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World Journal of Microbiology and Biotechnology (2020) 36:186

https://doi.org/10.1007/s11274-020-02963-7

ORIGINAL PAPER

The use of mesophilic and lactic acid bacteria strains as starter


cultures for improvement of coffee beans wet fermentation
Luciana Silva Ribeiro1 · Maria Gabriela da Cruz Pedrozo Miguel1 · Silvia Juliana Martinez1 ·
Ana Paula Pereira Bressani2 · Suzana Reis Evangelista1 · Cristina Ferreira Silva e Batista1 · Rosane Freitas Schwan1 

Received: 27 April 2020 / Accepted: 12 November 2020


© Springer Nature B.V. 2020

Abstract 
The use of starter cultures during food fermentation aims to standardize the process and to obtain a higher quality product.
The objectives were to study mesophilic bacteria (MB) and lactic acid bacteria (LAB) isolated from wet coffee processing
and evaluate their performance in a pulped coffee medium. Eighty-six bacteria isolates (59 MB and 27 LAB) were assessed
for pectinolytic activity, metabolite production, and pH value decrease in coffee-based culture (CPM). Seven bacteria strains
(3 MB and 4 LAB) were selected and used as starter cultures in the wet fermentation of pulped coffee. The MB and LAB
populations varied from 4.48 to 8.43 log CFU g−1 for MB and 3.54 to 8.72 log CFU g−1 for LAB during fermentation.
Organic acid concentration (ranged from 0.01 to 0.53 for succinic acid; 0.71 to 8.14 for lactic acid and 0.06 to 0.29 for acetic
acid), and volatile compounds (44 compounds were detected in green beans and 98 in roasted beans) were evaluated during
fermentation. The most abundant compounds found in roasted beans belong to furans [15], ketones and esters [14], pyridines
[13], and pyrazines [12]). Leuconostoc mesenteroides CCMA 1105 and Lactobacillus plantarum CCMA 1065 presented
volatile compounds important for coffee aroma. Isovaleric acid; 2,3-butanediol; phenethyl alcohol; β-linalool; ethyl linoleate;
and ethyl 2-hydroxypropanoate could improve cupping qualities.

Electronic supplementary material  The online version of this


article (https​://doi.org/10.1007/s1127​4-020-02963​-7) contains
supplementary material, which is available to authorized users.

* Rosane Freitas Schwan


rschwan@ufla.br
Luciana Silva Ribeiro
luciana.ufla@gmail.com
Maria Gabriela da Cruz Pedrozo Miguel
mgcpmiguel@gmail.com
Silvia Juliana Martinez
silvia292004@gmail.com
Ana Paula Pereira Bressani
paulinhabressani@hotmail.com
Suzana Reis Evangelista
suzanareise@gmail.com
Cristina Ferreira Silva e Batista
cristinafsb@ufla.br
1
Department of Biology, Federal University of Lavras,
Campus Universitário, Lavras, MG 3037, Brazil
2
Food Science Department, Federal University of Lavras,
Lavras, MG, Brazil

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Graphic abstract

Keywords  Acid lactic bacteria · Arabica · Coffee aroma · Coffee fermentation · Mesophilic bacteria · Volatile metabolites

Introduction precursors present in green beans before roasting. Differ-


ent concentrations of flavor precursors in green beans can
The mucilage of coffee fruits is an insoluble hydrogel rich in provide different profiles of coffee beverages. For example,
fermentable sugars and nitrogen that turn into a suitable sub- furans are among the predominant coffee flavor groups and
strate for microbial growth (Silva 2015). Along with micro- produce caramel-like odors (Batista and Chalfoun 2015).
bial reproduction, those molecules are either transformed in As furans, esters are associated with positive notes because
enzymes, acids, or volatile compounds. Previously described they positively influence beverage by producing fruity fla-
enzymes include the polygalacturonase (PG), which cata- vors (Toledo et al. 2016). These chemical variations are also
lyzes the hydrolysis of 1,4-glycosidic bonds in polygalac- influenced by the fermentation phase, just as reported in Lee
turonic acid. The pectin lyase (PL) that catalyzes pectin et al. (2015), Bressani et al. (2019), and Wang et al. (2019a),
breakdown by releasing galacturonic unsaturated acids. which showed differences in the non-volatile profile of green
Lastly, the pectin methylesterase (PME) that is responsible beans and the flavor profile.
for de-esterification of the methoxy group of pectin-forming Microorganisms have been used as starter cultures in dif-
pectic acid and methanol (Agate and Bhat 1966; Massawe ferent fermentative processes for thousands of years. The
and Lifa 2010; Silva et al. 2013; Haile and Kang 2019). evolution of taxonomy and identification methods has led
Mutual interaction of extracellular enzymes and organic to various extensions of these microorganisms’ use in fer-
acids leads to macromolecules’ hydrolysis (carbohydrates, mented foods (Bourdichon et al. 2012; Elhalish and Zhao
proteins, and polyphenols). It resulted in important aroma 2020). Yeasts’ use as starter cultures in natural and semi-
precursors, such as reducing sugars, proteins, amino acids, dry coffee has been documented (Evangelista et al. 2014;
and phenolic compounds (Lee et al. 2015). Ribeiro et al. 2017; Martinez et al. 2017; Bressani et al.
Changes of the volatiles profile and cupping qualities 2018); however, the use of bacteria in the wet process is still
in roasted coffee depend on the chemical composition of unknown. There are numerous bacterial species possibilities

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World Journal of Microbiology and Biotechnology (2020) 36:186 Page 3 of 15  186

as starter cultures that can and should be exploited, espe- ­MgSO4 0.02%, ­CaCl2 0.0002%, ­H3BO3 0.0002%, 0.0002%,
cially for wet processing. ­M nSO 4, 0.0014%, Z ­ nSO 47H 2O, 0.001%, C ­ uSO 45H 2O,
Microbial starter cultures produce coffee with different 0.0002% ­MoO3) for determination of the activity of the PG
aromas and flavors, leading to new perspectives on cof- enzyme. The determination of the PL enzyme activity was
fee quality. The relationship between coffee fermentation carried out using an MP7 medium; this had the same con-
and coffee aroma profile is very close (Jackels and Jackels stitution as described above, except for a substitution of
2005; Jackels et al. 2006; Gonzaléz-Rios et al. 2007; Lin polygalacturonic acid for the citrus pectin. A CTBA solu-
2010). With optimized parameters and selection of starter tion 1% (polygalacturonic acid and pectin with cetylmethyl
cultures to remove mucilage, controlled fermentation might ammonium bromide) was used as the revealed solution
confer specific desirable attributes to coffee beverages. The for the enzymatic assay, being considered positive when
targeted use of different bacteria species would lead to a there was the formation of clear halo around the colony.
greater diversification of flavors, which is already evident in The yeast Kluyveromyces marxianus CCT 3172 (Schwan
the fermented food and wine industry (Marshall and Mejia et al. 1997) was used as a positive control.
2011). Therefore, this work’s objective was to select bacteria
strains isolated from arabica coffee fruits capable of produc-
ing organic acids and volatile compounds during wet coffee Quantification of pectin lyase (PL) and pectin
fermentation. methylesterase (PME) activity

The activity of PL and PME was quantified in culture


Material and methods mediums with coffee, using only strains that showed posi-
tive qualitative pectinase results (test described above).
Bacteria isolates The PL activity was determined by increasing the absorb-
ance of the medium (Albersheim 1966), using the extinc-
The microorganisms were isolated during the wet process tion coefficient of 5550 M−1 cm−1. A pectin solution (3 mL
from three different coffee varieties (Coffea arabica L. citrus pectin 2.5% in 100 mM phosphate buffer, pH 6.8)
var. Ouro Amarelo, Mundo Novo, and Catuaí Vermelho) was mixed with 4.5 mL of culture supernatant. The mix-
(Ribeiro et al. 2018). A total of 86 coffee isolates (including ture was incubated at 40 °C, and 0.5 mL was collected at 0,
59 Mesophilic Bacteria (MB) and 27 Lactic Acid Bacteria 10, 15, 20, and 30 min; each time, the reaction stopped by
(LAB)) (Table 1). The MB was reactivated on nutrient broth adding 4.5 mL of 0.01 M HCl. The samples were analyzed
NB (Himedia, Mumbai, India). The LAB was maintained on at 235 nm. The equipment was calibrated with a pectin
MRS (Man Rugosa Sharp) broth (Merck, Darmstadt, Ger- solution and culture medium containing coffee without
many) during the experiment conduct, and both scored in inoculation.
an ultra-freezer at − 80 °C, containing 20% glycerol (w/w). The PL activity was expressed from the calculation of
the galacturonides concentration released by the PL action:
Experimental design
A = 𝜀 × l × C,
The work plan was conducted in two stages, as shown in where A = the absorbance of the sample at 235 nm; ε = the
Fig. 1. First, 86 isolates were tested for their ability to pro- molar extinction coefficient ­(M−1 cm−1); 1 (one) = the opti-
duce pectinase and metabolites using a coffee pulp medium cal path (1 cm); and C = analyte concentration, expressed
(CPM). Secondly, the best-selected strains were inoculated in M.
in wet coffee fermentation. The PME activity quantification was determined by
titration according to the methodology proposed by Bara-
Characterization and selection of best bacteria cat et al. (1989). The reaction was carried out with 3 mL of
strains the culture supernatant mixed with 20 mL of citrus pectin
1% (60% methoxylated or higher) in a solution of NaCl
Pectinase activity of microorganisms 0.1 M. The pH 7.5 was adjusted with NaOH 0.5 M. This
solution was incubated for 30 min at 30 °C, and the pH
The pectinolytic activity of the 86 strains was determined was maintained at 7.5 by the addition of NaOH 0.02 M.
as described in Schwan et  al. (1997) and Silva et  al. The PME activity was proportional to the NaOH volume
(2013). The strains were grown on plates containing MP5 spent to keep the pH at 7.5. PME activity was expressed
mineral medium (0.5% glucose, 0.5% polygalacturonic as the micro equivalent of polygalacturonic acid ­mL−1 h−1.
acid, 0.6% ­KH2PO4, 0.1% yeast extract, 0.2% ­(NH4) ­SO4, The analyzes were carried out in triplicate.
1.5% agar, and 0.1 mL of the solutions: F ­ eSO4 0.0001%,

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Table 1  Bacterial isolates used Species Number strain Species Number strain


in fermentative performance
in culture medium containing Bacillus subtilis group CCMA ­1228OA Rhizobium radiobacter CCMA ­1212MN
coffee peel and pulp CCMA ­1234 MN

CCMA ­1235CV Rhizobium pusense CCMA ­1200CV


CV
CCMA ­1236
CCMA ­1237CV Rhodococcus pyridinivorans CCMA ­1214CV
CV
CCMA ­1238 CCMA ­1282CV
CV
CCMA ­1239
CCMA ­1240CV Pantoea vagans CCMA ­1208OA
CV
CCMA ­1241 CCMA ­1209OA
CV
CCMA ­1242 CCMA ­1210OA
CV
CCMA ­1244
Bacillus pumilus group CCMA ­1248CV Pantoea agglomerans CCMA ­1211CV
CV
CCMA 1249 CCMA ­1277CV
CCMA ­1250MN Microbacterium paraoxydans CCMA ­1152CV
CCMA ­1251CV CCMA ­1153CFW
CCMA1252CV Microbacterium testaceum CCMA ­1147CFW
CCMA ­1272CV CCMA ­1148CFW
CCMA 1273 CV CCMA ­1150CFW
CCMA 1274 CV CCMA ­1151MN
Bacillus safensis CCMA ­1232OA CCMA ­1082OA
CCMA ­1083OA
OA
Bacillus megaterium CCMA ­1245 CCMA ­1084OA
VC
CCMA ­1246 CCMA ­1085OA
CCMA ­1087MN
OA
Bacillus clausii CCMA ­1229 Leuconostoc mesenteroides CCMA ­1089MN
OA
CCMA ­1230 CCMA ­1090MN
OA
CCMA ­1231 CCMA ­1105CV
OA
CCMA ­1283 CCMA ­1106CV
OA
Bacillus licheniformis CCMA ­1233 CCMA ­1108CV
CCMA ­1109CV
OA
Bacillus asahii CCMA ­1247 CCMA ­1110CV
CCMA ­1111CV
OA
Bacillus horneckiae CCMA ­1265 CCMA ­1112CV
CV
CCMA ­1266 CCMA ­1115CV
CCMA ­1117CV
MN
Bacillus humi CCMA ­1217 CCMA ­1120CV
MN
Bacillus simplex CCMA ­1216 Lactobacillus plantarum CCMA ­1058OA
CCMA ­1059OA
OA
Lysinibacillus fusiformis CCMA ­1263 CCMA ­1064OA
MN
CCMA ­1264 CCMA ­1065OA
CCMA ­1067MN
MN
Lysinibacillus macroides CCMA ­1280 CCMA ­1071CV
MN
CCMA ­1281 CCMA ­1072CV
CCMA ­1076CV
MN
Brevibacillus parabrevis CCMA ­1218 CCMA ­1078CV
CCMA ­1080CV
CV
Psychrobacillus psychrotolerans CCMA ­1215 Paenibacillus cookii CCMA ­1267OA
CFW
Paenibacillus illinoisensis CCMA ­1269 Paenibacillus lactis CCMA ­1268MN
OA
Paenibacillus konsidensis CCMA ­1253 Arthrobacter koreensis CCMA ­1157CV
CCMA ­1279CV
OA MN CV CFW
ISOLATED FROM: Coffea arabica var. Ouro Amarelo; Mundo Novo; Catuaí Vermelho; Cof-
fee fermentation water

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Fig. 1  Flowchart of the bacteria


selection process

Growth assessment in coffee‑based medium Organic acids

The bacteria fermentation were carried out in a culture Malic, lactic, acetic, butyric, propionic, citric, oxalic, suc-
medium containing coffee pulp (CPM) as described in cinic, and tartaric acid were analyzed by high-performance
Silva et al. (2013):100 g of coffee cherries were homog- liquid chromatography (HPLC). Samples of fermented
enized in a ­Stomacher ® with 1 L of distilled water for coffee medium were centrifuged (10.000 rpm at 4 °C for
10  min; it was then filtered, and 0.5% of glucose was 10 min), and the supernatant was filtered using a 0.22 μm
added. The pH value was adjusted to 5.5 with HCl (0.1 M) cellulose acetate filter. The extracts were analyzed using an
solution, and the media were sterilized in flowing steam HPLC system (Shimadzu, Japan). A Shimpack SCR-101H
for 20 min. (7.9 mm × 30 cm) column was used with a 100 mM solu-
The bacteria were grown up to a concentration of tion of perchloric acid with a flow rate of 0.6 mL/minute as
­10  CFU mL−1 in NB for MB and MRS for LAB. Subse-
7
the mobile phase. The oven temperature was kept at 50 °C,
quently, the cells were centrifuged and resuspended in ster- detected with a 210 nm UV detector. The compound quan-
ile peptone water (0.1%). The inoculum ­(107 CFU mL−1) tification was performed using calibration curves, differ-
was transferred separately to 500 mL flasks containing ent standard concentrations were analyzed using the same
CPM medium (100 mL) and kept at 30 °C for 48 h. Sam- conditions used for the samples, and the analyses were per-
ples were collected at intervals (12, 24, and 48 h of fer- formed in triplicate.
mentation and final drying) for chemical and microbio-
logical analysis. The fermentations were carried out in Second experimental stage
triplicate.
Coffee fermentation inoculated with bacteria

Microbiological analysis Selected bacteria strains were used to carry out fermenta-
tion on a larger scale and the control fermentation, which
Serial decimal dilutions were performed with sterile pep- is without inoculation. Coffee cherries of the Catuaí Ver-
tone water (0.1% bacteriological peptone) to assay the MB melho variety were mechanically harvested on a farm
and LAB population. The MB population was quantified on located in Lavras, Minas Gerais State, Brazil, at 900 m
nutrient agar, and LAB was quantified on MRS agar. The above sea level. Three kilograms of pulped coffee were
plates were incubated at 30 °C and 35 °C, respectively, for fermented in plastic buckets with 2 L of sterile distilled
48 h. water. A population of ­107 ­CFUg−1 of coffee of the cho-
sen strains was inoculated separately in each vessel. The
fermentation time was 48 h. After fermentation, the water

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was discarded, and coffee was transferred to suspended Results


terraces for sun drying until 11–12% moisture [Gehaka
model G650J]. Samples were collected for microbiologi- Evaluation of the fermentative performance
cal and chemical analysis. The coffee fermentation was of bacteria
performed in triplicate.
The first criterion was the ability to decrease the pH value,
the initial pH was 5.5, and a variation between the strains
Parameters evaluated in inoculated coffee tested was observed (Fig. 2), where some strains promoted
increased, others decreased the pH value. Microbacterium
The bacterial population and organic acid concentration testaceum CCMA 1147 and 1148 the strains that presented
in the inoculated coffee were assessed according to the the most considerable pH reduction, significantly different
above items. from the others (3.73 and 3.55, respectively). In compari-
Analyses of volatile compounds were done on green son, the LAB strains lowered the pH value to around 3.7
and roasted coffee by gas chromatography/mass spectrom- (Fig. 3). Leuconostoc mesenteroides CCMA 1082, 1105,
eter (GC/MS). Volatile compounds were extracted using a and 1117 were the strains that showed the most significant
manual headspace-solid-phase microextraction procedure pH reduction, significantly different from the others (3.68,
(HS-SPME), according to Evangelista et al. (2014). The 3.40, and 3.67, respectively). The decrease in pH values
compounds were analyzed using a Shimadzu QP2010 GC was from 26 to 38% in fermentation using LAB as a starter
model equipped with mass spectrometry (MS) and a silica culture, whereas fermentation inoculated with MB reduced
capillary Carbo-Wax 20 M (30 m × 0.25 mm × 0.25 mm) the pH values by up to 32%.
column. Operating conditions were performed as described The results population counting criterion showed that
by Ribeiro et  al. (2017). The volatile compounds were the initial population inoculated was 7 log CFU g−1(Fig. 2),
identified by comparing the mass spectra to the NIST11 strains that increase their population, or remain in the ini-
library. Besides, an alkane series (C10–C40) was used to tial community are of interest. Arthrobacter koreensis
calculate the retention index (RI) for each compound, which CCMA 1157 (8.66 CFU g−1), Microbacterium testaceum
was compared with RI values found in the literature data CCMA 1151 (8.84 CFU g−1), Leu. mesenteroides CCMA
(Czerny and Grosch 2000; Eom and Jung 2013; Piccino 1082, 1090, 1105 (8.05; 8.08; 8.04 CFU g−1, respectively)
et al. 2014). and Lactobacillus plantarum CCMA 1065 and 1072 (7.95
and 7.93 CFU g−1, respectively) were the strains that pre-
sented the largest final population, significantly different
Statistical analysis from the others (Figs. 2, 3).
Eighty-six bacterial isolates tested on plates, 22 strains
The organic acid data were evaluated by variance analy- showed a positive result for PL, and 4 showed a positive
sis (ANOVA), and the Scott–Knott test was used for com- outcome for PME, and the results were based on growth or
parison between means. An 8 × 4 factorial arrangement non-growth (data not shown). Only MB showed positive
of treatment was used to analyze the results of the organic results for pectinolytic activity, Bacillus subtilis CCMA
acid: ten treatments (control, CCMA 1234, CCMA 1251, 1234, 1236, and 1237, and Paenibacillus konsidensis
CCMA 1151, CCMA 1082, CCMA 1105, CCMA 1065, CCMA 1253 showed higher results for PL activity (0.073;
CCMA 1072) and five sample collection times (T12, T24, 0.064; 0.057 and 0.073 U/mL, respectively). B. subtilis
T48, dried coffee). The data were analyzed under the fol- CCMA 1238 and 1239 showed the highest results for PME
lowing model: activity of 0.483 and 0.450 micro equivalent m ­ L−1 h−1,
respectively (Table 2).
X = 𝜇 + Treatj + Timek + Treat × Timejk + ejk.
Metabolites results presented below are associated
where µ  =  global mean; Treatj  =  treatment effect with fermentation in coffee-based medium (Supplemen-
(j = control, CCMA 1234, CCMA 1251, CCMA 1151, tary Material). The citric acid production was mainly
CCMA 1082, CCMA 1105, CCMA 1065, CCMA 1072); characterized when inoculated with Bacillus pumilus
Timek = time collected effect (k = T12, T24, T48, dried CCMA 1248; B. pumilus CCMA 1251; and B. horneckiae
coffee); Treat × Timejk = effect of interaction between CCMA 1265, and Leuconostoc mesenteroides CCMA
treatment and time collection time; and ejk = experimen- 1105. Malic and tartaric acid production were associated
tal error. The tests were performed using Sisvar 5.6 soft- with Pantoea agglomerans CCMA 1277 and between the
ware (Ferreira 2014). The significance level was defined LAB, Leu. mesenteroides CCMA 1082 and Leu. mesenter-
at p < 0.05 level. oides CCMA 1106 was related to malic acid production.

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Fig. 2  Mesophilic bacterial population ­(Log10 CFU g-1 ) and pH (42) P. lactis; (43–44) A. koreensis; (45) R. radiobacter; (46) R. puse-
( ) of culture medium containing coffee pulp at final fermenta- nse; (47–48) M. paraoxydans; (49–52) M. testaceum; (53–54) R. pyri-
tion. (1–11) B. subtilis; (12–19) B. pumilus; (20) B. safensis; (21–22) dinivorans; (55–57) P. vagans; (58–59) P. agglomerans. The stand-
B. megaterium; (23–26) B. clausii; (27) B. licheniformis; (28) B. asa- ard deviation of the mean pH was less than 0.05. Error bars represent
hii; (29–30) B. horneckiae; (31) B. humi; (32) B. simplex; (33–34) L. standard deviations of means of population. There was a statistical
fusiformys; (35–36) L. macrolides; (37) B. parabrevis; (38) P. psy- difference at p < 0.05 by the Scott–Knott test
chrotolerans; (39) P. illinoisensis; (40) P. konsidensis; (41) P. cookie;

Fig. 3  Lactic acid bacterial population ­(Log10 CFU g-1 ) and pH ard deviation of the mean pH was less than 0.05. There was a statisti-
( ) of culture medium containing coffee pulp at final fermenta- cal difference at p < 0.05 by the Scott–Knott test
tion. (1–17) Leu. mesenteroides; (18–27) Lac. plantarum. The stand-

Arthrobacter koreensis CCMA 1157 and P. dispersa almost all Leu. mesenteroides (CCMA 1083, CCMA 1085,
CCMA 1278 were mainly characterized by propionic acid CCMA 1087, CCMA 1090, CCMA 1109, and CCMA 1112)
production. tested were characterized by acetic acid production.
Succinic and acetic acids were primarily associated with Microbancterium testaceum CCMA 1147 and 1148,
Microbacterium paraoxydans CCMA 1152, Rhizobium Lactobacillus plantarum CCMA 1065, and CCMA 1072
radiobacter CCMA 1212, and R. pusense CCMA 1200, and were characterized by lactic acid production. Strains

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Table 2  Pectin lyase (PL) No. Strain Species PLa (U/mL) PMEb ­(mL−1 h−1)
and pectin methyl esterase
(PME) activities quantified in 1 CCMA 1234 Bacillus subtilis 0.073 ± 0.01c 0.100 ± 0.01a
CPM medium fermented with
2 CCMA 1228 0.013 ± 0.03a 0.250 ± 0.00b
mesophilic and lactic acid
bacteria 3 CCMA 1236 0.064 ± 0.00c 0.070 ± 0.00a
4 CCMA 1237 0.057 ± 0.02c 0.100 ± 0.06a
5 CCMA 1238 0.033 ± 0.01b 0.483 ± 0.03d
6 CCMA 1239 0.021 ± 0.00b 0.450 ± 0.00d
7 CCMA 1240 0.024 ± 0.03b nd
8 CCMA 1241 0.005 ± 0.02a 0.250 ± 0.00b
9 CCMA 1242 0.029 ± 0.00b 0.383 ± 0.03c
10 CCMA 1244 0.001 ± 0.02a 0.250 ± 0.00b
11 CCMA 1248 Bacillus pumilus 0.016 ± 0.00a nd
12 CCMA 1251 0.025 ± 0.01b nd
13 CCMA 1273 0.010 ± 0.02a 0.250 ± 0.00b
14 CCMA 1253 Paenibacillus konsidensis 0.073 ± 0.01c 0.100 ± 0.06a
15 CCMA 1211 Pantoea agglomerans 0.033 ± 0.01b 0.070 ± 0.04a
16 CCMA 1278 Pantoea dispersa 0.055 ± 0.05b 0.633 ± 0.03e
17 CCMA 1279 Arthrobacter korensis 0.001 ± 0.00a nd

nd not detected. a–e mean values with different letters are significant at p < 0.05 for each treatment based
on the Scott–Knott test
a
 Expressed as the amount (in μmol) of unsaturated galacturonides/min per ml of culture supernatant U/mL)
b
 Expressed as micro equivalents of pectic acid released per ­ml−1 h−1)

Fig. 4  Population count (­log10 ­CFUg-1) of mesophilic bacteria (a) (----); Lac. plantarum CCMA 1065 (.....); Microbacterium testaceum
and lactic acid bacteria (b) during fermentation and drying of wet- CCMA 1151 (♦); Bacillus pumilus CMMA 1251 (▲) and Bacillus
processed coffee. Control (•); Leu. mesenteroide CCMA 1105 (*); subtilis CCMA 1234 (■)
Leu. mesenteroide CMMA 1082 (×); Lac. plantarum CCMA 1072

belonging to the Lac. plantarum species increased the Use of starter selected bacteria in wet coffee
lactic acid concentration by more than 50%. Based fermentation
on these criteria, the selected strains were B. subtilis
CCMA 1234, B. pumilus CCMA 1251, Microbacterium Three MB and four LAB strains were inoculated separately
testaceum CCMA 1151, Leu. mesenteroides CCMA in wet coffee fermentation. Among the MB count tested,
1082 and CCMA 1105, Lac. plantarum CCMA 1065 there was a significant difference (p < 0.05) in the treatments
and CCMA 1072. and fermentation time (Fig. 4a). During fermentation (T12
to T48), there was a significant decrease (p < 0.05) in MB in

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Fig. 5  Organic acid concentration (mg  g−1) of culture medium con- (×); Lac. plantarum CCMA 1072 (----); Lac. plantarum CCMA 1065
taining coffee pulp fermented with Mesophilic Bacteria at final fer- (.....); Microbacterium testaceum CCMA 1151 (♦); Bacillus pumilus
mentation. a Succinic acid; b lactic acid; c acetic acid. Control (•); CMMA 1251 (▲) and Bacillus subtilis CCMA 1234 (■)
Leu. mesenteroide CCMA 1105 (*); Leu. mesenteroide CMMA 1082

almost all the fermentations. However, in treatments inocu- in succinic acid concentration in all treatments. The fer-
lated with B. subtilis CCMA 1234 and B. pumilus CCMA mentation with Leu. mesenteroides CCMA 1105 presented
1251, there was an increase in population (from 4.91 to 5.34 the highest concentration of succinic acid (0.54 mg g−1),
and 5.34 to 6.04 log CFU g−1, respectively). After T48 of and Leu. mesenteroides CCMA 1082 presented the lowest
fermentation, the MB decreased its population. There was concentration (0.22 mg g−1).
a significant increase (p < 0.05) in the LAB population in There was an increase (p < 0.05) in lactic acid con-
fermentations inoculated with MB. The fermentation inocu- centration, with the highest increase in final drying time
lated with Lac. plantarum CCMA 1065, CCMA 1072, and (dried coffee) (Fig. 5b). The fermentation inoculated with
Leu. mesenteroide CCMA 1105 showed a decrease of the LAB showed a higher lactic acid concentration, which was
LAB population (reaching the end of fermentation [T48] already expected. The fermentation with MB showed 5.0
with an average population of 7,24; 6,85 and 6.65 log and 5.9 mg g −1 of lactic acid, while fermentation with
CFU g−1, respectively). LAB showed 7.6 and 8.1 mg g −1. The highest concen-
Succinic, lactic, and acetic acids were detected, and tration of acetic acid was found in fermentation without
there was a significant difference (p < 0.05) among treat- inoculation (control—0.18 mg g−1) in 48 h of fermenta-
ments (Fig. 5), and these acids, the lactic acid was pro- tion (Fig. 5c). All treatments showed an increase in ace-
duced in greater concentration in all fermentations. There tic acid concentration at the end of fermentation (T48)
was a decrease in the succinic acid concentration (Fig. 5a) (Fig. 5c). Acetic acid was not detected in the fermentation
inoculated with MB and Leu. mesenteroides CCMA1082. inoculated with Leu. mesenteroides CCMA 1105 at any
Inoculated fermentation with LAB (Leu. mesenteroides sampling time, and in fermentations with Lac. plantarum
CCMA 1105, Lac. plantarum CCMA 1065, and CCMA CCMA 1072 and 1065 presented low concentrations of
1072) showed an increase in the succinic acid concentra- this acid, which seems to be a positive point for the use of
tion (Fig. 5a). At the end of drying, there was an increase these starter cultures.

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Forty-four volatile compounds were detected by HS- Discussion


SPME GC–MS analysis in the green coffee fermented with
bacteria inoculation and spontaneous fermentation (Table 3). We used four criteria for selecting bacteria to be used as
Some compounds were detected in specific samples, such as starter cultures in wet coffee fermentation. And these were
1-phenoxypropan-2-ol (B. subtilis CCMA 1234), phytol, and (i) pH decrease, (ii) increase in bacteria population, (iii)
ethyl linoleate (C. cellulans CCMA 1186) and octadecane pectinases, and (iv) organic acids (lactic, malic, succinic,
(Leu. mesenteroides CCMA 1105). The fermentation with citric, and propionic acids) production in the coffee pulp
M. testaceum CCMA 1151 and Lac. plantarum CCMA 1065 medium. pH values decreased over the fermentation time
showed a higher percentage of aldehydes and ketones, pre- when evaluated in a coffee-based (CP) medium (Figs. 2,
dominately found after 48 h. Isovaleric acid was detected in 3). During coffee fermentation, the pH value decreased
spontaneous fermentation, Leu. mesenteroides CCMA 1105, due to acid production by microorganisms; thus, the ability
and d Lac. plantarum CCMA1065. While 2,3-butanediol to survive in a coffee fermentation medium is an essential
in coffee beans fermented by C. cellulans CCMA1186). feature for the starter culture’s viability maintenance. The
Phenethyl alcohol was detected in samples from coffee beans pH value decreased due to acid production by microorgan-
without inoculation, Leu. mesenteroides CCMA 1105, and isms (Elhalish and Zhao 2020); thus, the ability to survive
Lac. plantarum CCMA1065. β-linalool (Leu. mesenteroides in a coffee fermentation medium is essential for the starter
CCMA 1105); 2-hexenal (without inoculation and Leu. mes- culture’s viability maintenance. It is worth remembering
enteroides CCMA 1105); ethyl 2-hydroxypropanoate (with- that until now, Leu. mesenteroides CCMA 1105, in addi-
out inoculation and Leu. mesenteroides CCMA 1105); and tion to increasing its population during fermentation in a
tetracosane (Leu. mesenteroides CCMA 1105) influenced coffee-based medium, also decreased the pH value in the
coffee quality. first experimental stage performed in the present study.
A total of 98 volatile compounds was detected in the Species of the lactic acid bacteria group are increasingly
roasted coffee (Table 4). Among these compounds, acids being used in fermentation processes. These have shown
(6), aldehydes and ketones (14), esters (14), furans (15), lac- positive results as presented by Wang et al. (2019a), who
tones (4), phenols (4), pyrans (3), pyrazines (12), pyridines used LAB to ferment green coffee beans and evaluate
(13), pirroles (8) and other compounds (alkaloids, alcohol, changes in final roasted coffee flavors.
sulfur compounds and amines) were classified. Some com- In the present study, only mesophilic bacteria showed
pounds were detected in all samples, which means that they pectinolytic activities (Table 2). The low pectinase produc-
are compounds inherent in the coffee variety studied and tion occurred due to several factors: (i) the bacteria were
compounds naturally present in roasted coffee. Fermenta- isolated from pulped coffee where there was not a large
tion with Leu. mesenteroides CCMA1105 and B. pumilus amount of pectic substrate to be degraded, (ii) pectinolytic
CCMA1251 showed the highest percentages of aldehydes enzymes could be suppressed by excess or lack of mono-
and ketones. M. testaceum CCMA1151 had the highest rate saccharides (Schwan et al. 1997; Henick-Kling et al. 1998;
of esters. Leu. mesenteroides CCMA1082, Lac. plantarum Masoud and Jespersen 2006), (iii) lower availability of the
CCMA1072 and spontaneous fermentation (control) had a nitrogen source (Silva et al. 2013), (iv) rapid lowering of
higher percentage of furans. Fermentations inoculated with pH value (Figs. 2, 3), which made the enzymatic activity
Leu. mesenteroides CCMA1105 presented a higher rate of difficult (pH 3.5–5.5) (Silva 2015).
lactones, phenols, and pyrans, respectively. Like the MB, the LAB population showed a significant
Pyrazines and pyridines were shown in higher percent- difference (p < 0.05) (Fig.  5). The population of LAB
ages in the fermentations with M. testaceum CCMA1151 varies from ­104 to 1­ 08 log CFU g−1 (Avallone et al. 2002;
and Lac. plantarum CCMA1065. The Leu. mesenteroides Pereira et al. 2020; Evangelista et al. 2015). Haile and
CCMA1082 had a higher percentage of pyrrole. Some com- Kang (2019) reported that it would be better to use lac-
pounds were detected in a few samples, such as 2,3-octane- tic acid bacteria to remain as close as possible to natural
dione (B. subtilis CCMA1234); 2,4-pentanedione, 3-methyl- fermentation.
(Leu. mesenteroides CCMA1105); phthalic acid, hept-3-yl Production of metabolites was another important fea-
isobutyl ester (without inoculation); phthalic acid, hex-3-yl ture in selecting starter cultures for coffee fermentation of
isobutyl ester; phenol, 2-methoxy- (B. pumilus CCMA1251); the present study. Acetic, succinic, malic, tartaric, citric,
vinyl crotonate; dibutyl phthalate; pyrazine, 2-ethyl-methyl-; propionic, and lactic were detected during fermentation
ethanone, 1-(2-hydroxy-5-methylphenyl); 3-hydroxypyridine using a coffee-based medium (supplementary material).
monoacetate (M. testaceum CCMA1151); undecanoic acid The synthesis of some acids, such as acetic and propionic,
isopropyl ester; acetamide, N-(3-methyl-2-oxobutyl)- (Lac. occurs due to bacteria present on the fruit’s surface, which
plantarum CCMA1072); 1H-indole, 3-methyl- (Leu. mes- can migrate to the mucilage and pulp (Silva et al. 2013).
enteroides CCMA1082).

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World Journal of Microbiology and Biotechnology (2020) 36:186 Page 11 of 15  186

Table 3  Volatile compounds identified in green coffee at the end of spontaneous and inoculated wet fermentation via headspace-solid phase
microextraction/gas chromatography-mass spectrometry (HS-SPME/GC–MS)
Compounds Treatments*
A A1 B B1 C C1 D D1 E E1 F F1 G G1 H H1 I I1 J J1
Acids
Acetic acid
Isolvaleric acid
Hexadecanoic acid
Tetradecanoic acid
Hexanoic acid
Octanoic acid
Alcohols A A1 B B1 C C1 D D1 E E1 F F1 G G1 H H1 I I1 J J1
1-Hexadecanol
2-Heptanol
2,3-Butanediol
5-methyl-2-hexanol
Benzyl alcohol
1-phenoxypropan-2-ol
Phenethyl alcohol
Pentadecanol
Tetradecanol
Tridecanol
Dodecanol
β-linalool
Phytol
Aldehydes and Ketones A A1 B B1 C C1 D D1 E E1 F F1 G G1 H H1 I I1 J J1
Acetoin
Benzaldehyde
Pentadecanal
2-Hexenal
9,17-Octadecadienal, (Z)-
2-Pentadecanone, 6,10,14-
trimethyl-
(E)-Geranyl acetone
2,4-Hexadienal, (E,E)-
Esters A A1 B B1 C C1 D D1 E E1 F F1 G G1 H H1 I I1 J J1
Methyl hexadecanoate
Ethyl hexadecanoate
Diisobutyl phthalate
Ethyl 2-hydroxypropanoate
Ethyl linoleate
Ethyl benzeneacetate
Hydrocarbons A A1 B B1 C C1 D D1 E E1 F F1 G G1 H H1 I I1 J J1
Heptadecane
Hexadecane
Hexacosane
Tetracosane
Octadecane
Others** A A1 B B1 C C1 D D1 E E1 F F1 G G1 H H1 I I1 J J1
Methyl salicylate
Vanillin
Heneicosane
Caffeine
*Treatments: Spontaneous fermentation (A); B. subtilis CCMA1234 (B); B. pumilus CCMA1251 (C); C. cellulans
CCMA1186 (D); P. dispersa CCMA1203 (E); M. testaceum CCMA1151 (F); Leu. mesenteroides CCMA1082 (G); Leu.
mesenteroides CCMA1105 (H); Lac. plantarum CCMA1065 (I); Lac. plantarum CCMA1072 (J). Capital letters without
number: the beginning of fermentation; Capital letters with subscript number: end of fermentation. **Included: Alkaloids.
*Treatments: spontaneous fermentation (A); B. subtilis CCMA1234 (B); B. pumilus CCMA1251 (C); C. cellulans CCMA1186 (D); P. dispersa
CCMA1203 (E); M. testaceum CCMA1151 (F); Leu. mesenteroides CCMA1082 (G); Leu. mesenteroides CCMA1105 (H); Lac. plantarum
CCMA1065 (I); Lac. plantarum CCMA1072 (J). Capital letters without number: the beginning of fermentation; Capital letters with subscript
number: end of fermentation
**Included: alkaloids

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Table 4  Volatile compounds Compounds Treatments*


identified in roasted coffee A B C D E F G H I J
processed by spontaneous Acids
and inoculated wet Acetic acid
fermentation via headspace- Propanoic acid
solid phase microextraction/ 3-methyl-2-butenoic acid
gas chromatography-mass Isovaleric acid
Tetradecanoic acid
spectrometry (HS-SPME/
Hexadecanoic acid
GC–MS) Aldehydes and Ketones A B C D E F G H I J
1,2-Cyclopentanedione, 3-methyl-
2-Cyclopenten-1-one, 3-ethyl-2-hydroxy-
2-Propanone, 1-hydroxy-
2,3-Hexanedione
2,5-Hexanedione
2,3- Octanedione
2,5-Octanedione
Ethanone, 1-(2-hydroxy-5-methylphenyl)-
5,9-Dodecadien-2-one, 6,10-dimethyl-, (E,E)-
4-Methyl- 1,5-Heptanediene
1-Penten-3-one, 2,4-dimethyl-
2-Propanone
2,4-Pentanedione, 3-methyl-
Cyclobutane, 1,2-bis(methylene)-
Esters A B C D E F G H I J
Acetic acid, methyl ester
2-Butanone, 1-(acetyloxy)-
Acetic acid, (acetyloxy)-
Phthalic acid, hept-3-yl isobutyl ester
2-Propanone, 1-(acetyloxy)-
1,2-Benzenedicarboxylic acid, bis(2-methylpropyl) ester
1,2-Ethanediol, diacetate
Acetic acid ethenyl ester
1,2-Ethanediol, monoacetate
Phthalic acid, hex-3-yl isobutyl ester
Propanoic acid, 2-oxo-, ethyl ester
Vinyl crotonate
Dibutyl phthalate
Undecanoic acid isopropyl ester
Furans A B C D E F G H I J
Ethanone, 1-(2-furanyl)-
2-Furanmethanol, acetate
2-Furancarboxaldehyde, 5-methyl-
2-Furanone, 2,5-dihydro-3,5-dimethyl
2-Furanmethanol
trans-Furfurylideneacetone
Furan, 2,2'-[oxybis(methylene)]bis-
2,5-Dimethyl-4-hydroxy-3(2H)-furanone
Benzofuran, 2,3-dihydro-
5-Hydroxymethylfurfural
Bis(2-furfuryl)disulfide
Furan, 2-[(methyldithio)methyl]-
2-Furfurylthiol
3(2H)-Furanone, dihydro-2-methyl-
2-Furylmethyl formate
Lactones A B C D E F G H I J
Butyrolactone
2(5H)-Furanone
2(3H)-Furanone, dihydro-4-hydroxy-
2-hydroxy-gamma-butyrolactone
Phenols A B C D E F G H I J
Methyl salicylate
4-Hydroxy-2-methylacetophenone
Phenol, 2-methoxy-
4-Hydroxy-3-methylacetophenone
Pyrans A B C D E F G H I J

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World Journal of Microbiology and Biotechnology (2020) 36:186 Page 13 of 15  186

Table 4  (continued) Maltol
4H-Pyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl-
Ethanone, 1-(2-hydroxy-5-methylphenyl)
Pyrazines A B C D E F G H I J
Pyrazine, methyl-
Pyrazine, 2,6-dimethyl-
Pyrazine, 2-ethyl-6-methyl-
Pyrazine, trimethyl-
5H-5-Methyl-6,7-dihydrocyclopentapyrazine
1-(6-Methyl-2-pyrazinyl)-1-ethanone
Pyrazine, 2-ethyl-5-methyl-
Pyrazine, 2,5-dimethyl-
Pyrazine, 3-ethyl-2,5-dimethyl-
2-Butyl-3-methylpyrazine
2-Isoamyl-6-methylpyrazine
Pyrazine, 2-ethyl-methyl-
Pyridine A B C D E F G H I J
Pyridine
2-Pyridinecarboxylic acid
2-Pyridinecarboxaldehyde
Picolinamide
Fampridine
3-Pyridinol
4-Pyridinamine, N,N-dimethyl-
4(H)-Pyridine, N-acetyl-
1,2-Ethanediol, 1,2-di-pyridinyl-
2-Aminopyridine
3-Aminopyridine
3-Hydroxypyridine monoacetate
2-Pyridylhydroxymethanesulfonic acid
Pyrroles A B C D E F G H I J
1H-Pyrrole-2-carboxaldehyde, 1-methyl-
Ethanone, 1-(1H-pyrrol-2-yl)
1H-Pyrrole-2-carboxaldehyde
Indole
1H-Pyrrole, 1-(2-furanylmethyl)-
2-Pyrrolidinone, 1-butyl-
Pyrrole
1H-Indole, 3-methyl-
Others** A B C D E F G H I J
2-Thiophenemethanol
Diacetylsulphide
Caffeine
Cyclobutanol
Acetamide, N-(3-methyl-2-oxobutyl)-
*Treatments: Spontaneous fermentation (A); B. subtilis CCMA1234 (B); B. pumilus CCMA1251 (C); C. cellulans
CCMA1186 (D); P. dispersa CCMA1203 (E); M. testaceum CCMA1151 (F); Leu. mesenteroides CCMA1082 (G); Leu.
mesenteroides CCMA1105 (H); Lac plantarum CCMA1065 (I); Lac. plantarum CCMA1072 (J). Capital letters without
number: the beginning of fermentation; Capital letters with subscript number: end of fermentation **Included: Alkaloids,
sulfur compounds, alcohols, and amines.
*
 Treatments: Spontaneous fermentation (A); B. subtilis CCMA1234 (B); B. pumilus CCMA1251 (C); C.
cellulans CCMA1186 (D); P. dispersa CCMA1203 (E); M. testaceum CCMA1151 (F); Leu. mesenter-
oides CCMA1082 (G); Leu. mesenteroides CCMA1105 (H); Lac plantarum CCMA1065 (I); Lac. plan-
tarum CCMA1072 (J). Capital letters without number: the beginning of fermentation; Capital letters with
subscript number: end of fermentation **Included: Alkaloids, sulfur compounds, alcohols, and amines

These acids, such as acetic and succinic in high concentra- heterofermentative LAB (Swiegers et al. 2005), and yeast
tions (more significant than one mg mL−1), create negative (Martinez et al. 2017; Bressani et al. 2019). Stains of Bacil-
deterioration factors in coffee (onion flavor) and interfere lus subtilis and Pantoea dispersa were used as bacteria start-
in a deprecatory way in the final quality of the beverage ers in Martinez et al. (2019), showing that they produced
(Lopez et al. 1989). However, these acids were described succinic acid during wet fermentation. Wang et al. (2019b)
in the present study; they were detected in concentrations reported that this acid could remain higher even during cof-
below mg g −1. The variation of acids during fermenta- fee roasting.
tion due to microbial metabolism changed the pH value Lactic acid was the acid detected in the highest concentra-
and influenced the microbiota present, and the diffusion tion in coffee-based fermentation (Supplementary Material)
of these acids into the bean could affect the final bever- and bucket fermentation (Fig. 4) with the selected bacte-
age flavor and quality (Silva et al. 2013; Evangelista et al. ria. Evangelista et al. (2015) also found that lactic acid was
2014; Silva 2015). the primary acid detected in wet coffee fermentations. The
The succinic acid was detected in some fermentation high concentration of lactic acid produced by the LAB and
carried out in this study using the coffee-based medium. the consequent lowering of pH would cause the dissocia-
Succinic acid is obtained naturally during coffee process- tion of the bean mucilage. The high production of citric,
ing and contributes to the final product (Bressani et  al. succinic, and lactic acids, and the low production of acetic
2019; Wang et al. 2019b; Avallone et al. 2001). This acid and propionic acids in a coffee pulp medium were used as
may be produced by Bacillus spp. (Silva et al. 2013), by selection factors to determine the strains most suitable for

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186   Page 14 of 15 World Journal of Microbiology and Biotechnology (2020) 36:186

conducting the wet coffee fermentation. According to Mar- coffee. Future work should be conducted to evaluate these
tinez et al. (2019), lactic, acetic citric, and succinic acids strains in different coffee varieties and the sensory profiles
were produced when they inoculated bacteria of the genus produced.
Bacillus and Pantoea during wet fermentation. According
to Pothakos et al. (2020), LAB showed to be dominant and Acknowledgements  The authors thank the Brazilian agencies, Con-
selho Nacional de Desenvolvimento Científico e Tecnológico do Brasil
very important during coffee processing, from green coffee (CNPQ), Fundação de Amparo à Pesquisa do Estado de Minas Gerais
beans to coffee cupping. (FAPEMIG) and Coordenação de Aperfeiçoamento de Pessoal de Nível
Acids, alcohols, aldehydes, ketones, esters, hydrocarbons, Superior (CAPES) for financial support. We also thank Daterra farm,
and other compounds (phenols, alkanes, and alkaloids) were Patrocínio, Minas Gerais, Brazil, for collecting the samples.
classified in the study (Tables 3, 4). The volatile compounds
predominantly found in initial fermentation belong to alco- Compliance with ethical standards 
hols, aldehydes, and ketones. These compounds are pro-
Conflict of interest  The authors declared that there is no conflict of
duced during coffee processing due to the pectin and sugars interest.
degeneration, resulting in a decrease in pH (De Bruyn et al.
2017).
The presence of crucial flavor marker phenethyl alcohol
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