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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 the Lactobacillales order, subdivided into six families
multiple ecosystems (water, native soil, air, and plant) find in the (Aerococcaceae, Carnobacteriaceae, Enterococcaceae,
cherry pulp a rich environment for their development. They Lactobacillaceae, Leuconostocaceae, and Streptococca-
utilize pulp substrate as a source of carbon and nitrogen to ceae) and 40 genera (including Aerococcus, Alloiococcus,
produce significant amounts of lactic acid. This natural Carnobacterium, Dolosigranulum, Enterococcus, Fructobacil-
fermentation is purposely used by coffee growers to promote lus, Lactobacillus, Lactococcus, Lactovum, Leuconostoc,
an efficient removal of the mucilage layer adhering to the fruits, Oenococcus, Paralactobacillus, Pediococcus, Streptococcus, Tet-
before storage and transport of the coffee beans. Besides ragenococcus, Vagococcus, and Weissella) according to their
lactic acid, LAB metabolism produces a variety of compounds 16S rRNA gene sequences [2,3].
from the utilization of citrate and the catabolism of amino acids.
Recent studies have demonstrated that these metabolites have Although LAB are mainly associated with dairy matrices,
a complementary function in the formation of taste and flavor the origin of industrial strains is believed to be plant
precursors of coffee beverages. However, the possibility of material [4]. The ubiquity of LAB in nature often results
improving coffee quality by the use of LAB has largely been in opportunistic inoculation of food raw materials [5]. In
ignored. This review considers the importance of LAB coffee processing, LAB from multiple ecosystems find in
associated with coffee processing, exploring their diversity and coffee pulp a rich environment for their development.
metabolism and influences on coffee quality. The selection of Populations above 108 cells/mL of coffee pulp metabolize
appropriate LAB strains, alone or in combination with yeasts, is sugars and other minor constituents to form mainly lactic
a promising research line in a near future, leading to new acid, resulting in pH decrease. The lactic acid, in turn,
perspectives on coffee quality. assists in the breakdown of pectin, a complex carbohy-
drate present in high concentrations in coffee pulp [6].
Address These metabolic activities aid in the subsequent drying
Department of Bioprocess Engineering and Biotechnology, Federal
process by eliminating coffee mucilage constituents,
University of Paraná, Curitiba, Paraná, Brazil
causing reduction of the time required for post-harvest
Corresponding author: Soccol, Carlos R ([email protected]) processing from 21 to 7 days [7,8].

In addition to mucilage removal, LAB have been associ-

Current Opinion in Food Science 2020, 31:1–8
ated with the generation of bioactive compounds related
This review comes from a themed issue on Food bioprocessing to coffee quality. The flavor-forming capability of ‘wild-
Edited by Gabriele Rocchetti type’ LAB cultures in coffee fermentation has gained
For a complete overview see the Issue and the Editorial increased interest due to the diverse aromas such strains
Available online 17th July 2019
are capable of impacting. Some LAB-derived metabo-
lites, such as esters, ketones, higher alcohols, and alde-
https://doi.org/10.1016/j.cofs.2019.07.004
hydes, can influence sensory attributes of coffee bev-
2214-7993/ã 2019 Published by Elsevier Ltd. 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).

Introduction
Lactic acid bacteria (LAB) are a microbial group of Coffee processing
substantial economic importance, used extensively as a In the international market, coffee is classified according
starter culture in the production of fermented foods. to the postharvest processing technology used to remove
Metabolic-based definition classifies LAB by the forma- the outer layers adhered to the fruits: ‘natural coffee’,
tion of more than 50% lactic acid as end product of produced from coffee beans processed on the farm by the
carbohydrate utilization, besides being gram-positive, simple method of sun-drying, known as dry processing;
non-motile, and non-spore-forming bacteria with cocco- and ‘washed coffee’, produced from coffee beans that
bacilli or rods morphology [1]. The LAB are comprised by undergo a relatively complex series of steps, including

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2 Food bioprocessing

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

Figure 1
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ai
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u

hi
di

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Ca

Ha

Ch

Co
Ec

Th

Ta

Ta
Br

Et
In

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. 3

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

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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 situation. Another culture, Lcb. rhamnosus HN001,
designed for fermenting coffee beans, mainly due to the selected by Wang et al. [9], was also able to promote
physical and chemical peculiarities of this process [41]. A an efficient consumption of pulp substrate.
primary strategy for research in food applications is
screening from the natural ecosystem. Recently, the Impact on beverage quality
removal of coffee mucilage using lactic acid fermentation Coffee consumption has greatly increased all around the
was proposed by introducing a selected LAB, Lcb. plan- world. This is reflected by the growing number of coffee
tarum LPBR01, isolated from natural coffee fermentation bars and local brands in consuming countries. Thus,
[10]. This bacterium strain was able to promote an international competition within the coffee market is
accelerated coffee-pulp acidification process reducing providing new challenges for innovation in this sector.
the time required for mucilage removal into field 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 acid during fermentation process promotes the modifica-
ignored the possibility of controlling coffee fermentation tion in sensorial perception of acidity and body of coffee
during on-farm processing [42]. The complex metabolism beverages [7,10]. From citrate metabolism, the produc-
of LAB yields flavor-active metabolites that impact on tion of 2,3-butanedione and acetoin confers buttery-like
coffee quality (Table 1). The intense diffusion of lactic 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 citrate, and amino acids, and the key components pro-
catabolism of amino acids, specifically ethyl propionate, duced during their growth, are the main activities associ-
ethyl acetate, acetaldehyde, phenyl ethanol, and pheny- ated with coffee processing. They act by demuciling
lacetaldehyde, are known for increasing fruity and floral coffee fruits through pulp acidification, besides forming
perceptions in final beverage [30]. flavor-active metabolites that add quality to final coffee
products. However, the use of LAB in coffee processing
Undoubtedly, aroma is one of most important character- has largely been overlooked. To date, only two species,
istics that contribute to the quality of coffee. As in many Lcb. plantarum LPBR01 and Lcb. rhamnosus HN001, were
foods, coffee aroma is composed by over 1000 different evaluated under field conditions. This is a small fraction
volatile organic compounds with concentrations that can within the rich diversity of species involved in natural
vary between 845 and 1239 ppm [43]. The balance and fermentations. For example, Leuconostoc sp., a versatile
interaction of all of them determine the coffee aromatic microbial group with useful properties, have never been
quality. The use of LAB cultures was demonstrated to be recovered as a starter culture. Undoubtedly, the full
favorable for the production of coffee with distinctive potential of coffee related LAB has not been fully deter-
sensory profiles. Coffee beverages with high acidity and mined and many challenges are awaiting research, dis-
fruity and floral perceptions were produced by the use of semination, and industrial exploitation. Future research
the Lcb. plantarum LPBR01 [10], while caramelic and should be focused on the investigation of new LAB and
burnt characteristics were the sensory attributes for Lcb. the possibility of creating multi-purpose mixed cultures
rhamnosus HN001inoculated treatment. These coffee with yeast strains. As reported above, several features
beverages can strategically be used to supply specific influence LAB activities in coffee fermentation. To
coffee consumer regions or be used in blends to achieve obtain a more complete picture on LAB interaction in
desirable acidity and distinctive flavor. inoculated fermentation (pure and mixed with yeast) a
multifactorial approach using ‘omics’ methodologies
Functional genomic should be planned. Furthermore, the emerging field of
The recent development of high-throughput sequencing synthetic biology using the sinecology concept can be
technology has expanded the knowledge about LAB’s applied to understand and control intercellular interac-
metabolic potential and bioprocessing capabilities. The tion, spatiotemporal coordination, and stability of LAB
genome of LAB is among the best characterized to date. within microbial consortia of coffee fermentation.
However, only recently, the whole genome sequencing of
a LAB (P. acidilactici LPBC101) originated from coffee
fermentation was published [44]. This genome arrange-
Conflict of interest statement
Nothing declared.
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 Acknowledgement
of unique genes involved in the use of coffee pulp sugars The authors gratefully acknowledge the support provided by Brazilian
and encoding stress-related proteins (e.g. thiol peroxi- Council for Scientific and Technological Development (grant number
dase, glutathione reductases, NADH-oxidases, and alka- 303254/2017-3).
line-shock proteins). In addition, this coffee-related LAB
strain possesses a remarkable phenotypic diversity, pos- References and recommended reading
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tolase, and pentose-phosphate pathways [44]. The pres- have been highlighted as:
ence of these genes can be used as solid scientific  of special interest
evidence in searching LAB with potential applications  of outstanding interest
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