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Lactic acid bacteria: what coffee industry should know?
Gilberto V de Melo Pereira, Alexander da Silva Vale,
Dão Pedro de Carvalho Neto, Elisângela SM Muynarsk,
Vanete Thomaz Soccol and Carlos R Soccol
During coffee processing, lactic acid bacteria (LAB) from
multiple ecosystems (water, native soil, air, and plant) find in the
cherry pulp a rich environment for their development. They
utilize pulp substrate as a source of carbon and nitrogen to
produce significant amounts of lactic acid. This natural
fermentation is purposely used by coffee growers to promote
an efficient removal of the mucilage layer adhering to the fruits,
before storage and transport of the coffee beans. Besides
lactic acid, LAB metabolism produces a variety of compounds
from the utilization of citrate and the catabolism of amino acids.
Recent studies have demonstrated that these metabolites have
a complementary function in the formation of taste and flavor
precursors of coffee beverages. However, the possibility of
improving coffee quality by the use of LAB has largely been
ignored. This review considers the importance of LAB
associated with coffee processing, exploring their diversity and
metabolism and influences on coffee quality. The selection of
appropriate LAB strains, alone or in combination with yeasts, is
a promising research line in a near future, leading to new
perspectives on coffee quality.
Address
Department of Bioprocess Engineering and Biotechnology, Federal
University of Paraná, Curitiba, Paraná, Brazil
Corresponding author: Soccol, Carlos R (soccol@ufpr.br)
Current Opinion in Food Science 2020, 31:1–8
This review comes from a themed issue on Food bioprocessing
Edited by Gabriele Rocchetti
For a complete overview see the Issue and the Editorial
Available online 17th July 2019
https://doi.org/10.1016/j.cofs.2019.07.004
2214-7993/ã 2019 Published by Elsevier Ltd.
Introduction
Lactic acid bacteria (LAB) are a microbial group of
substantial economic importance, used extensively as a
starter culture in the production of fermented foods.
Metabolic-based definition classifies LAB by the forma-
tion of more than 50% lactic acid as end product of
carbohydrate utilization, besides being gram-positive,
non-motile, and non-spore-forming bacteria with cocco-
bacilli or rods morphology [1]. The LAB are comprised by
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the Lactobacillales order, subdivided into six families
(Aerococcaceae, Carnobacteriaceae, Enterococcaceae,
Lactobacillaceae, Leuconostocaceae, and Streptococca-
ceae) and 40 genera (including Aerococcus, Alloiococcus,
Carnobacterium, Dolosigranulum, Enterococcus, Fructobacil-
lus, Lactobacillus, Lactococcus, Lactovum, Leuconostoc,
Oenococcus, Paralactobacillus, Pediococcus, Streptococcus, Tet-
ragenococcus, Vagococcus, and Weissella) according to their
16S rRNA gene sequences [2,3].
Although LAB are mainly associated with dairy matrices,
the origin of industrial strains is believed to be plant
material [4]. The ubiquity of LAB in nature often results
in opportunistic inoculation of food raw materials [5]. In
coffee processing, LAB from multiple ecosystems find in
coffee pulp a rich environment for their development.
Populations above 108 cells/mL of coffee pulp metabolize
sugars and other minor constituents to form mainly lactic
acid, resulting in pH decrease. The lactic acid, in turn,
assists in the breakdown of pectin, a complex carbohy-
drate present in high concentrations in coffee pulp [6].
These metabolic activities aid in the subsequent drying
process by eliminating coffee mucilage constituents,
causing reduction of the time required for post-harvest
processing from 21 to 7 days [7,8].
In addition to mucilage removal, LAB have been associ-
ated with the generation of bioactive compounds related
to coffee quality. The flavor-forming capability of ‘wild-
type’ LAB cultures in coffee fermentation has gained
increased interest due to the diverse aromas such strains
are capable of impacting. Some LAB-derived metabo-
lites, such as esters, ketones, higher alcohols, and alde-
hydes, can influence sensory attributes of coffee bev-
erages with distinct floral, fruity, and buttery
perceptions [9,10]. This article discusses new direc-
tions for exploiting LAB in coffee fermentation. It covers
diversity, ecology, metabolism, and key influences on
coffee quality (Table 1).
Coffee processing
In the international market, coffee is classified according
to the postharvest processing technology used to remove
the outer layers adhered to the fruits: ‘natural coffee’,
produced from coffee beans processed on the farm by the
simple method of sun-drying, known as dry processing;
and ‘washed coffee’, produced from coffee beans that
undergo a relatively complex series of steps, including
Current Opinion in Food Science 2020, 31:1–8
2 Food bioprocessing

depulping, fermentation, and sun-drying, known as wet
processing. In an alternative method, referred to as semi-
dry processing, de-pulped cherries are sun-dried and
milled to release the green beans. Coffee originated from
the semi-dry processing are denominated as ‘pulped
natural’ [11].
In the wet processing, after harvesting and pulping, the
coffee beans are deposited in masonry tanks containing
large volumes of water. The microaerophilic environ-
ment and nutritional selectivity of coffee pulp cause the
development of microorganisms with fermentative
metabolism, mainly yeast and LAB. Microbial activities
degrade the components of mucilage (simple sugars,
complex carbohydrates, and proteins) and induce the
biochemical transformations necessary for natural fer-
mentation [12]. Many microbial species have been
reported from coffee beans fermentation, comprising
more than 80 genera, as reported by recent microbiome
studies [13,14,15]. These microbial groups harbor a
remarkable fermentation profile that includes produc-
tion of aromatic compounds, enzymes, and organic acids
[10,16].
Ecology and diversity of LAB in coffee
processing
The first comprehensive accounts of the association of
LAB with coffee processing were provided 73 years ago
by Pederson and Breed [17]. Since that time, LAB have
been recognized as an integral component of coffee
processing in most coffee-producing countries. The phy-
logenetic relationship of coffee-related LAB species is
shown in Figure 1. They are divided into four clades
(Leuconostoaceae, Lactobacillaceae, Streptococcaceae,
and Enterococcaceae families) occurring in the taxonomic
genera Leuconostoc, Fructobacillus, Weissela, Lactobacillus,
Pediococcus, Lactococcus, and Enterococcus. It is plausible
that LAB initially colonized coffee fermentation from
surface of coffee fruits. However, soil, water used in
the processing, coffee equipment, and insets are also
potential sources of LAB [13,18,19]. After assessing the
fermentation process, LAB quickly proliferate and
reached population of 108 cells/mL within 20 hours [6].
This accentuated growth is related for LAB’ adaptability
to the environment and stress factors of coffee processing,
such as pH variation, sugars availability, and competition
with other microorganisms [20].

Figure 1
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Leuconostoc sp.
L. pseudomesenteroides
L. mesenteroides dextranicum
L. mesenteroides
L. citreum
L. holzapfelli
Fructobacillus sp.
L. fallax
Leuconostocaceae Weissella sp.
W. thailandensis
W. cibaria
W. confuse
W. soli
Lactobacillus sp.
L. hordei
Pediococcus sp.
P. pentosaceus
P. acidilactici
L.brevis
L. plantarum
L. fermentum
L. vaccinostercus
Lactobacillaceae L. paracasei ssp. paracasei
Lactococcus lactis
L. lactis ssp. lactis
L. hircilastis
Enterococcus sp.
Streptococcaceae
E. hirae
E. faecium
Enterococcaceae E. casseliflavus
E. faecalis

Current Opinion in Food Science

16S rRNA Neighbor-joining tree showing the phylogenetic relationship of LAB species reported with coffee beans fermentation. The 16S rRNA
gene sequences were retrieved from GenBank database and aligned with ClustalW. The phylogenetic tree was constructed using MEGA
4 program. Black blocks indicate specie presence in the referred country, according to the studies of Avallone et al. [6], Carvalho Neto et al. [13],
De Bruyn et al. [45], De Bruyn et al. [15], Feng et al. [46], Hamdouche et al. [47], Leong et al. [27], Muynarsk et al. [44], Nasanit and Satayawut
[48], Pagnoncelli et al. [49], Pederson and Breed [17], Ribeiro et al. [50], Schillinger et al. [51], Silva et al. [52], Velmourougane [53], Vilela et al. [54],
Zhang et al. [14].

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 Lactic acid bacteria in coffee processing de Melo Pereira et al.
Leuconostoc is the ubiquitous microbial genera reported in
coffee fermentation from Brazil, Cameroon, Colombia,
China, Ecuador, Ethiopia, Hawaii, Mexico, Thailand, and
Tanzania biomes (Figure 1). Culture-dependent micro-
biology approaches also supported Leuconostoc sp. as the
most abundant microbial group through the coffee fer-
mentation process [6,21]. Plant materials (e.g. decaying
leaves, roots, and over ripened fruits) are natural ecologi-
cal habitat of Leuconostoc species [22–24]. They are com-
monly found in association with yeast in domestic appli-
cations (e.g. wine, cocoa, and kefir) [24]. The complex
nature of this interaction is highlighted by the observa-
tions that (i) the autolysis of yeasts release nutrients, such
as amino acids, polysaccharides and riboflavin, favorable
for bacterial growth [25,26], and that (ii) the acidification
of the fermentation media by LAB creates a prone envi-
ronment for yeast development [11]. These positive
interactions have been shown to promote desired sensory
attributes in wine, sourdough, and yogurt. However,
information about these mechanisms in coffee fermenta-
tion is scarce.
Other LAB members are commonly found in specific
coffee-producing regions, such as Lactobacillus hordei, Lcb.
vaccinostercus, Lactococcus hircilactis, Leuconostoc fallax, and
Pediococcus pentosaceus in Ecuador; Enterococcus hirae, Fruc-
tobacillus sp., Pediococcus sp., P. acidolactici, and Lcb. para-
casei subsp. paracasei in Brazil; Leu. mesenteroides subsp.
dextranicum in Mexico; Lcb. fermentum in Cameroon; and
Weissella thailandensis in Taiwan (Figure 1). Although
present in low proportions, this wide diversity indicates
a microbial activity specific to geographical region and
niche, and may impart flavors that yield clues to the terroir
of coffee growing regions.
Metabolism of LAB in coffee fermentation
The abundant sugar content present in coffee pulp,
including pentoses (xylose, ribose, and arabinose),
hexoses (glucose, fructose, galactose, and mannose) and
polysaccharides (pectin and cellulose), are primary carbon
and energy sources for LAB growth (Figure 2). Homo-
fermentative LAB species, such as Lcc. lactis, P. pentosa-
cesus, E. faecalis, and Lcb. hordei, ferment sugars by the
Embden–Meyerhoff–Parnas (EMP) pathway to pyruvate,
which is converted into lactic acid by lactate dehydroge-
nase [3,14,15,27]. However, it is possible to suppose
that, under coffee-related stress conditions (e.g. carbon
limitation and acid environment), these homofermenta-
tive species can shift into a mixed-acid metabolism [20].
Heterofermentative LAB, such as Leu. mesenteroides, Leu.
citreum, and Lcb. brevis, are also commonly found in coffee
fermentations [15,27,28]. These LAB species are able to
catabolize pentoses and hexoses present in coffee pulp
into a vast range of end-metabolites, including lactate,
acetate, CO2, and ethanol, via phosphoketolase or pen-
tose phosphate pathways pathway (Figure 2). Lastly,
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3
LAB are able to promote the breakdown of complex
carbohydrates through the production of different hydro-
lytic enzymes (e.g. pectin lyase, pectin methylesterase,
and exo-polygalacturonase) and acidification process
[6,29]. The hydrolysis of pectin releases simple sugars
(glucose, rhamnose, xylose, galactose, arabinose, and D-
galacturonate) as an additional carbon source for LAB
growth [30,31].
In addition to sugars, LAB species have the capability of
metabolizing citrate present in high concentration in the
coffee pulp (Figure 2). The metabolism of citrate by
LAB occurs through three processes: (i) citrate transport,
(ii) conversion of citrate into oxaloacetate, and (iii)
conversion of oxaloacetate into pyruvate and CO2
[32,33]. This process leads to the production of 4-carbon,
flavor-active compounds, including diacetyl, acetoin, and
2,3-butanediol. In addition, accumulation of pyruvate in
an acidic environment such as coffee pulp favors the
production of a-acetolactate, a precursor of 4-carbon
compounds [34]. Leuconostoc and Lactococcus species
found in coffee fermentation are reported as presenting
accentuated citrate metabolism [35,36].
Amino acid catabolism has an important role in LAB
physiology for obtaining energy in nutrient-limited condi-
tions and participating in pH homeostasis [20]. In addition,
LAB are auxotrophic for a variable number of amino acids,
depending on a rich environment for their growth. Coffee
pulp provides such conditions due a rich constitution in
leucine, valine, phenylalanine, threonine, and isoleucine
[30]. The catabolism of amino acids has implications with
the formation of low-molecular weight compounds, such as
and aldehydes, esters, carboxylic acids, and higher alcohols
(Figure 2). For instance, strains of Lcb. plantarum are able to
produce phenylacetaldehyde, phenylacetate, and pheny-
lethanol during the phenylalanine catabolism, while Lcc.
lactis strains are capable to metabolize leucine into
3-methylbutanal, 3-methylbutanol, and 3-methylbutyric
acid [37,38].
Impact on process efficiency
LAB metabolism primarily assists in the process of
removal of mucilage layer by the efficient use of pulp
sugars and acid lactic formation. The pulp acidification
process also changes swelling properties of the inner
mucilage layer, loosening the polysaccharide network
with a clear textural change [11]. It is not surprising that,
empirically, coffee growers use pH reduction to levels
below 4.5 as a method to determine the end of coffee
fermentation process [39]. Finally, LAB are able to pre-
vent the growth of fungi associated with poor beverage
quality (negative flavor modifications) and the production
of mycotoxins potentially harmful to consumers [40].
Numerous LAB strains have been developed with appli-
cations in the food industry. However, commercially
Current Opinion in Food Science 2020, 31:1–8
4 Food bioprocessing

Figure 2

Coffee pulp

Citric acid Sucrose Pectin Free fatty acids

Peptides

Glucose Fructose Arabinose Galacturonic acid Amino acids

Homofermentative

Ribulose-5-P α-keto acids

Glucose 6-P

Acetic acid
P Aldehydes
Glyceraldehyde 3-P Xylulose-5-P
Higher alcohols
Heterofermentative Ethanol

Oxaloacetate Pyruvate

2,3-butanediol Esters
α-acetolactate

Lactic acid
Diketones

LAB cell
Current Opinion in Food Science

Proposed schematic representation of the major metabolic pathways and metabolites generated by LAB during natural coffee fermentation from
existing precursors.

available LAB starter cultures are currently not directly
designed for fermenting coffee beans, mainly due to the
physical and chemical peculiarities of this process [41]. A
primary strategy for research in food applications is
screening from the natural ecosystem. Recently, the
removal of coffee mucilage using lactic acid fermentation
was proposed by introducing a selected LAB, Lcb. plan-
tarum LPBR01, isolated from natural coffee fermentation
[10]. This bacterium strain was able to promote an
accelerated coffee-pulp acidification process reducing
the time required for mucilage removal into field
situation. Another culture, Lcb. rhamnosus HN001,
selected by Wang et al. [9], was also able to promote
an efficient consumption of pulp substrate.
Impact on beverage quality
Coffee consumption has greatly increased all around the
world. This is reflected by the growing number of coffee
bars and local brands in consuming countries. Thus,
international competition within the coffee market is
providing new challenges for innovation in this sector.
So far, coffee industry has paid attention to the flavor

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 Lactic acid bacteria in coffee processing de Melo Pereira et al. 5

compounds formed during the roasting process and has
ignored the possibility of controlling coffee fermentation
during on-farm processing [42]. The complex metabolism
of LAB yields flavor-active metabolites that impact on
coffee quality (Table 1). The intense diffusion of lactic
acid during fermentation process promotes the modifica-
tion in sensorial perception of acidity and body of coffee
beverages [7,10]. From citrate metabolism, the produc-
tion of 2,3-butanedione and acetoin confers buttery-like
aroma in coffee beverages [9,30]. In addition, a vast

Table 1

Main metabolites produced by coffee-related LAB and their metabolic pathway and sensory influences

Metabolite Sensorial description Metabolic pathway Producing LAB References

Lactic acid Sour, acid Embden–Meyerhoff–Parnas, All species [3]
phosphoketolase or pentose
phosphate pathways
Benzaldehyde Fruity, cherry Tryptophan and phenylalanine O. oeni, Lcb. plantarum [55–57]
catabolism
Acetaldehyde Fruity Threonine catabolism Lcb. brevis, Lcb. casei [58]
delbrueckii subsp. bulgaricus and S.
thermophilus
3-Methyl-butanal Chocolate, nutty, leafy, cocoa Branched-chain amino acids Lcc. lactis, Lcb. helveticus [55,59]
catabolism
2-Nonenal Fatty with a citrus nuance Lipid oxidation Lcb. sanfranciscensis and Lcb. [60]
reuteri
Nonanal Citrus, with a fresh green lemon b-Oxidation of unsaturated free Lcb. sanfrancisco, Lcb. rhamnosus, [61–63]
peel-like nuance fatty acids Lcc. lactis ssp. cremosis, Lcc. lactis
ssp. lactis
Decanal Orange peel, citrus, and floral b-Oxidation of unsaturated free Lcc. lactis ssp. cremosis, Lcc. lactis [63]
fatty acids ssp. lactis
Ethyl acetate Fruity, grape Esterefication reaction between Lcc. lactis ssp. lactis, Lcb. [10,64]
alcohols and free fatty acids rhamnosus, Lcb. paracasei ssp.
paracasei, Lcb. plantarum, Leu.
lactis, Pediococcus sp.
Ethyl butanoate – Esterefication reaction between L. plantarum, L. rhamnosus, L. [10,65]
alcohols and free fatty acids fermentum, L. helveticus, L. casei
Pediococcus sp., Lcc. lactis, Lcc.
lactis ssp. lactis, Lcc. lactis ssp.
cremosis, S. salivarius ssp.
thermophiles, Leu. mesenteroides
ssp. cremoris, Leu. lactis.
Ethyl propionate Winey, grape, and fermented Esterefication reaction between Lcb. plantarum [10]
with an eggnog nuance alcohols and free fatty acids
Ethyl hexanoate Fruity, pineapple, banana Esterefication reaction between Lcc. lactis, Lcc. lactis ssp. lactis, [10,64,66]
alcohols and free fatty acids Lcb. rhamnosus, Lcb. paracasei
ssp. paracasei, Lcb. plantarum, Lcb.
helveticus, Lcb. casei, Leu. lactis,
Pediococcus sp.
3-Methyl-1-butanol Fruity, banana and molasses Branched-chain amino acids Lcc. Lactis, Lcb. sanfrancisco, Lcc. [55,61,67]
catabolism lactis ssp. lactis
2-Methyl-propanol Winey Valine catabolism Lcb. helveticus [59]
Phenyl ethanol Floral, rose, bready Phenylalanine catabolism S. termophillus, Lcb. rhamnosus [9,64]
2-Methyl-butanol Roasted, winey, fruity Isoleucine catabolism Lcb. brevis, Lcb. fermentum, Lcb. [67,68]
plantarum, Lcb. paracasei ssp.
paracasei, Lcb. delbruecki ssp.
delbrueckii, E. faecium, S.
Termophillus
1-Hexanol Green, fruity, apple-skin and oily 3-Keto-hexanoyl-CoA Lcb. plantarum [7,69]
conversion
2,3-Butanediol Fruity, creamy, buttery Citrate or aspartate assimilation Lcb. plantarum [7,70]
Phenylacetaldehyde Honey, floral, rose Phenylalanine catabolism O. oeni, Lcb. brevis, Lcb. casei, Lcb. [7,57]
plantarum, Lcc. Lactis
2-Phenethyl acetate Floral with a slight yeasty, honey Phenylalanine catabolism Lcb. plantarum [7]
note
Diacetyl Creamy, buttery Citrate or aspartate assimilation Lcb. plantarum, Lcb. rhamnosus [9]
Acetoin Dairy, milky Citrate or aspartate assimilation Lcb. rhamnosus [9]

The abbreviations of the LAB genera are as follows: Lactobacillus = Lcb.; Leuconostoc = Leu.; Lactococcus = Lcc.; Streptococcus = S.; Enter-
ococcus = E.; Oenococcus = O.; Pediococcus = P.

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6 Food bioprocessing
range of LAB-derived metabolites associated with the
catabolism of amino acids, specifically ethyl propionate,
ethyl acetate, acetaldehyde, phenyl ethanol, and pheny-
lacetaldehyde, are known for increasing fruity and floral
perceptions in final beverage [30].
Undoubtedly, aroma is one of most important character-
istics that contribute to the quality of coffee. As in many
foods, coffee aroma is composed by over 1000 different
volatile organic compounds with concentrations that can
vary between 845 and 1239 ppm [43]. The balance and
interaction of all of them determine the coffee aromatic
quality. The use of LAB cultures was demonstrated to be
favorable for the production of coffee with distinctive
sensory profiles. Coffee beverages with high acidity and
fruity and floral perceptions were produced by the use of
the Lcb. plantarum LPBR01 [10], while caramelic and
burnt characteristics were the sensory attributes for Lcb.
rhamnosus HN001inoculated treatment. These coffee
beverages can strategically be used to supply specific
coffee consumer regions or be used in blends to achieve
desirable acidity and distinctive flavor.
Functional genomic
The recent development of high-throughput sequencing
technology has expanded the knowledge about LAB’s
metabolic potential and bioprocessing capabilities. The
genome of LAB is among the best characterized to date.
However, only recently, the whole genome sequencing of
a LAB (P. acidilactici LPBC101) originated from coffee
fermentation was published [44]. This genome arrange-
ment provided insights on the mechanisms of adaptation
and metabolism of LAB in the environment of coffee
processing. P. acidilactici LPBC10 harbor a high number
of unique genes involved in the use of coffee pulp sugars
and encoding stress-related proteins (e.g. thiol peroxi-
dase, glutathione reductases, NADH-oxidases, and alka-
line-shock proteins). In addition, this coffee-related LAB
strain possesses a remarkable phenotypic diversity, pos-
sessing all enzymes required for glycolysis, phosphoke-
tolase, and pentose-phosphate pathways [44]. The pres-
ence of these genes can be used as solid scientific
evidence in searching LAB with potential applications
for coffee processing. However, genome information pro-
vides only a predictive model, because gene expression is
dependent on the environmental conditions. Thus, geno-
mic data must be confirmed by transcriptome, proteome,
and metabolome profiling and, ultimately, applications
under field conditions. These platforms should be
included in LAB selection studies to obtain a deep
understanding of the function and effects of selected
strain on coffee processing.
Conclusion and perspectives
LAB cultures have great potential to achieve control,
reproducibility, and quality consistency over coffee pro-
cessing. In particular, LAB metabolism of carbohydrates,
Current Opinion in Food Science 2020, 31:1–8
citrate, and amino acids, and the key components pro-
duced during their growth, are the main activities associ-
ated with coffee processing. They act by demuciling
coffee fruits through pulp acidification, besides forming
flavor-active metabolites that add quality to final coffee
products. However, the use of LAB in coffee processing
has largely been overlooked. To date, only two species,
Lcb. plantarum LPBR01 and Lcb. rhamnosus HN001, were
evaluated under field conditions. This is a small fraction
within the rich diversity of species involved in natural
fermentations. For example, Leuconostoc sp., a versatile
microbial group with useful properties, have never been
recovered as a starter culture. Undoubtedly, the full
potential of coffee related LAB has not been fully deter-
mined and many challenges are awaiting research, dis-
semination, and industrial exploitation. Future research
should be focused on the investigation of new LAB and
the possibility of creating multi-purpose mixed cultures
with yeast strains. As reported above, several features
influence LAB activities in coffee fermentation. To
obtain a more complete picture on LAB interaction in
inoculated fermentation (pure and mixed with yeast) a
multifactorial approach using ‘omics’ methodologies
should be planned. Furthermore, the emerging field of
synthetic biology using the sinecology concept can be
applied to understand and control intercellular interac-
tion, spatiotemporal coordination, and stability of LAB
within microbial consortia of coffee fermentation.
Conflict of interest statement
Nothing declared.
Acknowledgement
The authors gratefully acknowledge the support provided by Brazilian
Council for Scientific and Technological Development (grant number
303254/2017-3).
References and recommended reading
Papers of particular interest, published within the period of review,
have been highlighted as:
 of special interest
 of outstanding interest
1. Holzapfel WH, Wood BJB: Introduction to the LAB. In Lactic
Acid Bacteria: Biodiversity and Taxonomy. Edited by Holzapfel
WH, Wood BJB. Wiley Blackwell; 2014:1-12.
2. Salvetti E, Torriani S, Felis GE: The genus Lactobacillus: a
taxonomic update. Probiotics Antimicrob Proteins 2012, 4:217-
226.
3. Endo A, Dicks LMT: Physiology of the LAB. In Lactic Acid
Bacteria: Biodiversity and Taxonomy. Edited by Holzapfel WH,
Wood BJB. Wiley Blackwell; 2014:13-30.
4. Cavanagh D, Fitzgerald GF, Mcauliffe O: From field to
fermentation: the origins of Lactococcus lactis and its
domestication to the dairy environment. Food Microbiol 2015,
47:45-61.
5. Narvhus JA, Axelsson L: Lactic acid bacteria. In Encyclopedia of
Food Sciences and Nutrition. Edited by Caballero nai. CRC Press;
2003:3465-3472.
www.sciencedirect.com
 Lactic acid bacteria in coffee processing de Melo Pereira et al.
6. Avallone S, Brillouet JM, Guyot B, Olguin E, Guiraud JP:
Involvement of pectolytic micro-organisms in coffee
fermentation. Int J Food Sci Technol 2002, 37:191-198.
7. Carvalho Neto DP, Pereira GVM, Finco AMO, Letti LAJ, Silva BJG,
 Vandenberghe LPS, Soccol CR: Efficient coffee beans mucilage
layer removal using lactic acid fermentation in a stirred-tank
bioreactor: kinetic, metabolic and sensorial studies. Food
Biosci 2018, 26:80-87.
Coffee beans fermentation was set up in a stirred-tank reactor added
of Lactobacillus plantarum LPBR01 starter culture. This new fermentation
system showed potential reduction of the fermentation time from 24 to
10 hours.
8. Huch M, Franz CMAP: Coffee: Fermentation and Microbiota.
Woodhead Publishing; 2015.
9. Wang C, Sun J, Lassabliere B, Yu B, Zhao F, Zhao F, Chen Y,
 Liu SQ: Potential of lactic acid bacteria to modulate coffee
volatiles and effect of glucose supplementation: fermentation
of green coffee beans and impact of coffee roasting. J Sci Food
Agric 2019, 99:409-420.
The introduction of the Lactobacillus rhamnosus strain HN001 into field
condition led to modification of flavor-related constituents in green coffee
beans.
10. Pereira GVM, Carvalho Neto DP, Medeiros ABP, Soccol VT,
 Neto E, Woiciechowski AL, Soccol CR: Potential of lactic acid
bacteria to improve the fermentation and quality of coffee
during on-farm processing. Int J Food Sci Technol 2016,
51:1689-1695.
Accelerated coffee-pulp acidification process and production of high-
quality beverages by the introduction of Lactobacillus plantarum strain
LPBR01 under field conditions.
11. Pereira GVM, Soccol VT, Brar SK, Neto E, Soccol CR: Microbial
ecology and starter culture technology in coffee processing.
Crit Rev Food Sci Nutr 2017, 57:2775-2788.
12. Silva CF, Batista LR, Abreu LM, Dias ES, Schwan RF: Succession
of bacterial and fungal communities during natural coffee
(Coffea arabica) fermentation. Food Microbiol 2008, 25:951-957.
13. Carvalho Neto DP, Pereira GVM, de Carvalho JC, Soccol VT,
Soccol CR: High-throughput rRNA gene sequencing reveals
high and complex bacterial diversity associated with
Brazilian coffee bean fermentation. Food Technol Biotechnol
2018, 56:88-93.
14. Zhang SJ, De Bruyn F, Pothakos V, Torres J, Falconi C,
 Moccand C, Weckx S, De Vuyst L: Following coffee production
from cherries to cup: microbiological and metabolomic
analysis of wet processing of Coffea arabica. Appl Environ
Microbiol 2019, 85:1-22.
This comprehensive study monitored the evolution of microbial diversity
along the whole wet coffee processing chain. LAB was confirmed as the
prevalent microbial group during the fermentation step.
15. De Bruyn F, Zhang SJ, Pothakos V, Torres J, Lambot C, Moroni AV,
 Callanan M, Sybesma W, Weckx S, De Vuyst L: Exploring the
impacts of postharvest processing on the microbiota and
metabolite profiles during green coffee bean production. Appl
Environ Microbiol 2017, 83 e02398-16.
First study to apply high-throughput sequencing approach in coffee bean
fermentation. The results allowed the analysis of temporal distribution,
diversity, and composition of coffee-related microorganisms.
16. Leroy F, De Vuyst L: Lactic acid bacteria as functional starter
cultures for the food fermentation industry. Trends Food Sci
Technol 2004, 15:67-78.
17. Pederson CS, Breed RS: Fermentation of coffee. Food Res 1946,
11:99-100.
18. Chen Y-S, Yanagida F, Shinohara I: Isolation and identification
of lactic acid bacteria from soil using an enrichment
procedure. Lett Appl Microbiol 2005, 40:195-200.
19. Endo A, Salminen S: Honeybees and beehives are rich sources
for fructophilic lactic acid bacteria. Syst Appl Microbiol 2013,
36:444-448.
20. Mayo B, Aleksandrzak-Piekarczyk T, Fernández M, Kowalczyk M,
Álvarez-Martı́n P, Bardowski J: Updates in the metabolism of
lactic acid bacteria. In Biotechnology of Lactic Acid Bacteria:
www.sciencedirect.com
7
Novel Applications. Edited by Mozzi F, Raya RR, Vignolo GM.
Wiley-Blackwell; 2010:3-32.
21. Velmourougane K: Impact of natural fermentation on
physicochemical, microbiological and cup quality
characteristics of Arabica and Robusta coffee. Proc Natl Acad
Sci India Sect B Biol Sci 2013, 83.
22. Hemme D, Foucaud-Scheunemann C: Leuconostoc,
characteristics, use in dairy technology and prospects in
functional foods. Int Dairy J 2004, 14:467-494.
23. Huys G, Leisner J, Björkroth J: The lesser LAB gods:
Pediococcus, Leuconostoc, Weissella, Carnobacterium, and
affiliated genera. In Lactic Acid Bacteria: Microbiological and
Funcional Aspects. Edited by Lahtinen S, Ouwehand AC, Salminen
S, von Wright A. CRC Press; 2012:93-121.
24. Jouhten P, Ponomarova O, Gonzalez R, Patil KR: Saccharomyces
cerevisiae metabolism in ecological context. FEMS Yeast Res
2016, 16:1-8.
25. Fleet GH: Yeast interactions and wine flavour. Int J Food
Microbiol 2003, 86:11-22.
26. Alexandre H, Guilloux-Benatier M: Yeast autolysis in sparkling
wine – a review. Aust J Grape Wine Res 2006, 12:119-127.
27. Leong K-H, Chen Y-S, Pan S-F, Chen J-J, Wu H-C, Chang Y-C,
Yanagida F: Diversity of lactic acid bacteria associated with
fresh coffee cherries in Taiwan. Curr Microbiol 2014, 68:440-
447.
28. Avallone S, Guyot B, Brillouet JM, Olguin E, Guiraud JP:
Microbiological and biochemical study of coffee fermentation.
Curr Microbiol 2001, 42:252-256.
29. Silva CF, Vilela DM, de Souza Cordeiro C, Duarte WF, Dias DR,
Schwan RF: Evaluation of a potential starter culture for
enhance quality of coffee fermentation. World J Microbiol
Biotechnol 2013, 29:235-247.
30. Pereira GVM, Carvalho Neto DP, Júnior AIM, Vásquez ZS,
 Medeiros ABP, Vandenberghe LPS, Soccol CR: Exploring the
impacts of postharvest processing on the aroma formation of
coffee beans – a review. Food Chem 2019, 272:441-452.
This recent review reported the impacts of coffee processing chain on the
flavor formation of coffee beans. Among the different steps in postharvest
processing, microbial mucilage removal has a major influence on the
volatile composition of processed beans.
31. Avallone S, Guiraud JP, Guyot B, Olguin E, Brillouet JM:
Polysaccharide constituents of coffee-bean mucilage. J Food
Sci 2000, 65:1308-1311.
32. Hugenholtz J: Citrate metabolism in lactic acid bacteria. FEMS
Microbiol Rev 1993, 12:165-178.
33. Garcı́a-Quintáns N, Repizo G, Martı́n M, Magni C, López P:
Activation of the diacetyl/acetoin pathway in Lactococcus
lactis subsp. lactis bv. diacetylactis CRL264 by acidic growth.
Appl Environ Microbiol 2008, 74:1988-1996.
34. Snoep JL, De Mattos MJT, Starrenburg MJC, Hugenholtz J:
Isolation, characterization, and physiological role of the
pyruvate dehydrogenase complex and a-acetolactate
synthase of Lactococcus lactis subsp. lactis bv. diacetylactis.
J Bacteriol 1992, 174:4838-4841.
35. Drider D, Bekal S, Prévost H: Genetic organization and
expression of citrate permease in lactic acid bacteria. Genet
Mol Res 2004, 3:273-281.
36. Sánchez C, Neves AR, Cavalheiro J, dos Santos MM, Garcı́a-
Quintáns N, López P, Santos H: Contribution of citrate
metabolism to the growth of Lactococcus lactis CRL264 at low
pH. Appl Environ Microbiol 2007, 74:1136-1144.
37. Vermeulen N, Gánzle MG, Vogel RF: Influence of peptide supply
and cosubstrates on phenylalanine metabolism of
Lactobacillus sanfranciscensis DSM20451T and Lactobacillus
plantarum TMW1.468. J Agric Food Chem 2006, 54:3832-3839.
38. Smit BA, Vlieg JETVH, Engels WJM, Meijer L, Wouters JTM,
Smit G: Identification, cloning, and characterization of a
Lactococcus lactis branched-chain a-keto acid
Current Opinion in Food Science 2020, 31:1–8
8 Food bioprocessing
decarboxylase involved in flavor formation. Appl Environ
Microbiol 2005, 71:303-311.
39. Jackels SC, Jackels CF: Characterization of the coffee
mucilage fermentation process using chemical indicators: a
field study in Nicaragua. Food Chem Toxicol 2005, 70:321-325.
40. Pereira GVM, Beux M, Pagnoncelli MGB, Soccol VT, Rodrigues C,
Soccol CR: Isolation, selection and evaluation of antagonistic
yeasts and lactic acid bacteria against ochratoxigenic fungus
Aspergillus westerdijkiae on coffee beans. Lett Appl Microbiol
2016, 62:96-101.
41. Pereira GVM, Neto E, Soccol VT, Medeiros ABP,
Woiciechowski AL, Soccol CR: Conducting starter culture-
controlled fermentations of coffee beans during on-farm wet
processing: growth, metabolic analyses and sensorial effects.
Food Res Int 2015, 75:348-356.
42. Lee LW, Cheong MW, Curran P, Yu B, Liu SQ: Coffee
fermentation and flavor – an intricate and delicate
relationship. Food Chem 2015, 185:182-191.
43. Cheong MW, Tong KH, Ong JJM, Liu SQ, Curran P, Yu B: Volatile
composition and antioxidant capacity of Arabica coffee. Food
Res Int 2013, 51:388-396.
44. Muynarsk ESM, Pereira GVM, Mesa D, Thomaz-soccol V,
 Carvalho JC, Pagnoncelli MGB, Soccol CR: Draft genome
sequence of Pediococcus acidilactici strain LPBC161, isolated
from mature coffee cherries during natrual fermentation.
Microbiol Resour Announc 2019, 8 e00332-19.
First sequenced genome of a LAB culture isolated from coffee
fermentation.
45. De Bruyne K, Schillinger U, Caroline L, Boehringer B, Cleenwerck I,
Vancanneyt M, De Vuyst L, Franz CMAP, Vandamme P:
Leuconostoc holzapfelii sp. nov., isolated from Ethiopian
coffee fermentation and assessment of sequence analysis of
housekeeping genes from delineation of Leuconostoc
species. Int J Syst Evol Microbiol 2007, 57:2952-2959.
46. Feng X, Dong H, Yang P, Yang R, Lu J, Lv J, Sheng J: Culture-
dependent and -independent methods to investigate the
predominant microorganisms associated with wet processed
coffee. Curr Microbiol 2016, 73:190-195.
47. Hamdouche Y, Meile JC, Nganou DN, Durand N, Teyssier C,
 Montet D: Discrimination of post-harvest coffee processing
methods by microbial ecology analyses. Food Control 2016,
65:112-120.
The authors report LAB as a microbial marker that appears to be specific
to coffee origin, species or treatment.
48. Nasanit R, Satayawut K: Microbiological study during coffee
fermentation of Coffea arabica var. chiangmai 80 in Thailand.
Kasetsart J Nat Sci 2015, 49:32-41.
49. Pagnoncelli MGB, Brand D, Roussos S, Gaime-Perraud I, Augur C,
Soccol CR: Isolation and identification of lactic acid bacteria
from mature coffee cherries: potential application in coffee
husk ensiling. In New Horizons in Biotechnology. Edited by
Roussos S, Soccol CR, Pandey A, Augur C. Kluwer Academic
Publishers; 2003:321-333.
50. Ribeiro LS, Evangelista SR, Miguel MGCP, van Mullem J, Silva CF,
Schwan RF: Microbiological and chemical-sensory
characteristics of three coffee varieties processed by wet
fermentation. Ann Microbiol 2018, 68:705-716.
51. Schillinger U, Boehringer B, Wallbaum S, Caroline L, Gonfa A,
Huch M, Holzapfel WH, Franz CMAP: A genus-specific PCR
method for differentiation between Leuconostoc and
Weissella and its application in identification of
heterofermentative lactic acid bacteria from coffee
fermentation. FEMS Microbiol Lett 2008, 286:222-226.
52. Silva CF, Schwan RF, Dias ES, Wheals AE: Microbial diversity
during maturation and natural processing of coffee cherries of
Coffea arabica in Brazil. Int J Food Microbiol 2000, 60:251-260.
Current Opinion in Food Science 2020, 31:1–8
53. Velmourougane K: Impact of natural fermentation on
physicochemical, microbiological and cup quality
characteristics of Arabica and Robusta coffee. Proc Natl Acad
Sci India Sect B Biol Sci 2013, 83:233-239.
54. Vilela DM, Pereira GVM, Silva CF, Batista LR, Schwan RF:
Molecular ecology and polyphasic characterization of the
microbiota associated with semi-dry processed coffee
(Coffea arabica L.). Food Microbiol 2010, 27:1128-1135.
55. van Kranenburg R, Kleerebezem M, Vlieg JVH, Ursing BM,
Boekhorst J, Smit BA, Ayad EHE, Smit G, Siezen RJ: Flavour
formation from amino acids by lactic acid bacteria:
predictions from genome sequence analysis. Int Dairy J 2002,
12:111-121.
56. Nierop Groot MN, de Bont JAM: Conversion of phenylalanine to
benzaldehyde initiated by an aminotransferase in
Lactobacillus plantarum. Appl Environ Microbiol 1998, 64:3009-
3013.
57. Hernandez-Orte P, Cersosimo M, Loscos N, Cacho J, Garcia-
Moruno E, Ferreira V: Aroma development from non-floral
grape precursors by wine lactic acid bacteria. Food Res Int
2009, 42:773-781.
58. Ott A, Germond JE, Chaintreau A: Origin of acetaldehyde during
milk fermentation using 13C-labeled precursors. J Agric Food
Chem 2000, 48:1512-1517.
59. Klein N, Maillard M, Thierry A, Lortal S: Conversion of amino
acids into aroma compounds by cell-free extracts of
Lactobacillus helveticus. J Appl Microbiol 2001, 91:404-411.
60. Vermeulen N, Czerny M, Gänzle MG, Schieberle P, Vogel RF:
Reduction of (E)-2-nonenal and (E,E)-2,4-decadienal during
sourdough fermentation. J Cereal Sci 2007, 45:78-87.
61. Gobbetti M, Corsetti A: Lactobacillus sanfrancisco a key
sourdough lactic acid bacterium: a review. Food Microbiol
1997, 14:175-187.
62. Sgarbi E, Lazzi C, Tabanelli G, Gatti M, Neviani E, Gardini F:
Nonstarter lactic acid bacteria volatilomes produced using
cheese components. J Dairy Sci 2013, 96:4223-4234.
63. Ayad EHE, Verheul A, De Jong C, Wouters JTM, Smit G: Flavour
forming abilities and amino acid requirements of Lactococcus
lactis strains isolated from artisanal and non-dairy origin. Int
Dairy J 1999, 9:725-735.
64. Liu SQ, Holland R, Crow VL: Ester synthesis in an aqueous
environment by Streptococcus thermophilus and other dairy
lactic acid bacteria. Appl Microbiol Biotechnol 2003, 63:81-88.
65. Liu S-Q, Holland R, Crow VL: Ethyl butanoate formation by dairy
lactic acid bacteria. Int Dairy J 1998, 8:651-657.
66. Fenster KM, Rankin SA, Steele JL: Accumulation of short n-
chain ethyl esters by esterases of lactic acid bacteria under
conditions simulating ripening parmesan cheese. J Dairy Sci
2003, 86:2818-2825.
67. Gadaga TH, Mutukumira AN, Narvhus JA: The growth and
interaction of yeasts and lactic acid bacteria isolated from
Zimbabwean naturally fermented milk in UHT milk. Int J Food
Microbiol 2001, 68:21-32.
68. Muyanja CMBK, Narvhus JA, Treimo J, Langsrud T: Isolation,
characterisation and identification of lactic acid bacteria from
bushera: a Ugandan traditional fermented beverage. Int J Food
Microbiol 2003, 80:201-210.
69. Coda R, Rizzello CG, Trani A, Gobbetti M: Manufacture and
characterization of functional emmer beverages fermented by
selected lactic acid bacteria. Food Microbiol 2011, 28:526-536.
70. Paul BJ: Enhanced pyruvate to 2,3-butanediol conversion in
lactic acid bacteria. 2013, USPTO 8,455,224 B2 (Patent).
www.sciencedirect.com