Review

Microbial Characteristics and Functions in Coffee Fermentation:

A Review
Xiaojing Shen 1 , Qi Wang 1,2 , Hongsheng Wang 1 , Guoqing Fang 1 , Ying Li 1 , Jilai Zhang 1, * and Kunyi Liu 1,2, *

1 College of Science & College of Food Science and Technology & College of Resources and Environment,
Yunnan Agricultural University, Kunming 650201, China; 2013017@ynau.edu.cn (X.S.);
mumu202107@163.com (Q.W.)
2 School of Wuliangye Technology and Food Engineering, Yibin Vocational and Technical College,
Yibin 644100, China
* Correspondence: zhangjilai@ynau.edu.cn (J.Z.); ben.91@163.com (K.L.)

Abstract: Based on coffee’s unique and fascinating flavor, coffee has become the most
popular nonalcoholic drink in the world and is a significant agricultural economic crop
in tropical- and subtropical-planted coffee countries and regions. It is also beneficial for
human health because of its rich active compounds, such as caffeine, chlorogenic acids,
trigonelline, tryptophan alkaloids, diterpenes, melanoidins, etc. These compounds often
relate to the prevention of cardiovascular disease, Alzheimer’s disease, and antibacterial,
anti-diabetic, neuroprotection, and anti-cancer activities. The formation of coffee’s flavor
results from various influence factors, including genetics, shade, elevation, post-harvest
processing, fermentation, roasted methods, etc. The first stage of coffee production is
obtaining green coffee beans through the primary process. Fermentation is critical in the
primary process of coffee, which is often related to yeasts, bacteria, and filamentous fungi.
Therefore, microorganisms play a key role in coffee fermentation and coffee flavor. To
provide an understanding of the role of microorganisms in coffee fermentation, the coffee
fermentation overview and microbial characteristics in different coffee primary processing
methods and different coffee fermentation regions were reviewed in this paper. Brazil and
China are the main study countries in coffee fermentation, which contribute a large number
of technologies and methods to improve coffee flavor by fermentation. Different primary
processing methods (wet, dry, or semi-dry processing) and coffee producer countries had
Academic Editor: Antonio Morata
obvious microbial community characteristics. Moreover, the application of yeast and
Received: 22 November 2024 bacteria for improving coffee flavor by microbial fermentation was also introduced.
Revised: 18 December 2024
Accepted: 23 December 2024
Keywords: coffee fermentation; microbial characteristic; yeasts; bacteria; filamentous fungi;
Published: 25 December 2024
co-cultivation; coffee flavor
Citation: Shen, X.; Wang, Q.; Wang,
H.; Fang, G.; Li, Y.; Zhang, J.; Liu, K.
Microbial Characteristics and
Functions in Coffee Fermentation: A
1. Introduction
Review. Fermentation 2025, 11, 5.
https://doi.org/10.3390/ Coffee belongs to the Rubiaceae family and Coffea genus, which includes
fermentation11010005 139 species/taxa [1,2]. The cherries of Coffea liberica, Coffea robusta, and Coffea arabica,
Copyright: © 2024 by the authors. especially C. arabica and C. robusta, are often used to make coffee beverages [3]. In re-
Licensee MDPI, Basel, Switzerland. cent years, with the steady growth of the commercial importance and functional values
This article is an open access article of coffee, coffee has become the most popular beverage and the second-largest traded
distributed under the terms and commodity, following petroleum, around the world, originating from its rich and complex
conditions of the Creative Commons
flavor and other sensory characteristics, such as astringency, bitter flavor, sweet-caramel,
Attribution (CC BY) license
earthy, roast/sulfur, smoky, roasted, burnt/acrid, nutty, cocoa, musty/earthy, floral, fruity,
(https://creativecommons.org/
licenses/by/4.0/). sweet aromatic, sour aromatic, and pungent characteristics, etc. [4,5]. A new report from

Fermentation 2025, 11, 5 https://doi.org/10.3390/fermentation11010005

Fermentation 2025, 11, 5 2 of 20

International Coffee Organization (ICO) pointed out that world coffee exports amounted
to 11.13 million bags in October 2024 compared with 9.67 million in October 2023, and
exports throughout increased to 139.27 million bags in the 12 months ending October 2024
compared to 123.17 million bags in the same period in 2023 (https://ico.org/). In addi-
tion, the ICO Composite Indicator Price (I-CIP) averaged 258.90 US cents/lb in September
2024, above the September 2023 I-CIP with 153.13 US cents/Ib by 69.1%. Simultaneously,
according to the Coffee: World Markets and Trade from the United States Department of
Agriculture (USDA), world coffee production for 2024/25 is forecast to be 176.2 million
bags, global exports to be 123.1 million bags with additional supplies, and consumption
will increase 3.1 million bags higher, to 170.6 million. Thus, it can be seen the develop-
ment of the coffee industry has the potential to make an important contribution to local
economic development.
Moreover, coffee is a super-functional food based on its various health functions. The
main bioactive components in coffee include caffeine, chlorogenic acids, trigonelline, tryp-
tophan alkaloids, diterpenes, melanoidins, and some other second metabolites [6]. These
components are wildly bioactive. For example, caffeine can inhibit the adenosine receptors
to alleviate hypertension, enhance cognitive function, relieve Alzheimer’s disease, ease
anxiety, and treat congestive heart failure and polar renal dysfunction [6]. Chlorogenic
acids can prevent diseases caused by free radical damage (such as induced cardiovascu-
lar damage, nervous system damage, liver damage, and tumors), control inflammatory
response diseases (such as acute liver injury, and gastrointestinal disease), treat diabetes,
prevent obesity and cardiovascular disease, and lower blood pressure [6]. Melanoidins
can lower blood pressure and prevent colon cancer [6]. Moreover, green coffee bean ex-
tract could improve intestinal barriers and slow the progression of colorectal cancer [6].
Coffee consumption exhibits antiadipogenic, antidiabetic, antitumor, and neuroprotective
effects [7–10] based on coffee’s bioactivity components, including alkaloids, flavonoids,
diterpenes, and phenolic acids [11,12]. So, coffee consumption is beneficial to human
health, especially preventing chronic and degenerative diseases like cancer, cardiovascu-
lar disorders, diabetes, and Parkinson’s disease [13]. Moreover, coffee by-products have
potential applications as foods or novel foods [14,15], often used as food in Europe and
non-EU-member countries [15]. Therefore, coffee has important value on human health.
Coffee production is a series of processes from processing coffee cherries to brewing
roasted coffee beans [16]. Previous studies showed that the formation of complex coffee
flavors is the result of the interaction of many factors, such as coffee species, environment,
roast, storage, etc. [5]. A coffee bean is surrounded by skin, pulp, mucilage, parchment,
and silver skin from the surface to the interior [17]. Therefore, harvested coffee cherries
must be processed using a primary processing method (dry, wet, or semi-dry) to obtain
green coffee beans [17]. Then, these green coffee beans are roasted to form a distinct flavor
through Maillard, Strecker degradation, caramelization, and fragmentation reactions during
roasting [18]. In the coffee process, the primary processing method brings the fermentation
of coffee fruits by different microorganisms, which can affect coffee flavor and cupping
quality by changing the metabolites in coffee [19,20]. The dry processing method is the
easiest and oldest way and is generally used for C. robusta or in countries with less rainfall
and long periods of sunshine (such as Brazil, Paraguay, and Ethiopia) to obtain unwashed
or natural coffee [17,20,21]. In the dry processing method, the whole cherries are directly
dried for 14–30 days, during which coffee undergoes spontaneous fermentation [16]. The
second method is the wet processing method, in which de-pulped ripe fruits are fermented
in an underwater tank for 24–48 h, and then dried until they reach a final water content
of 10–12% [22]. This method is widely used in Colombia, Central America, Hawaii, and
China. This primary processing method is often used to improve coffee quality by involving
Fermentation 2025, 11, 5 3 of 20

organic acids, alcohols, esters, ketones, aldehydes, and other secondary metabolites of
fermentation [17,23]. Of course, this method is also used to produce robusta coffee in some
countries, such as India, Ivory Coast, Vietnam, Indonesia, and Uganda [24]. The third
method is semi-dry, a hybrid of wet and dry fermentation processing methods, which was
initially performed in Brazil. In this process, the fermentation process occurs directly under
the sun [25]. According to the reports, coffee flavor precursors are significantly different in
different primary processing methods. For example, low molecular weight sugars in the
wet processing method are significantly lower than in dry processing, while glutamic and
aspartic acids are higher [18].
Coffee fermentation in the primary coffee process is a natural and critical metabolic
process for removing the mucilage and reducing water content through enzymes that
naturally occur in the coffee fruit and microbiota acquired from the environment [17,26].
In addition, microbial metabolites in fermentation can migrate into the coffee and change
various physiological characteristics, such as water content, simple sugars, aroma, and other
flavor precursors. Therefore, the controlled microbial fermentation of coffee has become
an important and popular way to improve coffee flavor or produce coffee beverages with
special aromas and flavors, such as sweet, citrus, and fruity [22]. Yeast, bacteria, and
filamentous fungi such as Leuconostoc, Lactobacillus, Erwinia, Bacillus, Pseudomonas, Klebsiella,
Pichia, and Aspergillus are the main microorganisms in coffee fermentation. They play a
major role in degrading mucilage by producing various enzymes, alcohols, acids, and
microbial metabolites [27].
Fascinating coffee flavor is the most important factor supporting the development and
consumption of coffee in the economic market. The key role of microorganisms in coffee
flavor by fermentation has been understood in recent years. However, microorganisms
are easily influenced by the environment. Although previous reviews have introduced
and reviewed microbiology and its functions in coffee primary processing fermentation,
microbial characteristics in different coffee plantation and process countries or regions
are still unreported. In addition, special microorganisms used for coffee fermentation
have become an effective and popular way to improve coffee flavor. This review aims
to provide useful information for the further study on coffee flavor and reference for the
application of microorganisms in the coffee study yield. Therefore, based on the reported
literature, the study’s overview of coffee fermentation, microbial characteristics, and the
application in coffee fermentation were introduced in this review, which will provide a
clear understanding of the role of microbiota in coffee production and is beneficial for
further studies on improving coffee quality and flavor.

2. The Study Survey of Coffee Fermentation Using Bibliometric Analysis

Coffee is a popular food around the world and close attention to its flavor, healthy
functions, planting ecosystem, etc. has been paid. A total of 22,198 documents have
been conducted in the Science Citation Index Expanded within the Web of Science (WOS)
from 2014 to the present (8 November 2024) using “coffee” as the topic. However, only
95 documents were researched from 1986 to 2013. The search results mean that coffee
has become a hot study topic, especially in the last four years. Simultaneously, coffee
fermentation has also become a hot research orientation based on the important function
of forming coffee flavor by directly contributing to the precursor metabolites of volatile
compounds. Although the function and mechanism of coffee fermentation are complex
and still poorly understood, studies clearly show that enzymes from microorganisms can
degrade the mucilage of coffee cherries [17]. Mucilage comprises proteins, sugar, cellulose,
pectin, water, fiber, and ash [17]. Among these components, pectin occupies 0.91% and
comprises about 60% galacturonic acids [17]. Therefore, the degraded production of
 understood, studies clearly show that enzymes from microorganisms can degrade the mu
Fermentation 2025, 11, 5 cilage of coffee cherries [17]. Mucilage comprises proteins, sugar, cellulose,4 pectin, of 20 water
fiber, and ash [17]. Among these components, pectin occupies 0.91% and comprises abou
60% galacturonic acids [17]. Therefore, the degraded production of mucilage and micro
mucilage and
bialmicrobial metabolites
metabolites may migrate may into
migrate into the
the coffee coffee
beans andbeans
reactand react to flavor
to produce producecompound
flavor compounds by Maillard, Strecker degradation, caramelization, and fragmentation
by Maillard, Strecker degradation, caramelization, and fragmentation during roasting
during roasting [17,18].
[17,18]. Different
Different fermentation
fermentation techniques
techniques are used aretoused to produce
produce differentdifferent
flavors of high
flavors of high-quality coffee [28]. Fermentation technologies are in full
quality coffee [28]. Fermentation technologies are in full development and providedevelopment
and provide a promising
promising technology
technology for producing
for producing sensory
sensory characteristics
characteristics of coffee
of coffee and
and corroboratin
corroborating
thethe growing
growing pace
pace of of coffee
coffee consumption
consumption [28].A Atotal
[28]. totalofof763
763documents
documentshave havebeen con
ducted
been conducted using
using “coffee”
“coffee” andand “fermentation”
“fermentation” as topic
as the the topic
in theinScience
the Science Citation
Citation IndexIndex Ex
pandedWeb
Expanded within within Web of(WOS)
of Science Sciencefrom
(WOS)2014from
to the2014 to the(8present
present November (8 November
2024), as 2024), a
shown1.in Figure 1.
shown in Figure

Figure 1. Study documents on coffee and coffee fermentation from 2014 to November 2024. Red
Figure 1. Study documents on coffee and coffee fermentation from 2014 to November 2024. Re
column represents the study documents on coffee fermentation, blue column represents the study
column represents the study documents on coffee fermentation, blue column represents the stud
documents on coffee.
documents on coffee.
Then, bibliometric analysis, a study field using quantitative and statistical methods
Then, bibliometric
to analyze the production analysis, a of
and dissemination study field using
research quantitative
literature [29], wasand statistical
employed to method
gain furthertoinformation
analyze theon production and dissemination
coffee fermentation. of research
VOSviewer 1.6.20.0literature
was used[29], was employed t
to perform
gain further information on coffee fermentation. VOSviewer 1.6.20.0
co-authorship and keyword co-occurrence analyses and visualizations. Countries’ collabo- was used to perform
co-authorship
rative networks includingand keyword co-occurrence
a co-authorship (Figure 2A),analyses and
citation visualizations.
analysis Countries’
(Figure 2B), and collab
orative networks including a co-authorship (Figure
bibliographic coupling (Figure 2C) of countries were shown in Figure 2. 2A), citation analysis (Figure 2B), and
bibliographic coupling (Figure 2C) of countries were shown in Figure 2.
To reflect the critical themes in coffee fermentation research, these research countries were
grouped into different clusters. Closely related countries were clustered together. Figure 2
shows Brazil and China are the predominant countries in coffee fermentation research yield.
Coffee is an important agricultural economic crop cultivated in Brazil, Colombia, Ethiopia,
Honduras, Peru, Mexico, China, and other countries worldwide [30]. Coffee fermentation
research has spanned 78 countries around the world. However, the top contributors to
this study field were Brazil (166 documents, accounting for 21.76%; 3843 citations), China
(105 documents, 13.76%; 2816 citations), Spain (63 documents, 8.26%; 1624 citations), Colombia
(59 documents, 7.73%; 890 citations), the USA (48 documents, 6.29%; 2362 citations), India
(43 documents, 5.64%; 2286 citations), Mexico (40 documents, 5.24%; 626 citations), South
Korea (40 documents, 5.24%; 1372 citations), Japan (35 documents, 4.59%; 819 citations), and
Italy (31 documents, 4.06%; 733 citations) comparing with 82.57%.
Fermentation 2025, 11, 5 5 of 20
Fermentation 2025, 11, x FOR PEER REVIEW 5 of 20

Figure 2. National publication analyses about coffee fermentation ((A): co-authorship analysis; (B):
Figure 2. National publication analyses about coffee fermentation ((A): co-authorship analysis;
citation analysis; (C): bibliographic coupling analysis. The different colors represented different na-
(B): citation analysis; (C): bibliographic coupling analysis. The different colors represented different
tional clusters).
national clusters).

Brazil is the largest coffee-producing and exporting country forecasting 69.9 million
bags (60 kg per bag) and 46.65 million, respectively, in 2024/25 from the USDA (United
States Department of Agriculture) Foreign Agricultural Service, and it is also a vibrant
active country in the coffee fermentation research field. A report also showed that Brazil
is the leading contributor to coffee bean fermentation focused on the design of controlled
fermentations and the evaluation of the influence of microorganisms and process conditions
on the sensory quality and composition of coffee [31]. Although coffee total production
from China was only 1.9 million bags in 2024/25, China is the second main research country
 Fermentation 2025, 11, 5 6 of 20

in coffee fermentation. In China, coffee is one of the most important cash crops in Yunnan
Province, which is the biggest producer of high-quality coffee of China [32]. Silva et al.
pointed out that Brazil and China were the main countries with a high amount of research,
scientific collaborations, and international cooperation from 2012 to 2022, and their current
study focused on sensory modulation [28]. Based on the Coffee: World Markets and Trade
from the United States Department of Agriculture (USAD), Vietnam is the second-largest
coffee producer in the world. Robusta coffee is the main plantation coffee species, occupying
over 95 percent of total output. Only nine documents were found from Vietnam.
Keyword co-occurrence under author keywords at five minimum number of occur-
rences of a keyword is shown in Figure 3. In keyword co-occurrence analyses, 3694 key-
words were classed into 335 items, 4 clusters, 9049 links, and 16,692 total link strength. In
Figure 3, the different colors represented different keyword clusters. Therefore, based on
the keyword co-occurrence, “fermentation” was the most frequent keyword, with 274 occur-
rences, demonstrating its importance in the relevant literature. “Coffee” followed closely
with 112 occurrences. “Spent coffee grounds” was the third most important frequent key-
word with 81 occurrences. Coffee fermentation mainly focused on arabica coffee, which
had 90 occurrences. Yeast and lactic acid bacteria were fourth and sixth with 57 and 45,
respectively. In addition, the “fermentation” group focused on the application of flavor
and quality, fermentation methods (such as solid-state, processing optimization), active
chemical compounds (such as chlorogenic acid, polyphenols, and flavonoids), 7etc.
Fermentation 2025, 11, x FOR PEER REVIEW of Coffee
20
by-products are also researched in coffee fermentation, focusing on using active values to
improve coffee values.

Figure
Figure 3. Keyword
3. Keyword co-occurrence
co-occurrence aboutabout coffee
coffee fermentation.
fermentation. The The different
different colors
colors represented
represented different
differ-
keyword clusters.
ent keyword clusters.

3. The Microbiota Characteristics in Coffee Fermentation

3.1. The Microbiota Characteristics in Different Coffee Primary Processing Methods
The primary process in coffee production is a key stage, which not only eliminates
coffee cherry pulp to obtain green coffee beans but also affects coffee quality and flavor
[33,34]. The traditional processes include wet, dry, and semi-dry processing methods. In
recent years, the optimization of primary processes and reformational primary processes
Fermentation 2025, 11, 5 7 of 20

3. The Microbiota Characteristics in Coffee Fermentation

3.1. The Microbiota Characteristics in Different Coffee Primary Processing Methods
The primary process in coffee production is a key stage, which not only eliminates coffee
cherry pulp to obtain green coffee beans but also affects coffee quality and flavor [33,34].
The traditional processes include wet, dry, and semi-dry processing methods. In recent
years, the optimization of primary processes and reformational primary processes have been
used in the coffee primary process to improve coffee flavor [33,34]. It is well known that
microorganisms play a crucial role in producing enzymes to degrade pectin and metabolites
to change chemical compounds in coffee fermentation [35]. Although microorganisms were
influenced by environmental factors [35], they still show some specific characteristics in
coffee fermentation.
Microbial communities showed special characteristics in different primary process meth-
ods based on the basic process. For example, in the wet processing method, microorganisms
are the richest. Elhalis et al. published a review of the microbial species in primary coffee
processing methods [17]. They pointed out that the sources of microorganisms were wide,
and microbial communities were varied in coffee fermentation. Based on the review, a net-
work between microbial species and coffee primary processing methods shows the microbial
characteristics in different coffee primary processing methods (Figure 4). Firstly, the micro-
bial species in the wet processing method are the richest, followed by the dry and semi-dry
processing in Figure 4. Then, Lactobacillus, Pseudomonas, Klebsiella, and Enterobacter were wide
bacteria, Pichia is the widest yeast, and Aspergillus and Fusarium were the widest filamen-
tous fungi in the primary coffee process. Pichia caribbica (yeast), Lactiplantibacillus brevis
(bacteria), and Aspergillus ochraceus (filamentous fungi) were common microbial species
in wet and semi-dry processing methods. Bacillus megaterium (bacteria) and Cladosporium
cladosporioides (filamentous fungi) were common microbial species in dry and semi-dry
processing methods. Penicillium crustosum was the common filamentous fungi in dry and
wet processing methods. However, some predominant microbiotas were also different. For
example, Leuconostoc, Streptococcus, Flavobacterium, Proteus, Escherichia, Paracolobactrum, and
Weissela were the main bacteria genera; Hanseniaspora, Saccharomyces, and Candida were the
main yeast genera; Acremonium, Eurotium, Giberrlla, Penicillium, and Pseudozyma, were the
main filamentous fungi genera in the wet primary process. The main bacteria included
Erwinia, Tatumella, Proteus, Bacillus, Acinetobacter, and Leconostoc in the dry primary process.
Debaryomyces and Arula were the main yeast genera; Cladosporium, Pestalotia, Paecelomyces,
and Penicillium were the main filamentous fungi genera. In the semi-dry primary process,
the main bacteria genera included Escherichia, Bacillus, Acinetobacter, Serratia, Saccharomyses,
and Shizosaccharomyces. Candida, Rhodotorula, Hanseniaspore, and Kluyveromyces were the
main yeast genera; Cladosporium and Penicillium were the main filamentous fungi genera.
In addition, Klebsiella ozaenae, Klebsiella oxytoca, Klebsiella herbiola, Leuconostoc mesenteroides,
and Lactiplantibacillus brevis were the main microbial species in the wet process. Cryptococcus
laurentii, Cryptocccus albidus, and Candida guilliermondii were the main yeasts; and Klebsiella
pneumoniae and Erwinia herbicola were the main bacteria [17].
However, in Brazil, the microbial flora of C. arabica in dry processing was more varied
and complex than in wet fermentations. Bacteria were the most abundant group, followed by
filamentous fungi, and yeasts in dry processing [36]. The genus of Aeromonas, Pseudomonas,
Enterobacter, Serratia, and Cellulomonas were the most common and main bacteria. Yeast
included Pichia, Candida, Arxula, and Saccharomycopsis. In addition, Cladosporium, Fusarium,
and Penicillium were the main fungal isolates. While in the semi-dry process, Bacillus subtilis,
Escherichia coli, Bacillus cereus, Enterobacter agglomerans, and Klebsiella pneumoniae were the
predominant bacteria. Pichia anomala, Torulaspora delbrueckii, and Rhodotorula mucilaginosa were
the dominant yeasts; and Aspergillus was the most common filamentous fungal [22].
 main yeast genera; Cladosporium, Pestalotia, Paecelomyces, and Penicillium were the main
filamentous fungi genera. In the semi-dry primary process, the main bacteria genera in-
cluded Escherichia, Bacillus, Acinetobacter, Serratia, Saccharomyses, and Shizosaccharomyces.
Fermentation 2025, 11, 5 Candida, Rhodotorula, Hanseniaspore, and Kluyveromyces were the main yeast genera; 8 of 20
Cladosporium and Penicillium were the main filamentous fungi genera.

Figure4.4.The
Figure Themicrobiota
microbiota characteristics
characteristics of
of different
differentprimary
primarycoffee
coffeeprocessing
processingmethods
methods of of
coffee
coffee
cherries.The
cherries. The red
red hexagon
hexagonrepresented
represented different primary
different processing
primary methods,
processing and theand
methods, different color
the different
circles
color represented
circles microorganisms
represented microorganisms(green(green
was bacteria, purplepurple
was bacteria, was yeast,
was and light
yeast, andred wasred
light fila-
was
filamentous fungi).
mentous fungi).

Furthermore, the microbial

In addition, Klebsiella community
ozaenae, is a dynamic
Klebsiella oxytoca, change
Klebsiella process
herbiola, duringmesen-
Leuconostoc primary
processing [37].
teroides, and Lactiplantibacillus Acetobacteraceae
For example,brevis were the main (Acetobacter, Gluconobacter,
microbial species and
in the wet Kozakia),
process.
Cryptococcus laurentii,
Enterobacteria, Cryptocccus albidus,
L. pseudomesenteroides, and Candida
P. kluyveri, guilliermondii
Hanseniaspora were the
uvarum, andmain yeasts;
C. quercitrusa
andhigh
had Klebsiella
counts pneumoniae
during the andpooling,
Erwinia de-pulping,
herbicola wereandthe main bacteria [17].
fermentation in wet processing in
China. Then, lactic acid bacteria kept the quantitative prevalence andwas
However, in Brazil, the microbial flora of C. arabica in dry processing moreand
counts varied
com-
and complex than in wet fermentations. Bacteria were the most abundant
munities of yeasts relatively stable. Starmerella bacillaris became more pronounced as group, followed
by filamentous
fermentation fungi, and yeasts
progressed. At theinsame
dry processing [36]. The genus
time, Saccharomycopsis of Aeromonas,
crataegensis, L. Pseudo-
fallaxwas,
Pediococcus pentosaceus were sporadically encountered. L. pseudomesenteroides, bacteria.
monas, Enterobacter, Serratia, and Cellulomonas were the most common and main P. kluyver,
Yeast
and includedwere
H. uvarum Pichia, Candida,
prominent Arxula,during
members and Saccharomycopsis.
the soaking stage.InFinally,
addition, Cladosporium,
microorganisms were
decreased during the drying stage [38]. The dynamic change in the microbial community using
a semi-dry processing method showed that Staphylococcus, Klebsiella, Brevundimonas, and
Tatumella were the dominant bacterial genus at the beginning of fermentation. Then, Staphylococ-
cus decreased, whereas Tatumella increased. Subsequently and finally, Staphylococcus gradually
decreased while Staphylococcus, Klebsiella, and Brevundimonas increased [39].
Therefore, different primary processing methods have mainly influence in determining
coffee flavor because of the different microorganism fermentation from different environ-
ments, which showed a special community.

3.2. The Microbiota Characteristics in Coffees from Different Countries

In general, harvesting mature coffee cherries must be immediately processed using one
of the traditional postharvest primary processing methods of coffee. For example, whole
harvesting coffee cherries are spread on platforms or the floor in dry processing, in which
fermentation and drying occurring simultaneously. Wet processing employs de-pulped
coffee cherries, which are subjected to submerged fermentation. Therefore, microorganisms
found during coffee fermentation mainly originate from coffee cherries, soil, water, air, and
Fermentation 2025, 11, 5 9 of 20

other environmental factors [17]. Coffee needs plants in Brazil, Indonesia, India, Colombia,
Ethiopia, Honduras, Peru, Mexico, Guatemala, Nicaragua, China, Vietnam, Costa Rica,
Uganda, Papua New Guinea, and other tropical and subtropical countries and regions,
especially the Equatorial region at an altitude of 200–1600 m and at 18–22 ◦ C [40,41].
Although many microorganisms are common in coffee fermentation from different regions,
the microbiota showed a region-specific character as shown in Table 1.

Table 1. The microbial characteristics of coffee fermentation from different countries.

Primary Processing
Country Microorganisms Reference
Method
Pichia fermentans, P. kluyveri, P. caribbica, P. guilliermondii,
Candida glabrata, Saccharomyces sp., Wet processing method [23]
Brazil Hanseniaspora opuntiae
Meyerozyma guilliermondii Dry processing method [42]
Kazachstania, gamospora, K. humilis, Leuconostoc,
Colombia Wet processing method [43]
Acetobacter, Lactobacillus
Australia H. uvarum, P. kudriavzevii, L. mesenteroides, L. lactis Wet processing method [44]
Saccharomyces, Shizosaccharomyces, Bacillus, Lactobacillus,
India Leuconostoc, Pseudomonas, Flavobacterium, Aspergillus Wet processing method [24]
terreus, A. nidulans, A. tamarii
Enterobacter cowanii, E. sakazakii, E. ludwigii, Bacillus
subtilis, B. cereus, B. megaterium, Pseudomonas fluorescens,
Wet processing method [45]
P. fulva, Gluconobacter frateurii, G. oxydans, G. cerinus,
Kluyvera intermedia, K. cryocrescens

China Achromobacter, Tatumella, Weissella, Streptococcus,

Trichocoleus, Cystofilobasidium, Hanseniaspora, Lachancea, Wet processing method [46]
Wickerhamomyces, Aspergillus
Tatumella, Staphylococcus, Klebsiella, Brevundimonas,
Semi-dry
Gluconobacter, Candida, Hannaella, Hanseniaspora, [39]
processing method
Pichia, Lachancea
Wickerhamomyces anomalus, Saccharomycopsis fibuligera,
Republic of Korea Saccharomyces cerevisiae, Papiliotrema flavescens, [47]
P. kudriavzevii
P. kluyveri, P. anomala, P. ohmeri, H. uvarum,
Tanzania Kluyveromyces marxianus, C. pseudointermedia, Wet processing method [48]
Issatchenkia orientalis, Torulaspora delbrueki
Klebsiella pneumoniae, Erwinia herbicola, L. mesenteroides,
Mexico Wet processing method [49]
L. brevis

In Brazil, yeasts were diverse in the spontaneous coffee fermentation process. A total
of 144 yeasts were identified in the wet processing method, and P. fermentans was the
first isolated dominant yeast, and P. kluyveri was the most frequent isolate. Other main
yeasts include C. glabrata, C. quercitrusa, Saccharomyces sp., P. guilliermondii, P. caribbica, and
H. opuntiae [23]. However, Bacillus, Pichia, Candida, and Meyerozyma were found in the dry
processing method. Among them, Meyerozyma guilliermondii was the most frequent yeast
and P. kluyveri was found only in coffee cherries from 600 m in altitude [42].
Colombia is the third-largest coffee producer in the world behind Brazil and Viet-
nam. In Colombia, the microbial richness in the north was higher than in south-west. In
Northern Colombia, lactic acid bacteria were the predominant bacteria, and Kazachstania
was the predominant yeast during coffee fermentation, such as Kazachstania gamospora and
Fermentation 2025, 11, 5 10 of 20

K. humilis [43]. Kazachstania was the first reported in coffee fermentation that could produce
isoamyl alcohol, and propionic, isobutyric, and hexanoic acids. These compounds were
related to the fruity, floral, sweet, and caramel attributes of coffee flavor.
In Australia, Citrobacter was the predominant genus. H. uvarum and P. kudriavzevii were
the dominant yeasts in wet fermentation. L. mesenteroides and L. lactis were the dominant
lactic acid bacteria [44].
In India, yeast was the dominant microflora, followed by bacteria in the fermentation
of arabica and robusta beans. The genera of Saccharomyces, and Shizosaccharomyces in yeast,
Bacillus, Lactobacillus, Leuconostoc, Pseudomonas, and Flavobacterium in bacteria were the
dominant genera during the initial fermentation stages. In addition, Aspergillus genera,
such as A. niger, A. terreus, A. nidulans, and A. tamarii were dominant fungi [24].
In China, 15 genera and 27 different species were identified in the wet processing of
C. arabic L. Enterobacter was the main predominant genus, including E. cowanii, E. sakazakii,
E. ludwigii. Then, Bacillus, such as B. subtilis, B. cereus, and B. megaterium, was the second
most common genus. In addition, Pseudomonas fluorescens, P. fulva, Gluconobacter frateurii,
G. oxydans, G. cerinus, Kluyvera intermedia, and K. cryocrescens were also present [45]. In
addition, Zhang et al. [37] found that lactic acid bacteria and aerobic microorganisms were
the most prevalent microbial groups, while yeasts and enterobacteria were less common.
Even filamentous fungi were not found. Leuconostoc was the most prevalent lactic acid bac-
teria genus, especially L. pseudomesenteroides, L. mesenteroides, and L. holzapfelii. Lactococcus
lactis was a frequent Lactococcus during fermentation, and C. humilis and H. uvarum also
were widely percent. In addition, Shen et al. found that the top predominant microorgan-
isms in C. arabica fermentation were Achromobacter, Tatumella, Weissella, Streptococcus, and
Trichocoleus for bacteria and Cystofilobasidium, Hanseniaspora, Lachancea, Wickerhamomyces,
and Aspergillus for fungi in the wet processing [46]. Tatumella, Staphylococcus, Klebsiella,
Brevundimonas, and Gluconobacter were the most prevalent bacteria genera, and Candida,
Hannaella, Hanseniaspora, Pichia, and Lachancea were the most abundant fungal genera in
the semi-dry processing of C. arabica [39].
In Korea, 28 yeasts were isolated from C. arabica. Wickerhamomyces anomalus, S. fibuligera,
Papiliotrema flavescens, P. kudriavzevii, and Saccharomyces cerevisiae could produce pectinase
enzymes. S. fibuligera and W. anomalu produced great polygalacturonase and pectin lyase
potential. In addition, S. cerevisiae could produce high pectin methylesterase [47].
In Tanzania, P. kluyveri, P. anomala, and H. uvarum were the predominant yeasts in the
wet processing of C. arabica [48]. Meanwhile, H. uvarum was predominant during fermen-
tation. While P. kluyveri was predominant during the whole process. Other yeast species,
including Kluyveromyces marxianus, C. pseudointermedia, Issatchenkia orientalis, P. ohmeri, and
T. delbrueki were found at a low level.
In Mexico, Gram-negative bacilli were the main aerobic bacteria of C. arabica fermenta-
tion, especially Klebsiella pneumoniae and E. herbicola. They produced a low level of organic
acids. L. mesenteroides and Lactobacillus brevis could produce acetic and lactic acids. Kloeckera,
Candida, and Cryptococcus genera in yeasts had a good fermentative capacity with ethanol
production [49].
There were distinct differences between the dominant microbial species in different
coffee countries. L. meseuteroides, G. cerinus, L. lactis, P. fluorescens, and E. ludwigiiare were
the common dominant microbial species in Australia and China. H. uvarum was common in
Australia, China, and Tanzania. P. kudriavzevii and W. anomalus were common in Australia
and Korea. P. kluyeri was a common dominant microorganism in Brazil and Tanzania.
Saccharomyces sp. was common in Brazil and India. K. pneumoniae was common in Australia
and Mexico.
Fermentation 2025, 11, 5 11 of 20

Therefore, the different planted countries and regions show different environmental
factors and produce unique coffee fermentation microbial characteristics.

4. Effect of Microbiota on Flavor Quality in Coffee Fermentation

4.1. Effect of Yeast on Coffee Fermentation
Coffee flavor precursors (such as sugar, proteins, amino acid, and phenolic compounds)
change to coffee aroma compounds including through Maillard, Strecker degradation,
caramelization, and fragmentation reactions during roasting [18]. More than 1000 volatile
compounds have been identified in coffee, including hydrocarbons, alcohols, aldehydes,
ketones, carboxylic acids, esters, pyrazines, pyrroles, and pyridines. However, only a small
number of them contribute to the coffee flavor and aroma, such as furanones (e.g., furfural,
furfuryl acetate, 5-methylfurfural, 5-hydroxymethylfurfural, etc.), phenolic compounds (e.g.,
vanillin, 4-ethylguaiacol, 2-methoxy-4-vinylphenol, guaiacol, 4-vinylguaiacol etc.), sulfur-
containing compounds (e.g., 3-methyl-2-butene-1-thiol, 2-furfurylthiol, 2-methyl-3-furanthiol,
etc.), and pyrazines (e.g., 2,5-dimethylpyrazine, 2,6-dimethylpyrazine, 2-ethylpyrazine,
2,3-dimethylpyrazine, etc.) [5]. The relationship between coffee fermentation and coffee
aroma is intricate and delicate. In general, multifarious ways involve the influence of
fermentation on coffee flavor. One is that the production of microbial metabolites migrates
into the coffee beans to change the compounds of coffee beans. Second, the residual content
of free sugars and amino acids are key flavor precursors of coffee and are determined by
microbial activity during fermentation. In addition, fermentation affects the endogenous
metabolic activity of coffee seeds with resultant changes in the chemical composition of
the bean. Therefore, the change in coffee bean compounds from microbial metabolites
or metabolic activity can directly or indirectly impact the flavor under roasting [17]. The
coffee flavor was easily influenced by the fermentation process [18]. Yeast plays a crucial
role in coffee fermentation and coffee quality. In general, yeasts require intermediate water
activity microorganisms, which have potential pectinolytic activity and production of or-
ganic acids [50], and have been applied to food fermentation to improve flavor [51,52]. For
example, K. exiguawas, P. kudriavzevii, S cerevisiae, Zyosaccharomyces bailii, Geotrichum silvicola,
and Trichosporon ovoides can promote the formation of ethyl alcohol [52]. For example, coffee
with S. cerevisiae-fermentation had a higher sensory point and correlated with body, while
T. delbrueckii-fermentation correlated with sweetness and acidity [53]. Therefore, yeast
became an effective starter for producing specialty sensory characteristics in coffee during
the coffee fermentation stage. Usually, coffee beans fermented with yeast have higher
sensory scores of fragrances, flavor, acidity, body, and overall score. Yeast can improve the
production of lactic acid, isoamyl alcohol, ethanol, acetaldehyde, and other coffee flavor
compounds [54].
P. fermentans can increase the production of specific volatile aroma compounds, such
as ethanol, acetaldehyde, ethyl acetate, and isoamyl acetate. In these compounds, isoamyl
acetate is related to a banana-like aroma, and ethyl acetate is related to a pineapple-like
aroma. Therefore, P. fermentans could be used as an attractive yeast to enhance coffee beans’
aromatic value by producing high-quality coffees with distinctive characteristics, such as a
vanilla taste and floral aroma [46,55].
Saccharomyces strains can produce high amounts of ethanol, and the strongest power
of ethanol production. Saccharomyces sp. also is an excellent pectinase-producing strain.
Therefore, the co-culture of P. fermentans and Saccharomyces sp. could produce a pectinolytic
effect and high acetaldehyde (floral and fruity note) [23].
H. uvarum, P. fermentans, P. kudriavzevii, C. railenensis, C. xylopsoci, and W. anomalus
could produce critical aromatic compounds, including isoamyl alcohol, 2-phenylethyl alco-
hol, ethanol, ethyl acetate, acetaldehyde, and 2-propanone [55]. Among them, H. uvarum
Fermentation 2025, 11, 5 12 of 20

and P. kudriavzevii showed higher pectinase, amylase, cellulase, and protease activity pro-
duction effects than others. At the same time, the concentrations of total alcohols, esters,
and aldehydes produced were also higher than others. Moreover, P. kudriavzevii increased
the contents of sugar, protein, polyphenol, chlorogenic acids, caffeine, and trigonelline fer-
mentation compared with natural fermentation, and increased the volatile profile exhibited,
such as furans, ketones, pyrazines, lactone complexes [56]. And the inoculated H. uvarum
and P. kudriavzevii promoted the utilization of sugars in the mucilage, with resultant high
concentrations of metabolites such as glycerol, alcohols, aldehydes, esters, and organic
acids in the fermented green beans [57]. The result would reduce coffee’s honey, malt, and
berry notes [56].
So, H. uvarum and P. kudriavzevii had strong potential as starter cultures in cof-
fee fermentation [23,58]. 4-ethenyl-1,2-dimethoxybenzene, heptadecanol, 4-hydroxy-2-
methylacetophenone, and 1-butanol,2-methyl were found in coffee beans inoculated by
S. cerevisiae, C. parapsilosis, and Torulaspora delbrueckii [55].
C. arabica treated by self-induced anaerobic fermentation using S. cerevisiae, C. parapsilosis,
and T. delbrueckii had high scores. Among them, the score from T. delbrueckii was the highest
in pulped coffee, and C. parapsilosis received the highest in natural coffee. Coffee flavor
characteristics were citrus, caramel, honey, chocolate, and chestnut [59].
Coffee cherries inoculated with S. cerevisiae, C. parapsilosis, and P. guilliermondii that
were washed and non-washed showed higher sensations of flavors than unfermented
coffee using microorganisms, indicating increased sensory quality. The fermentation with
C. parapsilosis showed a dominance rate that was higher for the sensation of caramel. The
coffee inoculated with C. parapsilosis and S. cerevisiae by the dry method had a special aroma
of caramel, herbs, and fruits [60].
Green coffee beans generated fruity esters by S. cerevisiae and P. kluyveri fermentation.
In these fermented green coffee beans, ethyl octanoate only existed in S. cerevisiae. While
isoamyl acetate existed in fermented green coffee beans with P. kluyveri. A high level of
2-phenylethyl acetate was detected in the fermented roasted coffee beans, while ethyl
octanoate was found in the S. cerevisiae-fermented coffee. These fruity esters in green coffee
beans were directly transferred to the volatile profiles formed after roasting, enhancing the
fruity attribute in the roasted coffees, especially S. cerevisiae-fermented coffee. Moreover,
S. cerevisiae-fermented coffee had a high production of N-heterocyclic volatiles contributing
to elevated nutty and roasted aromas of coffee [61].
A mixed culture of W. anomalus and K. humilis significantly exhibited markedly in-
creased levels of acetic acid, lactic acid, ethanol, linalool, benzyl alcohol, and acetophenone,
thereby augmenting acidity, alcoholic notes, and a floral-fruity aroma in cascara coffee
beverages [62].
These reports demonstrated that yeast has great potential as a starter culture for
producing high-quality coffee with novel and desirable flavor profiles. Overall, P. fermentans,
P. kudriavzevii, P. guilliermondii, H. uvarum, C. parapsilosis, and Saccharomyces sp. will be
favored to produce an exceptional brew for improving coffee quality.

4.2. Effect of Bacteria in Coffee Fermentation

Bacteria are also common microorganisms during coffee fermentation. Erwinia, Kleb-
siella, Aerobacter, Escherichia, and Bacillus are usually used. Ester methyl salicylate was
found in bacterial fermentation, which often contributes to the esterification of methyl
salicylate. Guaiacol was produced by inoculated with B. subtilis. Malic, lactic, and acetic
acid were detected in inoculated coffee beans with bacteria (Pantoea dispersa, B. subtilis, and
Arthrobacter koreensis) [63].
Fermentation 2025, 11, 5 13 of 20

Furthermore, lactic acid bacteria are a group of Gram-positive bacteria, which predom-
inantly produce lactic acid as the main end-product of carbohydrate fermentation [63,64].
Among these, Lactobacillus stands out as a key genus within the lactic acid bacteria fam-
ily, having been extensively utilized as a starter culture in food production to enhance
nutritional value and flavor [65]. In coffee fermentation, the metabolic activities of lac-
tic acid bacteria are pivotal in removing mucilage and metabolizing sugars to produce
coffee-quality metabolites [66]. Coffee fermentation using L. plantarum, a safe, beneficial,
and probiotic microorganism, produced decanol; 2-undecanone; phenol, 2-methyl-, with
a high cupping score and a fruity, sour flavor and a dominant caramel-honey-like aroma,
while maintaining a non-toxic fermentation process [66]. In addition, L. plantarum with
other bacteria, such as T. delbrueckii, and S. cerevisiae, can also enhance coffee flavor [67–69].
L. mesenteroides fermentation coffee also achieved the best sensory scores [64]. 2-cyclopenten-
1-one, 3-ethyl-2-hydroxy-4-methyl in roasted coffee, and benzothiazole in green coffee were
detected in fermentations with L. plantarum and L. mesenteroides. Of course, some bacteria
will cause a bad flavor. For example, Enterobacteriaceae and Pantoea could cause a potato-like
flavor by forming 2-isopropyl-3-methoxypyrazine [70]. Despite the extensive application of
lactic acid bacteria in fermented foods, the use of specific starters, particularly L. plantarum,
to enhance coffee quality remains underexplored. L. plantarum is prevalent in various food
sources, including vegetables, meat, wine, and dairy products, and has been employed in
fermented foods for a considerable duration [71,72]. Consequently, L. plantarum-fermented
coffee presents substantial potential for improving the flavor quality of coffee through
fermentation methods.
Yeast and bacteria are the most popular starters for obtaining a good coffee flavor,
Fermentation 2025, 11, xhave
and they been
FOR PEER wildly used in improving coffee flavor. The effect of different
REVIEW 14 of 20 single
microbial cultures on volatile compounds in coffee beans was shown in Figure 5.
ethyl acetate
1-pentanol furfuryl formateethyl acetete
1-butanol,2-methyl benzaldehyde

1-octanol 2-furanmethanol, propanoate

7-methyl-4-octanol 4-hydroxy-2-methylacetophenone

2-hexanol Torulaspore delbrueckii isoamyl acetate

Candida parapsilosis
Bacillus subtilis Saccharomyces cerevisiae
acetaldehyde 3-methylbutanal
Leuconostoc mesenteroides Candida xylopsoci
1-decanol heptadecanol

Pichia kluyveri Sacharomyces sp.

caprylic acid 1-nonanol

Pichia guilliermondii Candida railenensis

guaiacol 4-ethenyl-1,2-dimethoxybenzene

2,2-dimethylhexanal 2-phenylethyl alcohol

Arthrobacter koreensis Wickerhamomyces anomalus

hexanal phenol, 2-methyl-

Hanseniaspora opunitiae Hanseniaspora uvarum
2-furancarboxaldehyde, 5-methyl- phenethyl alcohol
Candida glabrata Lactiplantibacillus plantarum
ester methyl salicylate ethanol
Pentoea dispersa Pichia kudriazevii
2,3-butanedione Pichia fermentans 2-undecanone
1H-pyrrole-2-carboxaldehyde, 1-methyl- isoamyl alcohol
2-propanone decanol
N-butyl acetete 2,5-dimethyl-4-hydroxy-3(2H)-furanone
2-ethyl-6-methyl-pyrazine

Figure 5. Effect of different single microbial culture on volatile compounds in coffee beans.
Figure 5. Effect of different single microbial culture on volatile compounds in coffee beans.
4.3. Effect of Filamentous Fungi in Coffee Fermentation
4.3. Effect of Filamentous Fungi fungi
Filamentous in Coffee Fermentation
are also present in different stages of the coffee primary process.
FilamentousAfungi
total of 263 isolates of filamentous fungi were identified, 38 species belonged to the
are also present in different stages of the coffee primary process.
genera of Pestalotia, Paecelomyces, Cladosporium, Fusarium, Penicillium, and Aspergillus [63].
A total of 263 isolates of filamentous
Water activity decreases withfungi
drying, were
and theidentified, 38 speciesis belonged
growth of microorganisms inhibited to the
[63,73]. Therefore, in the dry processing method, fungi counts were increased slowly from
harvest to drying. The species’ distribution varied during fermentation and drying, while
the Aspergillus species was predominated during the storage period [64]. Acremonium spp.,
Cladosporium spp., Aspergillus sp., Fusarium sp., and Penicillium spp. were detected in coffee
fermentation, while, Penicillium spp. was the most common filamentous fungi [74].
Specific fungi produce specific compounds and show significant strain-specific
Fermentation 2025, 11, 5 14 of 20

genera of Pestalotia, Paecelomyces, Cladosporium, Fusarium, Penicillium, and Aspergillus [63].

Water activity decreases with drying, and the growth of microorganisms is inhibited [63,73].
Therefore, in the dry processing method, fungi counts were increased slowly from harvest
to drying. The species’ distribution varied during fermentation and drying, while the
Aspergillus species was predominated during the storage period [64]. Acremonium spp.,
Cladosporium spp., Aspergillus sp., Fusarium sp., and Penicillium spp. were detected in coffee
fermentation, while, Penicillium spp. was the most common filamentous fungi [74].
Specific fungi produce specific compounds and show significant strain-specific aroma
compounds. For example, pyrazines significantly increased in A. oryzae fermented coffee,
and furans were higher in Mucor plumbeus-fermented coffee [75].

4.4. Effect of Co-Cultivation of Different Microbiota in Coffee Fermentation

Microbiota usually co-exist and cooperate in coffee fermentation [66]. Therefore, co-
cultivation has become a popular fermentation method in the coffee process for producing
specific compounds, especially in recent years, which is shown in Figure 6 and Table 2.
Fermentation 2025, 11, x FOR PEER REVIEWacid, caffeine, trigonelline, chlorogenic acid, and volatile compounds are
Organic 15influenced
of 20

by different microbiota co-cultivations.

1H-indole, 3-methyl-
2,6-dimethylpyrazine
2-butanone,1-(acetyloxy)
1,2-cyclo pentanedione,3-methyl
2(5H)-furanone
2-cyclopenten-1-one, 3-ethyl-2-hydroxy-
ethyl 9-hexadecenoate
1-hexanone, 1-(2-thienyl)-
Leuconostoc mesenteroides and Torulaspora delbrueckii 1H-pyrrole, 1-butyl-
hexadecanal
Leuconostoc mesenteroides and Saccharomyces cerevisiae phenol, 4-ethyl-
Lactiplantibacillus plantarum and Torulaspora delbrueckii 1H-pyrrole-2-carboxaldehyde, 1-methyl-
2,5-dimethyl-4-hydroxy-3(2H)-furanone
2-ethyl-6-methyl-pyrazine
2-furancarboxaldehyde, 5-methyl-
2-thiophenemethanol
pantolactone
Lactiplantibacillus plantarum and Saccharomyces cerevisiae 1-nonadecanol
2-hydroxy-gamma butyrolactone
3-hexen-2-one, 5-methyl-
Leuconostoc mesenteroides and Lactiplantibacillus plantarum 4-hydroxy-2-methylacetophenone
4-methyl-5H-furan-2-one
benzoic acid, ethyl ester
furan, 2,2′-methylenebis-
glycerol
4-methylpyrrolo[1,2-a]pyrazine
9,12-octadecadienoic acid, methyl ester
benzyl benzoate
geraniol
tetradecane
1-octanol
2,3-butanedione
2-hexanone
2-methyl-1-butanol
acetaldehyde
Pichia fermentans and Sacharomyces sp. diethyl succinate
ethanol
ethyl actate
ethyl octonoate
hexanal
isoamyl acetate

Figure 6. Effect of different co-cultivation microbial on volatile compounds in coffee beans.

Figure 6. Effect of different co-cultivation microbial on volatile compounds in coffee beans.

Table 2. Mixed microorganism co-cultivation in coffee fermentation.

Microorganisms Related Compounds Reference

2-furancarboxaldehyde, 5-methyl-; 1H-pyrrole-2-carboxaldehyde, 1-methyl-; 2-ethyl-6-
Leuconostoc mesenteroides with
methyl-pyrazine; 2,5-dimethyl-4-hydroxy-3(2H)-furanone; 2-butanone,1-(acetyloxy); 4- [66]
Lactiplantibacillus plantarum
methylpyrrolo[1,2-a]pyrazine
2-furancarboxaldehyde, 5-methyl-; 1H-pyrrole-2-carboxaldehyde, 1-methyl-;
Leuconostoc mesenteroides with
2-ethyl-6-methyl-pyrazine; 2,5-dimethyl-4-hydroxy-3(2H)-furanone; 2,6-dimethylpyra- [66]
Torulaspora delbrueckii
zine; 1H-indole, 3-methyl-
2-furancarboxaldehyde, 5-methyl-; 1H-pyrrole-2-carboxaldehyde, 1-methyl-; 2-ethyl-6-
Leuconostoc mesenteroides with methyl-pyrazine; 2,5-dimethyl-4-hydroxy-3(2H)-furanone; 2-butanone,1-(acetyloxy); 2-
[66]
Saccharomyces cerevisiae thiophenemethanol; 1,2-cyclopentanedione,3-methyl; 2-cyclopenten-1-one, 3-ethyl-2-hy-
droxy-; 2 (5H)-furanone; ethyl 9-hexadecenoate
2-furancarboxaldehyde, 5-methyl-; 1H-pyrrole-2-carboxaldehyde, 1-methyl-; 2-ethyl-6-
Fermentation 2025, 11, 5 15 of 20

Table 2. Mixed microorganism co-cultivation in coffee fermentation.

Microorganisms Related Compounds Reference

2-furancarboxaldehyde, 5-methyl-;
1H-pyrrole-2-carboxaldehyde, 1-methyl-;
Leuconostoc mesenteroides with
2-ethyl-6-methyl-pyrazine; [66]
Lactiplantibacillus plantarum
2,5-dimethyl-4-hydroxy-3(2H)-furanone;
2-butanone,1-(acetyloxy); 4-methylpyrrolo[1,2-a]pyrazine
2-furancarboxaldehyde, 5-methyl-;
1H-pyrrole-2-carboxaldehyde, 1-methyl-;
Leuconostoc mesenteroides with
2-ethyl-6-methyl-pyrazine; [66]
Torulaspora delbrueckii
2,5-dimethyl-4-hydroxy-3(2H)-furanone; 2,6-dimethylpyrazine;
1H-indole, 3-methyl-
2-furancarboxaldehyde, 5-methyl-;
1H-pyrrole-2-carboxaldehyde, 1-methyl-;
2-ethyl-6-methyl-pyrazine;
Leuconostoc mesenteroides with
2,5-dimethyl-4-hydroxy-3(2H)-furanone; [66]
Saccharomyces cerevisiae
2-butanone,1-(acetyloxy); 2-thiophenemethanol;
1,2-cyclopentanedione,3-methyl; 2-cyclopenten-1-one,
3-ethyl-2-hydroxy-; 2 (5H)-furanone; ethyl 9-hexadecenoate
2-furancarboxaldehyde, 5-methyl-;
1H-pyrrole-2-carboxaldehyde, 1-methyl-;
Lactiplantibacillus plantarum with 2-ethyl-6-methyl-pyrazine;
[66]
Torulaspora delbrueckii 2,5-dimethyl-4-hydroxy-3(2H)-furanone;
1-hexanone,1-(2-thienyl)-; 1H-pyrrole,1-butyl-; hexadecanal;
phenol,4-ethyl-
2-furancarboxaldehyde, 5-methyl-;
1H-pyrrole-2-carboxaldehyde, 1-methyl-;
2-ethyl-6-methyl-pyrazine;
Lactiplantibacillus plantarum with
2,5-dimethyl-4-hydroxy-3(2H)-furanonepantolactone; [66]
Saccharomyces cerevisiae
2-thiophenemethanol; 1-nonadecanol; 3-hexen-2-one, 5-methyl-;
4-hydroxy-2-methylacetophenone; furan, 2,2′ -methylenebis-;
4-methyl-5H-furan-2-one; 2-hydroxy-gammabutyrolactone
Ethanol; isoamyl acetate; ethyl acetate; acetaldehyde; 1-octanol;
Pichia fermentans with
caprylic acid; 2-hexanone; diethyl succinate; ethyl octonoate; [21]
Saccharomyces sp.
2-methyl-butanol

2-furancarboxaldehyde, 5-methyl-; 1H-pyrrole-2-carboxaldehyde, 1-methyl-; 2-ethyl-6-

methyl-pyrazine; and 2,5-dimethyl-4-hydroxy-3(2H)-furanone were common volatile com-
pounds in co-cultivation. In addition, 2-butanone,1-(acetyloxy); and 4-methylpyrrolo[1,2-
a]pyrazine were only detected in co-cultivation of L. mesenteroides with L. plantarum. 1H-
indole,3-methyl- and 2,6-dimethylpyrazine were found in the co-cultivation of L. mesenteroides
with T. delbrueckii. Coffee fermentation in co-cultivation of L. mesenteroides with S. cerevisiae had
an outstanding fragrance attribute, and 2-butanone,1-(acetyloxy);
1,2-cyclopentanedione,3-methyl-; 2-cyclopenten-1-one,3-ethyl-2-hydroxy-; 2 (5H)-furanone;
2-butanone, 1-(acetyloxy); pantolactone; and 2-thiophenemethanol were detected.
1-hexanone,1-(2-thienyl)-; 1H-pyrrole,1-butyl-; hexadecanal; and phenol,4-ethyl were the
characteristic compounds in the co-cultivation of L. plantarum with T. delbrueckii, which had
the sensory characteristics of chocolate, dark chocolate, nutty, fruity, and spice. Pantolac-
tone; 2-thiophenemethano; 1-nonadecanol; 2-hydroxy-gamma butyrolactone-; 3-hexen-2-
one,5-methyl-; 4-hydroxy-2-methylacetophenone; 4-methyl-5H-furan-2-one; and furan, 2,2′ -
methylenebis were specific compounds in co-cultivation of L. plantarum with S. cerevisiae,
which had dark chocolate, caramel, nutty, and spice characteristics [66].
Fermentation 2025, 11, 5 16 of 20

Lactic acid bacteria and yeast co-cultivation in coffee fermentation is a common

technology, especially in recent years [68,76]. Co-cultivation of Saccharomyces cerevisiae with
L. mesenteroides and L. plantarum could improve malic acid consumption. Co-cultivation of
L. mesenteroides with S. cerevisiae could improve chlorogenic acid and caffeine contents and
produce ethyl 9-hexadecenoate. While the co-cultivation of L. plantarum with S. cerevisiae
reduced trigonelline and produced glycerol, benzoic acid, and ethyl ester were detected.
At the same time, lactic acid concentration was the highest, and succinic acid concentration
increased with the co-cultivation fermentation of L. mesenteroides with L. plantarum [66].
Coffee fermentation using co-cultivation with P. fermentans and Saccharomyces. sp. found
ten different volatile compounds [21].
Furthermore, novel fermentation technologies are also important to improve coffee
flavor quality. For example, self-induced fermentation in a solid-state fermentation can
significantly improve coffee flavor with fermentation duration change [77].

5. Conclusions
Coffee is a popular nonalcoholic drink and an important agricultural economic crop,
which has important beneficial functions for human health and economic development in
tropical and subtropical planted coffee countries and regions. Microorganisms play a key
function in fermentation during primary processes, which degrade the mucilage layer of
coffee cherries to obtain green coffee beans. According to the existing reports, Brazil and
China are the main study countries on coffee fermentation. These studies provide some
technologies and methods to improve coffee flavor by fermentation. Moreover, this review
pointed out that microbiota show special characteristics in different process methods and
plantation and processing regions. Although the mechanism of microbiota during coffee fer-
mentation is still not completely clear, the microbiota improves or changes the coffee flavor
through the changed chemical compounds of roasted coffee beans. Special microorganisms,
such as P. fermentans, P. kudriavzevii, P. guilliermondii, H. uvarum, C. parapsilosis, L. plantarum,
L. mesenteroides, and S. cerevisiae can certainly be developed to obtain specialty coffee.

Author Contributions: Conceptualization, X.S. and K.L.; methodology, X.S., Q.W. and J.Z.; software,
H.W., G.F. and Y.L.; resources, H.W., G.F. and Y.L.; data curation, X.S., Q.W. and J.Z.; writing—original
draft preparation, X.S. and J.Z.; writing—review and editing, Q.W. and K.L.; funding acquisition, X.S.
and K.L. All authors have read and agreed to the published version of the manuscript.

Funding: This research was funded by the Project of Yunnan Province Agricultural Basic Research
Joint Foundation (No. 202101BD070001-046), the Reserve Talent Project of Young and Middle-aged
Academic and Technical Leaders Yunnan Province (No. 202405AC350064), the Talent Cultivation
Project at Yunnan Province (No. XDYC-QNRC-2022-0039), the Innovation and Entrepreneurship
Project of University Students Yunnan Province (Nos. S202310676052, S202410676038), the Science and
Technology Innovation Team Project of Yibin Vocational and Technical College (No. ybzy21cxtd-03),
the Scientific Research Project of Yibin Vocational and Technical College (No. ZRZD24-12).

Institutional Review Board Statement: Not applicable.

Informed Consent Statement: Not applicable.

Data Availability Statement: The experimental data provided in this work are available in articles.

Conflicts of Interest: The authors declare no conflicts of interest.

Fermentation 2025, 11, 5 17 of 20

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