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Post-harvest processing · Science

Microorganisms in coffee processing

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.

Across the chain: Science

Source-checkedby Coffearium verification pass· Last source-checked 8 Oct 2026· Prepared with AI assistance· 13 sources (13 tier A)· 2 contested· Updated 8 Oct 2026
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Contents

What lives on a coffee cherry#

A 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:

  • Lactic acid bacteria – Leuconostoc, Lactococcus, Lactobacillus and Weissella. They dominate most wet fermentations.1,6
  • Yeasts – the yeast community often includes Candida, Hanseniaspora, Pichia and Saccharomyces.1 Torulaspora delbrueckii appears sporadically.2
  • Acetic acid bacteria – Acetobacter and Gluconobacter, most abundant in dry processing.1
  • Enterobacteria – genera such as Pantoea, Erwinia and Klebsiella.8 Their numbers rise at the start of wet fermentation and then fall.2
  • Bacillus – one of several bacterial genera with pectin-degrading activity.4
  • Filamentous fungi – moulds such as Aspergillus, Penicillium, Fusarium, Mucor and Rhizopus.4,11 Their presence is undesirable.11

What the microbes do#

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

Consume sugars. In wet fermentation, microbes use sucrose first, then glucose and fructose, then citric and malic acid.3

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

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

Succession in wet and dry processing#

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

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  1. Enterobacteria. Present at the start of the standard 16-hour fermentation, then declining steadily.3
  2. Acetic acid bacteria. Present early to a lesser degree than enterobacteria, then declining steadily.3
  3. Leuconostoc. The prevalent lactic acid bacterium of the standard fermentation; lactic acid bacteria were already prevalent before fermentation began.3
  4. Lactococcus lactis. A transient peak during the standard fermentation.3
  5. Lactobacilli. In the extended 64-hour fermentation they take over from L. pseudomesenteroides: Lactobacillus vaccinostercus, L. brevis and L. plantarum.3
  6. Yeast Pichia kluyveri. An important community member, whether or not the beans were soaked afterwards.3
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.

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

Place, altitude and method#

The 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

Altitude 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

Reference table: key taxa by group and role#

The table brings together the taxa most often reported in the sources, with their main role. It is not a complete list.

Group Key taxa Main role in processing Where reported Source
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
Lactic acid bacteria Lactococcus lactis Transient during the standard fermentation in Ecuador; frequent in Yunnan Wet processing Zhang et al.2,3
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
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
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
Yeasts Hanseniaspora uvarum, Candida humilis Widespread in wet fermentation; sugar use, volatiles Wet processing Zhang et al.2, Elhalis et al.10
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
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
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
Bacillus Bacillus spp., B. licheniformis Pectinolytic activity; tested as a starter in Canephora Various Elhalis et al.4, Bernardes et al.11
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
Filamentous fungi Aspergillus section Nigri, Penicillium crustosum Mouldy, earthy off-flavours Processing Elhalis et al.4
Filamentous fungi Fusarium, Mucor, Rhizopus, Penicillium Negative sensory traits Semi-dry Canephora Bernardes et al.11

Reference values#

Parameter Value reported Source
Share of lactic acid bacteria in Colombian wet fermentation Over 60% at all sampling times de Oliveira Junqueira et al.6
Peak share of Leuconostoc 84% at 24 h de Oliveira Junqueira et al.6
Starting temperature, wet fermentation in Yunnan About 15 °C Zhang et al.2
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
Acetic acid giving a vinegary taste Above 2 mg/ml in the beverage Elhalis et al.4
Water activity range in which OTA-producing fungi grow on the drying yard 0.80–0.95 Codex5
Water activity below which they produce no OTA / cannot grow 0.80 / 0.76–0.78 Codex5
Recommended fermentation time (Codex) As short as possible, 12–36 h Codex5

Metabolic pathways#

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

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

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

How microbes are studied#

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

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

Starter cultures#

A starter culture is a selected strain added to steer fermentation. The main studies so far:

  • 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
  • Wet processing on-farm – Pichia fermentans YC5.2 gave coffees with intense vanilla taste and floral aromas.9
  • 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
  • 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

Risks and defects#

  • 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
  • Over-fermentation – high acetic acid gives a vinegary taste; propionic and butanoic acids give an onion flavour.4
  • Mould off-flavours – Aspergillus section Nigri and Penicillium crustosum produced mouldy, earthy flavours.4

Open questions#

  • How much the metabolites that reach the seed shape flavour after roasting is still being researched.4
  • Whether a starter truly takes over, or coexists with the resident community, differs between studies (see Contested).9,10
  • Many genera recently found by sequencing have unknown roles in coffee.6

Key studies#

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.

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

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.

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

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.

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

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.

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

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.

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

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
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Sources

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  12. ALópez-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. (2025). Probiotic potential of lactic acid bacteria and yeast isolated from cocoa and coffee bean fermentation: A review. Fermentation 11(2), 95. doi:10.3390/fermentation11020095 · other copies
  13. AOstry, V.; Malir, F.; Ruprich, J. (2013). Producers and Important Dietary Sources of Ochratoxin A and Citrinin. Toxins 5(9), 1574–1586. doi:10.3390/toxins5091574 · other copies

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