800 and 1,000 m and more acetic acid at 1,200 and 1,400 m; the cold-adapted yeast *Cystofilobasidium* was the main fungus at all altitudes.7\n\n\n\n## Reference table: key taxa by group and role\n\nThe table brings together the taxa most often reported in the sources, with their main role. It is not a complete list.\n\n| Group | Key taxa | Main role in processing | Where reported | Source |\n|---|---|---|---|---|\n| Lactic acid bacteria | *Leuconostoc pseudomesenteroides*, *L. mesenteroides*, *L. holzapfelii* | Early, dominant acidifiers; heterofermentative (mannitol) | Wet processing, Ecuador, China, Colombia | De Bruyn et al.1, Zhang et al.2,3, de Oliveira Junqueira et al.6 |\n| Lactic acid bacteria | *Lactococcus lactis* | Transient during the standard fermentation in Ecuador; frequent in Yunnan | Wet processing | Zhang et al.2,3 |\n| Lactic acid bacteria | *Lactobacillus brevis*, *L. vaccinostercus*, *Lactiplantibacillus plantarum* | Take over from *Leuconostoc* in extended fermentation; pectinolytic activity reported for *Lactobacillus* | Wet processing | Zhang et al.2,3, Elhalis et al.4 |\n| Lactic acid bacteria | *Weissella* (e.g. *W. soli*) | Present in wet fermentation; dominant at lower altitude in one study | Wet and anaerobic fermentations | De Bruyn et al.1, Zhang et al.2, Martinez et al.7 |\n| Yeasts | *Pichia kluyveri*, *P. nakasei*, *P. kudriavzevii*, *P. anomala* | Polygalacturonase (some strains), acetaldehyde, esters | Wet and dry processing | Zhang et al.3, Elhalis et al.4,10, de Oliveira Junqueira et al.6 |\n| Yeasts | *Hanseniaspora uvarum*, *Candida humilis* | Widespread in wet fermentation; sugar use, volatiles | Wet processing | Zhang et al.2, Elhalis et al.10 |\n| Yeasts | *Saccharomyces cerevisiae*, *Torulaspora delbrueckii* | Alcoholic fermentation; tested as starters | *T. delbrueckii* sporadic in spontaneous wet fermentation; both used in semi-dry and Canephora trials | Zhang et al.2, Evangelista et al.8, Bernardes et al.11 |\n| Acetic acid bacteria | *Acetobacter*, *Gluconobacter* | Gluconic acid in drying cherries; ethanol oxidation to acetic acid (shown in cocoa) | Dry processing, heaped cherries | De Bruyn et al.1, Martinez et al.7, López-Palestino et al.12 |\n| Enterobacteria | *Pantoea*, *Erwinia*, *Klebsiella* | Early growth; pectinolytic activity in *Erwinia* and *Klebsiella* | Start of fermentation | Zhang et al.2, Elhalis et al.4, Evangelista et al.8 |\n| *Bacillus* | *Bacillus* spp., *B. licheniformis* | Pectinolytic activity; tested as a starter in Canephora | Various | Elhalis et al.4, Bernardes et al.11 |\n| Filamentous fungi | *Aspergillus* section *Circumdati* (*A. ochraceus*, *A. westerdijkiae*, *A. steynii*) and section *Nigri* (*A. niger*, *A. carbonarius*) | Ochratoxin A | Drying and storage | Codex5, Ostry et al.13 |\n| Filamentous fungi | *Aspergillus* section *Nigri*, *Penicillium crustosum* | Mouldy, earthy off-flavours | Processing | Elhalis et al.4 |\n| Filamentous fungi | *Fusarium*, *Mucor*, *Rhizopus*, *Penicillium* | Negative sensory traits | Semi-dry Canephora | Bernardes et al.11 |\n\n## Reference values\n\n| Parameter | Value reported | Source |\n|---|---|---|\n| Share of lactic acid bacteria in Colombian wet fermentation | Over 60% at all sampling times | de Oliveira Junqueira et al.6 |\n| Peak share of *Leuconostoc* | 84% at 24 h | de Oliveira Junqueira et al.6 |\n| Starting temperature, wet fermentation in Yunnan | About 15 °C | Zhang et al.2 |\n| Maximum yeast population, inoculated vs spontaneous (wet, lab scale) | About 10.0 vs 8.0 log CFU/ml (as given in the abstract) | Elhalis et al.10 |\n| Acetic acid giving a vinegary taste | Above 2 mg/ml in the beverage | Elhalis et al.4 |\n| Water activity range in which OTA-producing fungi grow on the drying yard | 0.80–0.95 | Codex5 |\n| Water activity below which they produce no OTA / cannot grow | 0.80 / 0.76–0.78 | Codex5 |\n| Recommended fermentation time (Codex) | As short as possible, 12–36 h | Codex5 |\n\n\n\n## Metabolic pathways\n\n**Homofermentative and heterofermentative lactic acid bacteria.** Homofermentative lactic acid bacteria turn sugars mainly into lactic acid. Heterofermentative ones also produce ethanol, esters and diacetyl.4 In coffee, *Leuconostoc*, *Lactobacillus* and *Lactococcus* are named among the heterofermentative producers of alcohols, aldehydes and esters.4 A rise in mannitol in the mucilage is a marker of heterofermentative *Leuconostoc* activity.1\n\n**Alcoholic fermentation by yeasts.** In fermented foods generally, yeasts ferment sugars mainly to ethanol and carbon dioxide, with higher alcohols, esters and aldehydes as secondary products.4 Inoculating *Pichia fermentans* raised ethanol, acetaldehyde, ethyl acetate and isoamyl acetate and lowered lactic acid.9 Dominant inoculated yeasts used the mucilage sugars faster and more completely, giving two to three times more glycerol, alcohols, aldehydes, esters and organic acids in the fermented green beans.10\n\n**Acetic oxidation.** In cocoa fermentation, acetic acid bacteria (most often *Acetobacter pasteurianus*) oxidise the ethanol made by yeasts and convert lactic acid into acetic acid and acetoin.12 In dry-processed coffee, acetic acid bacteria were linked with gluconic acid and sugar alcohols building up in the drying outer layers of the cherry.1 At lower concentrations acetic acid tastes clean and sweet; at high concentrations it becomes vinegary.4\n\n## How microbes are studied\n\n**Culture-dependent methods** grow microbes on selective agar media, count them and identify isolates. Zhang et al. used this approach for five target groups.3 In Yunnan it found *Leuconostoc* as the most prevalent lactic acid bacterium.2 Isolates obtained this way can later be tested as starters.10\n\n**Culture-independent methods** read DNA directly from the sample. Earlier work used DGGE fingerprinting.8 Current studies use amplicon sequencing of marker genes – the V4 region of the bacterial 16S rRNA gene and the fungal ITS1 region2 or the 18S rRNA gene.6 These methods can reveal wide diversity: the Colombian study found 160 bacterial genera from 10 phyla.6 The Ecuadorian and Chinese studies combined both approaches.2,3\n\n## Starter cultures\n\nA starter culture is a selected strain added to steer fermentation. The main studies so far:\n\n- **Semi-dry processing, Arabica** – *Saccharomyces cerevisiae* (two strains), *Candida parapsilosis* and *Pichia guilliermondii*. The inoculated yeasts persisted throughout fermentation, and the inoculated coffee showed a caramel flavour absent from the control.8\n- **Wet processing on-farm** – *Pichia fermentans* YC5.2 gave coffees with intense vanilla taste and floral aromas.9\n- **Wet processing, Australia (lab)** – *Hanseniaspora uvarum* and *Pichia kudriavzevii*, isolated from coffee fermentations. The inoculated coffees, especially with *P. kudriavzevii*, scored higher for flavour, aroma and acidity, though for most attributes, including the overall score, the differences were not statistically significant.10\n- **Canephora** – *Leuconostoc mesenteroides*, *Lactiplantibacillus plantarum*, *Torulaspora delbrueckii* and *Saccharomyces cerevisiae* have been tested alone and in co-culture; in another trial *Bacillus licheniformis*, alone and with the yeast *Meyerozyma guilliermondii*, correlated with volatiles such as 5-methylfurfural, which the review links to almond, caramel and chocolate notes.11\n\n## Risks and defects\n\n- **Ochratoxin A** – in coffee only *Aspergillus* species produce it: *A. ochraceus* and relatives, *A. niger* and relatives, and *A. carbonarius*.5 These belong to sections *Circumdati* and *Nigri*.13 *Penicillium* species also make OTA, but mainly in temperate and colder zones; they are not involved in coffee.5,13 *Penicillium* on coffee matters for off-flavours, not OTA.4 The key control is to limit the time coffee spends on the drying yard at a water activity of 0.80–0.95.5\n- **Over-fermentation** – high acetic acid gives a vinegary taste; propionic and butanoic acids give an onion flavour.4\n- **Mould off-flavours** – *Aspergillus* section *Nigri* and *Penicillium crustosum* produced mouldy, earthy flavours.4\n\n## Open questions\n\n- How much the metabolites that reach the seed shape flavour after roasting is still being researched.4\n- Whether a starter truly takes over, or coexists with the resident community, differs between studies (see Contested).9,10\n- Many genera recently found by sequencing have unknown roles in coffee.6\n\n## Key studies\n\n
\n

De Bruyn et al., 2017 – Microbiota of wet and dry processing. Follows Typica coffee in Ecuador through wet and dry variants with DNA sequencing and metabolite analysis. Lactic acid bacteria led wet processing; acetic acid bacteria and yeasts led dry processing, and several microbial metabolites reached the seed.

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Applied and Environmental Microbiology 83(1), e02398-16 · doi:10.1128/AEM.02398-16

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Zhang et al., 2019 – From cherry to cup. Tracks the microbiota and metabolites of wet processing in Ecuador with plating and amplicon sequencing. Lactic acid bacteria were already prevalent before fermentation; enterobacteria and acetic acid bacteria were present early and then declined, Leuconostoc led the standard fermentation with a transient Lactococcus peak, and lactobacilli took over in extended fermentation. Longer-fermented coffee had more notes preferred by consumers.

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Applied and Environmental Microbiology 85(6), e02635-18 · doi:10.1128/AEM.02635-18

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de Oliveira Junqueira et al., 2019 – Colombian fermentation by sequencing. The first amplicon-sequencing study of spontaneous Colombian fermentation. It found very high bacterial diversity, Leuconostoc dominance and Pichia nakasei as the main yeast.

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Scientific Reports 9, 8794 · doi:10.1038/s41598-019-45002-8

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Evangelista et al., 2014 – Yeast starters in semi-dry processing. Inoculates Arabica with four yeast strains and follows them with DGGE. The starters persisted and gave a caramel note not found in the control.

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Food Microbiology 44, 87–95 · doi:10.1016/j.fm.2014.05.013

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Elhalis et al., 2021 – Yeast starters in wet fermentation. Compares fermentations inoculated with Hanseniaspora uvarum or Pichia kudriavzevii with a spontaneous control. The starters used sugars faster and raised flavour metabolites in the beans; cup scores were higher, but most differences were not statistically significant.

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Frontiers in Microbiology 12, 713969 · doi:10.3389/fmicb.2021.713969

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" }