Diversity of Lactic Acid Bacteria Associated with Fresh Coffee Cherries in Taiwan

Microbiota of arabica coffee: insights from soil to fruit

Studies have shown that a diverse and metabolically active microbiota exists throughout different stages of coffee processing, from pre- to post-harvest. This microbiota originates from both the cultivation and processing environments. Additionally, microorganisms from the soil can be found on the fruit due to the transfer between them. This study reviews the microbiota present in Arabica coffee fruits and the soils where the plants are grown. It examines how microbial profiles are related to coffee variety, altitude, cultivation region, and processing method, and establishes a connection between the microbiota in soil and fruit. A diverse microbiota was observed in both coffee fruits and soils, with similar microorganisms identified across different growing regions, processing methods, and coffee varieties. However, exclusive detections of some microorganisms were also observed. These differences highlight the influence of terroir on coffee's microbial composition, confirming that environmental conditions, genetic factors, and processing methods shape coffee microbiota. Since microbial development during coffee fermentation can affect the beverage's quality, the data presented in this review offer valuable insights for researchers and producers. Understanding the influence of processing methods, coffee varieties, and cultivation regions on coffee microbiota enables the selection of specific fermentation conditions or starter cultures to enhance terroir characteristics or adjust microbial populations to favor or introduce microorganisms beneficial for coffee quality.

The Relationship between Microbial Communities in Coffee Fermentation and Aroma with Metabolite Attributes of Finished Products

Coffee is a critical agricultural commodity and is used to produce premium beverages enjoyed by people worldwide. The microbiome of coffee beans has proven to be an essential tool that improves the flavor profile of coffee by creating aromatic flavor compounds through natural fermentation. This study investigated the natural microbial consortium during the wet process fermentation of coffee onsite in Thailand in order to identify the correlation between microbial diversity and biochemical characteristics including flavor, aroma, and metabolic attributes. Our study found 64 genera of bacteria and 59 genera of yeast/fungi present during the fermentation process. Group of microbes, mainly yeast and lactic acid bacteria, that predominated in the process were significantly correlated with preferable flavor and aroma compounds, including linalyl formate, linalool, cis-isoeugenol, trans-geraniol, and (-)-isopulegol. Some of the detected metabolites were found to be active compounds which could play a role in health.

Refermentation with yeast and lactic acid bacteria isolates: a strategy to improve the flavor of green coffee beans

BACKGROUND

Yeast and lactic acid bacteria (LAB) play an important part in the post-harvest fermentation of coffee. This study applied lab-scale fermentation to commercial green coffee beans using dry coffee pulp as the substrate, with the aim of modifying coffee-bean flavor. In addition to spontaneous fermentation, yeast and LAB isolated from coffee beans and dried coffee pulp were added during fermentation.

RESULTS

Co-inoculation of yeast and LAB showed a significant effect on the chlorogenic acid content after between 24 and 72 h of fermentation. Acetic, citric, malic, lactic, and quinic acids were shown to be affected significantly (P < 0.05) by fermentation and inoculation. Gas chromatography detected that esters, alcohols, aldehydes, furans, and pyrazines were the primary compounds in the coffee beans. Certain volatile groups were present in greater concentrations and broader varieties within the inoculated beans. The highest cupping scores were given to beans that had been co-inoculated with yeast and LAB.

CONCLUSION

Overall, the use of yeasts and LAB starters showed potential to create coffee beverages with desirable characteristics by standardized fermentation. © 2024 Society of Chemical Industry.

Exploring the microbiome of coffee plants: Implications for coffee quality and production

Coffee stands as one of the world's most popular beverages, and its quality undergoes the influence of numerous pre- and post-harvest procedures. These encompass genetic variety, cultivation environment, management practices, harvesting methods, and post-harvest processing. Notably, microbial communities active during fermentation hold substantial sway over the ultimate quality and sensory characteristics of the final product. The interaction between plants and microorganisms assumes critical significance, with specific microbes assuming pivotal roles in coffee plant growth, fruit development, and, subsequently, the fruit's quality. Microbial activities can synthesize or degrade compounds that influence the sensory profile of the beverage. However, studies on the metabolic products generated by various coffee-related microorganisms and their chemical functionality, especially in building sensory profiles, remain scarce. The primary aim of this study was to conduct a literature review, based on a narrative methodology, on the current understanding of the plant-microorganism interaction in coffee production. Additionally, it aimed to explore the impacts of microorganisms on plant growth, fruit production, and the fermentation processes, directly influencing the ultimate quality of the coffee beverage. Articles were sourced from ScienceDirect, Scopus, Web of Science, and Google Scholar using specific search terms such as "coffee microorganisms", "microorganisms-coffee interactions", "coffee fermentation", "coffee quality", and 'coffee post-harvest processing". The articles used were published in English between 2000 and 2023. Selection criteria involved thoroughly examining articles to ensure their inclusion was based on results about the contribution of microorganisms to both the production and quality of the coffee beverage. The exploration of microorganisms associated with the coffee plant and its fruit presents opportunities for bioprospecting, potentially leading to targeted fermentations via starter cultures, consequently generating new profiles. This study synthesizes existing data on the current understanding of the coffee-associated microbiome, its functionalities within ecosystems, the metabolic products generated by microorganisms, and their impacts on fermentation processes and grain and beverage quality. It highlights the importance of plant-microorganism interactions in the coffee production chain.

Yeasts are essential for mucilage degradation of coffee beans during wet fermentation

During wet fermentation, mucilage layers in coffee cherries must be removed completely. To explain mucilage degradation, several controversial hypotheses have been proposed. The aim of this work was to improve our understanding of the kinetics of mucilage breakdown. Pulped coffee beans were wet fermented with seven different treatments for 36 h. Endogenous bacteria and yeasts are selectively suppressed, and pectinases or lactic acid are added. They also involve maintaining the beans at pH 7 throughout fermentation and using spontaneous fermentation without additives as a control. During spontaneous fermentation, yeast and lactic acid bacteria were detected and significantly increased to 5.5 log colony-forming units (CFU)/mL and 5.2 log CFU/mL, respectively. In the first 12 h of fermentation, there was a significant degree of endogenous pectinolytic activity, which resulted in partly destroyed beans in the absence of microorganisms. By adding pectinase and lactic acid to the fermentation mass, the breakdown process was accelerated in less than 8 h. When yeast was present throughout the fermentation, complete degradation was achieved. Bacteria played no critical role in the degradation. Klebsiella pneumoniae and Erwinia soli were found in a lower population and showed weaker pectinolytic activities compared to Hanseniaspora uvarum and Pichia kudriavzevii. During wet fermentation, mucilage degradation appears to be mediated by endogenous enzymes at the early stage, whereas microbial contributions, mainly yeasts, occur subsequently. H. uvarum and P. kudriavzevii may be promising candidates to be tested in future studies as coffee starter cultures to better control the mucilage degradation process.

Microbial Diversity of Anaerobic-Fermented Coffee and Potential for Inhibiting Ochratoxin-Produced Aspergillus niger

Coffee flavor considerably depends on the fermentation process, with contributing factors including fermentation temperature, oxygen concentration, and microbial diversity. Efficient controlling of the fermentation can improve the quality of coffee beverages. Therefore, several studies on coffee fermentation processes have been conducted in various regions. The objective of this study was to assess the microbial diversity of coffee beans undergoing anaerobic fermentation at various temperatures (4 °C or 37 °C) and fermentation durations (12 h or 36 h) using full-length 16S rRNA sequencing. This analysis aimed to evaluate the inhibitory effects of the fermented metabolites against ochratoxin-producing Aspergillus niger. From our results, Acetobacter was identified as the dominant microbial community at higher fermentation temperatures, whereas Leuconostoc and Gluconobacter were the dominant genera at lower temperatures. However, at lower temperatures, changes in microbial communities were relatively slow. This study expands our knowledge of the microbial diversity involved in the anaerobic fermentation of coffee beans in Taiwan. The findings of this study can be used in future research to cultivate microorganisms linked to the quality and improve the quality of coffee beverages through fermentation.

Isolation of Yeast and LAB from Dry Coffee Pulp and Monitoring of Organic Acids in Inoculated Green Beans

Yeast and lactic acid bacteria (LAB) are known to play an important role in the fermentation process of coffee post-harvest. This study aimed to isolate and screen yeast and LAB to be applied in lab-scale refermentation of commercial green coffee beans and coffee pulp with the aim of modifying the composition of organic acids (OAs) in coffee beans. Yeast and LAB strains were isolated from green coffee beans and dry coffee pulp and identified, and their effect on OA concentration in the coffee beans was quantified. In addition, the effects of different fermentation conditions (additional carbon source, different inoculum dose, and different types of coffee pulp) were evaluated based on OA quantification. Nine yeast isolates of Rhodotorula mucilaginosa and Wickerhamomyces anomalus were identified, and 11 LAB isolates of the species Enterococcus mundtii were identified. Of the 7 OAs quantified, quinic acid was the most abundant. The inoculation of isolated yeasts and LAB led to higher concentrations of OAs, showing the potential to realize modification of the OA composition of green coffee beans by re-fermentation with coffee-originated isolates.

Effect of isolated lactic acid bacteria on the quality and bacterial diversity of native grass silage

Objective

The objective of this study was to isolate lactic acid bacteria (LAB) from native grasses and naturally fermented silages, determine their identity, and assess their effects on silage quality and bacterial communities of the native grasses of three steppe types fermented for 60 days.

Methods

Among the 58 isolated LAB strains, Limosilactobacillus fermentum (BL1) and Latilactobacillus graminis (BL5) were identified using 16S rRNA sequences. Both strains showed normal growth at 15- 45°C temperature, 3-6.5% NaCl concentration, and pH 4-9. Two isolated LAB strains (labeled L1 and L5) and two commercial additives (Lactiplantibacillus plantarum and Lentilactobacillus buchneri; designated as LP and LB, respectively) were added individually to native grasses of three steppe types (meadow steppe, MS; typical steppe, TS; desert steppe, DS), and measured after 60 d of fermentation. The fresh material (FM) of different steppe types was treated with LAB (1 × 10⁵ colony forming units/g fresh weight) or distilled water (control treatment [CK]).

Results

Compared with CK, the LAB treatment showed favorable effects on all three steppe types, i.e., reduced pH and increased water-soluble carbohydrate content, by modulating the microbiota. The lowest pH was found in the L5 treatment of three steppe types, at the same time, the markedly (p < 0.05) elevated acetic acid (AA) concentration was detected in the L1 and LB treatment. The composition of bacterial community in native grass silage shifted from Pantoea agglomerans and Rosenbergiella nectarea to Lentilactobacillus buchneri at the species level. The abundance of Lentilactobacillus buchneri and Lactiplantibacillus plantarum increased significantly in L1, L5, LP, and LB treatments, respectively, compared with CK (p < 0.05).

Conclusion

In summary, the addition of LAB led to the shifted of microbiota and modified the quality of silage, and L. fermentum and L. graminis improved the performance of native grass silage.

Enterococcus alishanensis sp. nov., a novel lactic acid bacterium isolated from fresh coffee beans

A coccus-shaped organism, designated ALS3T, was isolated from fresh coffee cherries collected at a farm located in the Ali Mountain region of Taiwan. Sequence analysis of its 16S rRNA gene indicated that strain ALS3T belongs to the genus Enterococcus and has more than 98.5 % sequence similarity to Enterococcus pallens and Enterococcus hermanniensis . When comparing the ALS3T genome with these two type strains, the average nucleotide identity values and digital DNA–DNA hybridization values were 72.6–73.3 and 19.2 %, respectively. The G+C content of the genomic DNA from strain ALS3T was 35.6 mol%. Results of sequence analysis, together with enzymatic activities and characteristics of carbohydrate metabolism, indicated that strain ALS3T is distinct and represents a novel species, for which the name Enterococcus alishanensis sp. nov. is proposed. The type strain is ALS3T (=NBRC 109593T=BCRC 80605T).

The Altitude of Coffee Cultivation Causes Shifts in the Microbial Community Assembly and Biochemical Compounds in Natural Induced Anaerobic Fermentations

Coffee harvested in the Caparaó region (Minas Gerais, Brazil) is associated with high-quality coffee beans resulting in high-quality beverages. We characterize, microbiologically and chemically, fermented coffees from different altitudes through target NGS, chromatography, and conventional chemical assays. The genera Gluconobacter and Weissella were dominant in coffee’s fruits from altitudes 800 and 1,000 m. Among the Eukaryotic community, yeasts were the most dominant in all altitudes. The most dominant fungal genus was Cystofilobasidium, which inhabits cold environments and resists low temperatures. The content of acetic acid was higher at altitudes 1,200 and 1,400 m. Lactic acid and the genus Leuconostoc (Pearson: 0.93) were positively correlated. The relative concentration of volatile alcohols, especially of 2-heptanol, was high at all altitudes. Bacteria population was higher in coffees from 800 m, while at 1,000 m, fungi richness was favored. The altitude is an important variable that caused shifts in the microbial community and biochemical compounds content, even in coffees belonging to the same variety and cultivated in the same region under SIAF (self-induced anaerobic fermentation) conditions. Coffee from lower altitudes has higher volatile alcohols content, while high altitudes have esters, aldehydes, and total phenolics contents.

Fermentation of Coffea canephora inoculated with yeasts: Microbiological, chemical, and sensory characteristics

This work aimed to evaluate Coffea canephora's microbiological, chemical, and sensory characteristics at 300 and 600 m elevation plantations processed by the natural method inoculated with yeasts. The coffee was spread on suspended terraces and sprayed with approximately 10⁷ cfu/mL of Meyerozyma caribbica CCMA 1738 or Pichia kluyveri CCMA 1743, separately. Cherries containing bark and parchment were collected during fermentation for microbial groups counting, qPCR, quantification of organic acids, and sugars (HPLC). Volatile compounds (GC-MS) and sensory analyses, cupping test with expert coffee tasters and triangular test with consumers, were performed on roasted coffee beans. The inoculated yeasts persisted during the entire fermentation process. M. caribbica reduced the filamentous fungal population by 63% and 90% in the 300- and 600-m coffees, respectively. The 300-m coffee fruits showed higher concentrations of organic acids in all fermentation times when compared to the 600-m reaching out to 8 times more. Twenty-four volatile compounds were identified in the roasted coffee beans, with the predominance of pyrazines. The 600-m coffee inoculated with M. caribbica showed an increase of more than one point in the score given by certified tasters. Consumers noticed the M. caribbica inoculation in the 300- and 600-m-elevation coffees. M. caribbica is a promising starter culture for Conilon coffee with the potential to increase the beverage quality.

Microbial diversity and chemical characteristics of Coffea canephora grown in different environments and processed by dry method

This study aimed to assess the microbial diversity in Coffea canephora grown in four different environments of Espirito Santo state, Brazil. Coffee cherries of two different altitudes (300 and 600 m) and two terrain aspects (Southeast-facing and Northwest-facing slopes) were processed by the dry method. Samples were collected during the drying/fermentation process. Microorganisms were counted, isolated, and identified by MALDI-TOF, followed by sequencing of the ribosomal region. Sugars and organic acids were quantified by HPLC and volatile compounds of the roasted coffees were evaluated by GC-MS. Bacteria population presented a significant number of isolates as well as higher counts during the drying/fermentation process with respect to the population of yeasts. The principal genera of microorganisms found were Bacillus, Pichia, Candida, and Meyerozyma. Meyerozyma guilliermondii was the most frequent yeast in all environments. On the other hand, Pichia kluyveri was found only in coffee cherries from the 600 m altitude. The highest concentration of acetic and succinic acids observed was 6.06 mg/g and 0.84 mg/g, respectively. Sucrose concentrations ranged from 0.68 to 5.30 mg/g, fructose from 1.30 to 4.60 mg/g, and glucose from 0.24 to 1.25 mg/g. Thirty-six volatile compounds, belonging to the groups of pyrazines, alcohols, aldehydes, ketones, and furans were identified in roasted coffee, with differences between altitude and terrain aspects. Information about microbial diversity is crucial to better understand the coffee quality and distinct characteristics of coffee produced in different environments.

Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

Intensive coffee production is accompanied by several environmental issues, including soil degradation, biodiversity loss, and pollution due to the wide use of agrochemical inputs and wastes generated by processing. In addition, climate change is expected to decrease the suitability of cultivated areas while potentially increasing the distribution and impact of pests and diseases. In this context, the coffee microbiota has been increasingly studied over the past decades in order to improve the sustainability of the coffee production. Therefore, coffee associated microorganisms have been isolated and characterized in order to highlight their useful characteristics and study their potential use as sustainable alternatives to agrochemical inputs. Indeed, several microorganisms (including bacteria and fungi) are able to display plant growth-promoting capacities and/or biocontrol abilities toward coffee pests and diseases. Despite that numerous studies emphasized the potential of coffee-associated microorganisms under controlled environments, the present review highlights the lack of confirmation of such beneficial effects under field conditions. Nowadays, next-generation sequencing technologies allow to study coffee associated microorganisms with a metabarcoding/metagenomic approach. This strategy, which does not require cultivating microorganisms, now provides a deeper insight in the coffee-associated microbial communities and their implication not only in the coffee plant fitness but also in the quality of the final product. The present review aims at (i) providing an extensive description of coffee microbiota diversity both at the farming and processing levels, (ii) identifying the “coffee core microbiota,” (iii) making an overview of microbiota ability to promote coffee plant growth and to control its pests and diseases, and (iv) highlighting the microbiota potential to improve coffee quality and waste management sustainability.

Evaluation of lactic acid bacteria strains isolated from fructose-rich environments for their mannitol-production and milk-gelation abilities

Mannitol is a sugar alcohol, or polyol, widely used in the food industry because of its low-calorie properties. Industrial production of mannitol is difficult and expensive. However, certain bacterial species are known to produce mannitol naturally, including certain lactic acid bacteria and fructophilic lactic acid bacteria (LAB). In this study, bacterial strains isolated from fructose-rich sources, including flowers, leaves, and honey, were identified by 16S rRNA sequence analysis as Leuconostoc, Fructobacillus, Lactococcus, and Lactobacillus species and 4 non-LAB species. DNA profiles generated by pulsed-field gel electrophoresis discriminated 32 strains of Leuconostoc mesenteroides and 6 Fructobacillus strains. Out of 41 LAB strains isolated, 32 were shown to harbor the mdh gene, which encodes the mannitol dehydrogenase enzyme, and several showed remarkable fructose tolerance even at 50% fructose concentrations, indicating their fructophilic nature. Several of the strains isolated, including Leuconostoc mesenteroides strains DPC 7232 and DPC 7261, Fructobacillus fructosus DPC 7237, and Fructobacillus fructosus DPC 7238, produced higher mannitol concentrations than did the positive control strain Limosilactobacillus reuteri DSM 20016 during an enzymatic screening assay. Mannitol concentrations were also examined via HPLC in 1% fructose de Man, Rogosa, and Sharpe medium (FMRS) or 1% fructose milk (FM). Among the strains, Fructobacillus fructosus DPC 7238 displayed high fructose utilization (9.27 g/L), high mannitol yield (0.99 g of mannitol/g of fructose), and greatest volumetric productivities (0.46 g/L per h) in FMRS. However, Leuconostoc mesenteroides DPC 7261 demonstrated the highest fructose utilization (8.99 g/L), mannitol yield (0.72 g of mannitol/g of fructose), and volumetric productivities (0.04 g/L per h) in FM. Storage modulus G' (>0.1 Pa) indicated a shorter gelation time for Limosilactobacillus reuteri DSM 20016 (8.73 h), followed by F. fructosus DPC 7238 (11.57 h) and L. mesenteroides DPC 7261 (14.52 h). Our results show that fructose-rich niches can be considered important sources of fructophilic LAB strains, with the potential to be used as starter cultures or adjunct cultures for the manufacture of mannitol-enriched fermented dairy products and beverages.

Fermentation of coffee pulp using indigenous lactic acid bacteria with simultaneous aeration to produce cascara with a high antioxidant activity

Coffee pulp which is a by-product of coffee production contains considerable amounts of phenolic compounds that can be valorised to produce cascara as an antioxidant beverage. The fermentation and drying conditions of the coffee pulp have a great influence on the bioactive compounds in the cascara. This study aimed to investigate the effect of natural fermentation with simultaneous aeration on the phenolic content and antioxidant activity of cascara. A systematic study was carried out using a response surface methodology with a face-centered central composite design to determine the effect of fermentation time (0-8 h) and temperature (27-37 °C) on the number of bacteria in the coffee pulp after natural fermentation with simultaneous aeration (an air flowrate of 4 m/s) as well as phenolic content and antioxidant activity of cascara. The experimental dataset was modelled with an empirical model using multi-variable non-linear regression. A good agreement between model and experimental data was obtained. At the optimum conditions (4.2 h, 31.8 °C), the phenolic content was 6.72% whereas the antioxidant activity was 27.6%. Indigenous lactic acid bacteria were also isolated from the coffee pulp and determined as Leuconostoc pseudomesenteroides. The isolated bacteria can be used as a starter for controlled fermentation of coffee pulp as it increased the antioxidant activity up to 15% higher than the antioxidant activity of cascara obtained at the optimum conditions for natural fermentation with simultaneous aeration and 30% higher from the fresh coffee pulp.

Microbial Community Dynamics and Natural Fermentation Profiles of Ensiled Alpine Grass Elymus nutans Prepared From Different Regions of the Qinghai-Tibetan Plateau

Feed deficiency during the long cold period of a year is one of the major problems that the traditional year-round animal grazing system has faced on the Qinghai-Tibetan plateau (QTP) since ancient time. Therefore, ensiling the grasses from grassland could be a desirable feeding regime to preserve high quality forage and to alleviate the seasonal unbalanced feed supply problem on this plateau. The present study was designed to investigate dynamics of bacterial community and natural fermentation quality of ensiled Elymus nutans collected from grasslands in four different areas with different elevations [Tianzhu County (TZ), 2965 m; Golog Prefecture (GL), 3763 m; Damxung County (DX), 4228 m, and Nagqu Prefecture (NQ), 4752 m] on the QTP. The bacterial community was characterized by using the PacBio single molecule with real-time sequencing technology (SMRT). The harvested fresh E. nutans grasses were ensiled in vacuum-sealed polyethylene bags for 14, 30, 60, and 90 days. Obvious differences in the epiphytic bacterial community of the fresh E. nutans samples from the four areas were observed, which resulted in various bacterial community dynamics and fermentation qualities of ensiled E. nutans. Higher fermentation quality was observed in silage samples from Nagqu than in those from the other areas (P < 0.05). Lactic acid bacteria (LAB) involved in fermentation of E. nutans from low altitude areas consisted of Pediococcus pentosaceus, Lactobacillus sp., Leuconostoc mesenteroides, and Lactobacillus coryniformis, whereas major LAB species involved in the fermentation of E. nutans silage from high altitudes included L. mesenteroides, Lactobacillus brevis, and Lactobacillus sp. Correlation analysis between bacterial composition and fermentation quality of E. nutans silages made from the four different areas in the QTP indicated that the LAB species responsible for silage fermentation in different areas were totally different, which was mainly due to the different epiphytic bacterial compositions in fresh E. nutans before ensiling. The present results provide important information on revealing the bacterial communities and fermentation quality of ensiled E. nutans, and on future screening of LAB isolates for making high quality silage in order to alleviate feed shortage of the traditional year-round grazing system on the QTP.

Leuconostoc litchii sp. nov., a novel lactic acid bacterium isolated from lychee

A novel lactic acid bacterium, strain MB7^T, was isolated from lychee in Taiwan. MB7^T is Gram-staining-positive, catalase-negative, non-motile, non-haemolytic, facultatively anaerobic, coccoid-shaped, heterofermentative and mainly produces d-lactic acid from glucose. Comparative analysis of 16S rRNA, pheS and rpoA gene sequences has demonstrated that the novel strain represented a member of the genus Leuconostoc. 16S rRNA gene sequencing results indicated that MB7^T had the same sequence similarity of 99.25 % to four type strains of members of the genus Leuconostoc: Leuconostoc mesenteroides subsp. dextranicum DSM 20484^T, Leuconostoc mesenteroides subsp. jonggajibkimchii DRC 1506^T, Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293^T and Leuconostoc suionicum DSM 20241^T. Additionally, high 16S rRNA sequence similarities were also observed with Leuconostoc mesenteroides subsp. cremoris ATCC 19254^T (99.12 %) and Leuconostoc pseudomesenteroides NRIC 1777^T (98.69 %). When comparing the genomes of these type strains, the average nucleotide identity values and digital DNA-DNA hybridization values of MB7^T with these type strains were 76.57-80.53 and 22.0-22.6 %, respectively. MB7^T also showed different phenotypic characteristics to other most closely related species of the genus Leuconostoc, such as carbohydrate metabolizing ability, halotolerance and growth at various pHs. On the basis of phenotypic and genotypic properties, strain MB7^T represents a novel species belonging to the genus Leuconostoc, for which the name Leuconostoc litchii sp. nov. is proposed. The type strain is MB7^T (=BCRC 81077^T=NBRC 113542^T).

Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria

Lactic acid bacteria (LAB) are essential for many fruit, vegetable and grain food and beverage fermentations. However, the numbers, diversity and plant-specific adaptions of LAB found on plant tissues prior to the start of those fermentations are not well understood. When measured, these bacteria have been recovered from the aerial surfaces of plants in a range from <10 CFU g^-1 to over 10^8.5 CFU g^-1 of plant tissue and in lower quantities from the soil and rhizosphere. Plant-associated LAB include well-known generalist taxa such as Lactobacillus plantarum and Leuconostoc mesenteroides, which are essential for numerous food and beverage fermentations. Other plant-associated LAB encompass specialist taxa such as Lactobacillus florum and Fructobacillus, many of which were discovered relatively recently and their significance on plants and in foods is not yet recognized. LAB recovered from plants possess the capacity to consume plant sugars, detoxify phenolic compounds and tolerate the numerous biotic and abiotic stresses common to plant surfaces. Although most generalist and some specialist LAB grow rapidly in food and beverages fermentations and can cause spoilage of fresh and fermented fruits and vegetables, the importance of living plants as habitats for these bacteria and LAB contributions to plant microbiomes remain to be shown.

Ecological diversity, evolution and metabolism of microbial communities in the wet fermentation of Australian coffee beans

The microbial ecology in the fermentation of Australian coffee beans was investigated in this study. Pulped coffee beans were kept underwater for 36 h before air dried. Samples were collected periodically, and the microbial communities were analyzed by culture-dependent and independent methods. Changes in sugars, organic acids and microbial metabolites in the mucilage and endosperm of the coffee beans during fermentation were monitored by HPLC. Culture-dependent methods identified 6 yeast and 17 bacterial species, while the culture-independent methods, multiple-step total direct DNA extraction and high throughput sequencing, identified 212 fungal and 40 bacterial species. Most of the microbial species in the community have been reported for wet fermentation of coffee beans in other parts of the world, but the yeast Pichia kudriavzevii was isolated for the first time in wet coffee bean fermentation. The bacterial community was dominated by aerobic mesophilic bacteria (AMB) with Citrobacter being the predominant genus. Hanseniaspora uvarum and Pichia kudriavzevii were the predominant yeasts while Leuconostoc mesenteroides and Lactococcus lactis were the predominant LAB. The yeasts and bacteria grew significantly during fermentation, utilizing sugars in the mucilage and produced mannitol, glycerol, and lactic acid, leading to a significant decrease in pH. The results of this study provided a preliminary understanding of the microbial ecology of wet coffee fermentation under Australian conditions. Further studies are needed to explore the impact of microbial growth and metabolism on coffee quality, especially flavour.

Coffee growing altitude influences the microbiota, chemical compounds and the quality of fermented coffees

The objective of this work was to evaluate the influence of different altitudes on the epiphytic microbiota of coffee beans and on sensorial and chemical quality of coffees grown at 800, 1000, 1200, and 1400 m in Serra do Caparaó, Espírito Santo, Brazil. For microbiological analysis, the population counts of mesophilic bacteria, lactic acid bacteria (LAB), and yeasts were performed from the surface plating. The isolates were grouped and identified from the Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and sequencing of the ribosomal region was used. The chemical composition of the green grains was evaluated by Raman spectroscopy, and the sensory analysis of the roasted grains was performed using temporal dominance of sensations (TDS). During fermentation, there was a decrease in the LAB in pulped coffee from 800 and 1000 m altitude, while an increase was observed at 1200 and 1400 m. In natural coffee, there was an increase of LAB population at all altitudes. The highest diversity of mesophilic bacteria and yeast were identified in natural 1400 m and 1000 m, respectively. However pulped coffee treatments it was at 1200 m and 800 m. The chlorogenic acid and fatty acids in the green bean changed with altitude variation and processing. The floral attribute was detected only at altitude 1400 m. Caramel, chocolate and almond attributes were most frequently detected in coffees at different altitudes and processing. Therefore, pulped coffee processing was most suitable at low altitude while at high altitudes, both processes can be conducted to obtain a beverage with unusual sensory profile.

First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing

In Colombia, coffee growers use a traditional method of fermentation to remove the cherry pulp surrounding the beans. This process has a great influence on sensory quality and prestige of Colombian coffee in international markets, but has never been studied. Here we use an Illumina-based amplicon sequencing to investigate bacterial and fungal communities associated with spontaneous coffee-bean fermentation in Colombia. Microbial-derived metabolites were further analysed by high-performance liquid chromatography and gas chromatography-mass spectrometry. Highly diverse bacterial groups, comprising 160 genera belonging to 10 phyla, were found. Lactic acid bacteria (LAB), mainly represented by the genera Leuconostoc and Lactobacillus, showed relative prevalence over 60% at all sampling times. The structure of the fungal community was more homogeneous, with Pichia nakasei dominating throughout the fermentation process. Lactic acid and acetaldehyde were the major end-metabolites produced by LAB and Pichia, respectively. In addition, 20 volatile compounds were produced, comprising alcohols, organic acids, aldehydes, esters, terpenes, phenols, and hydrocarbons. Interestingly, 56 microbial genera, associated with native soil, seawater, plants, insects, and human contact, were detected for the first time in coffee fermentation. These microbial groups harbour a remarkable phenotypic diversity and may impart flavours that yield clues to the terroir of Colombian coffees.

Diversity and Functional Properties of Lactic Acid Bacteria Isolated From Wild Fruits and Flowers Present in Northern Argentina

Lactic acid bacteria (LAB) are capable of converting carbohydrate substrates into organic acids (mainly lactic acid) and producing a wide range of metabolites. Due to their interesting beneficial properties, LAB are widely used as starter cultures, as probiotics, and as microbial cell factories. Exploring LAB present in unknown niches may lead to the isolation of unique species or strains with relevant technological properties. Autochthonous rather than allochthonous starter cultures are preferred in the current industry of fermented food products, due to better adaptation and performance of autochthonous strains to the matrix they originate from. In this work, the lactic microbiota of eight different wild tropical types of fruits and four types of flowers were studied. The ability of the isolated strains to produce metabolites of interest to the food industry was evaluated. The presence of 21 species belonging to the genera Enterococcus, Fructobacillus, Lactobacillus, Lactococcus, Leuconostoc, and Weissella was evidenced by using culture-dependent techniques. The isolated LAB corresponded to 95 genotypically differentiated strains by applying rep-PCR and sequencing of the 16S rRNA gene; subsequently, representative strains of the different isolated species were studied for technological properties, such as fast growth rate and acidifying capacity; pectinolytic and cinnamoyl esterase activities, and absence of biogenic amine biosynthesis. Additionally, the strains' capacity to produce ethyl esters as well as mannitol was evaluated. The isolated fruit- and flower-origin LAB displayed functional properties that validate their potential use in the manufacture of fermented fruit-based products setting the background for the design of novel functional foods.

Genetic and technological characterization of lactic acid bacteria isolated from tropically grown fruits and vegetables

Phyllosphere microorganisms are common contaminants of fruit or vegetable containing foods. The aim of this study was to identify and characterize lactic acid bacteria isolated from fruits and vegetables from Reunion Island, regarding possible application in food. Among 77 isolates, a large diversity of species was observed, with isolates belonging to Lactobacillus plantarum (3 isolates), other species of Lactobacillus (3), Lactococcus lactis (13), Leuconostoc pseudomesenteroides (25), Leuconostoc lactis (1), Leuconostoc mesenteroides (7), Leuconostoc citreum (14), Weissella cibaria (4), Weissella confusa (4), other species of Weissella (2) and Fructobacillus tropaeoli (1). Several of these species, although belonging to lactic acid bacteria, are poorly characterized, because of their low occurrence in dairy products. Lactobacillus, Lactococcus, Leuconostoc and Weissella isolates were classified by (GTG)₅ fingerprinting in 3, 6, 21 and 10 genetic groups, respectively, suggesting a large intra-species diversity. Several Weissella and Lactobacillus isolates were particularly tolerant to acid and osmotic stress, whereas Lc. pseudomesenteroides 60 was highly tolerant to oxidative stress. Isolates of Weissella 30, 64 and 58, Leuconostoc 60 and 12b, Lactobacillus 75 and Fructobacillus 77 present relevant characteristics for their use as starters or as preservative cultures for fruits and vegetables.

Exploring the impacts of postharvest processing on the aroma formation of coffee beans - A review

The aim of this review is to describe the volatile aroma compounds of green coffee beans and evaluate sources of variation in the formation and development of coffee aroma through postharvest processing. The findings of this survey showed that the volatile constituents of green coffee beans (e.g., alcohols, aldehydes, and alkanes) have no significant influence on the final coffee aroma composition, as only a few such compounds remain in the beans after roasting. On the other hand, microbial-derived, odor-active compounds produced during removal of the fruit mucilage layer, including esters, higher alcohols, aldehydes, and ketones, can be detected in the final coffee product. Many postharvest processing including drying and storage processes could influence the levels of coffee aroma compositions, which remain to be elucidated. Better understanding of the effect of these processes on coffee aroma composition would assist coffee producers in the optimal selection of postharvest parameters that favor the consistent production of flavorful coffee beans.

Diversity of Lactic Acid Bacteria Associated with Banana Fruits in Taiwan

Banana is a popular fruit worldwide. The lactic acid bacteria (LAB) microflora in banana fruits has not been studied in detail. A total of 164 LAB were isolated from banana fruits in Taiwan. These isolates were initially divided into nine groups (r1 to r9) using restriction fragment length polymorphism analysis and 16S ribosomal DNA sequencing. Isolates belonging to Lactobacillus plantarum group were further divided into three additional groups using multiplex PCR assay targeting the recA gene. The most common bacterial genera found in banana fruits were Lactobacillus and Weissella. The distribution of LAB indicated that, in most cases, neighboring regions shared common strains, but there were still some differences between regions. On the basis of phylogenetic analysis of 16S rRNA, rpoA, and pheS gene sequences, two strains included in the genera Lactobacillus were identified as potential novel species or subspecies. In addition, a total 36 isolates were found to have bacteriocin-producing abilities. These results suggest that various LAB are associated with banana fruits in Taiwan. This is the first report describing the distribution and varieties of LAB associated with banana fruits. In addition, one potential novel LAB species was also found in this study.

High-Throughput rRNA Gene Sequencing Reveals High and Complex Bacterial Diversity Associated with Brazilian Coffee Bean Fermentation

Coffee bean fermentation is a spontaneous, on-farm process involving the action of different microbial groups, including bacteria and fungi. In this study, high-throughput sequencing approach was employed to study the diversity and dynamics of bacteria associated with Brazilian coffee bean fermentation. The total DNA from fermenting coffee samples was extracted at different time points, and the 16S rRNA gene with segments around the V4 variable region was sequenced by Illumina high-throughput platform. Using this approach, the presence of over eighty bacterial genera was determined, many of which have been detected for the first time during coffee bean fermentation, including Fructobacillus, Pseudonocardia, Pedobacter, Sphingomonas and Hymenobacter. The presence of Fructobacillus suggests an influence of these bacteria on fructose metabolism during coffee fermentation. Temporal analysis showed a strong dominance of lactic acid bacteria with over 97% of read sequences at the end of fermentation, mainly represented by the Leuconostoc and Lactococcus. Metabolism of lactic acid bacteria was associated with the high formation of lactic acid during fermentation, as determined by HPLC analysis. The results reported in this study confirm the underestimation of bacterial diversity associated with coffee fermentation. New microbial groups reported in this study may be explored as functional starter cultures for on-farm coffee processing.

Isolation, selection and evaluation of antagonistic yeasts and lactic acid bacteria against ochratoxigenic fungus Aspergillus westerdijkiae on coffee beans

In this study, yeasts and lactic acid bacteria (LAB) were isolated from coffee fruits and identified via biochemical and molecular approaches. The isolates represented the Pichia, Debaryomyces, Candida, Clavispora, Yarrowia, Sporobolomyces, Klyveromyces, Torulaspora and Lactobacillus genera. Four isolates, namely Pichia fermentans LPBYB13, Sporobolomyces roseus LPBY7E, Candida sp. LPBY11B and Lactobacillus brevis LPBB03, were found to have the greatest antagonist activity against an ochratoxigenic strain of Aspergillus westerdijkiae on agar tests and were selected for further characterization. Applications of P. fermentans LPBYB13 in coffee cherries artificially contaminated with A. westerdijkiae showed efficacy in reducing ochratoxin A (OTA) content up to 88%. These results highlight that P. fermentans LPBYB13 fulfils the principle requirements of an efficient biological control of aflatoxigenic fungi in coffee beans and may be seen as a reliable candidate for further validation in field conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Studies based on microbial ecology and antagonistic interactions are important for the development of new strategies in controlling aflatoxin contamination of crops and are relevant to further biotechnological applications. This study shows that coffee fruit is a potential source for the isolation of microbial strains with antifungal ability. A new yeast strain, Pichia fermentans LPBYB13, showed efficacy in reducing growth and ochratoxin A production of Aspergillus westerdijkiae in coffee beans. Our results should encourage the use of this yeast strain on a large scale for biocontrol of aflatoxigenic fungi in coffee beans.

Diversity and Variation of Bacterial Community Revealed by MiSeq Sequencing in Chinese Dark Teas

Chinese dark teas (CDTs) are now among the popular tea beverages worldwide due to their unique health benefits. Because the production of CDTs involves fermentation that is characterized by the effect of microbes, microorganisms are believed to play critical roles in the determination of the chemical characteristics of CDTs. Some dominant fungi have been identified from CDTs. In contrast, little, if anything, is known about the composition of bacterial community in CDTs. This study was set to investigate the diversity and variation of bacterial community in four major types of CDTs from China. First, the composition of the bacterial community of CDTs was determined using MiSeq sequencing. From the four typical CDTs, a total of 238 genera that belong to 128 families of bacteria were detected, including most of the families of beneficial bacteria known to be associated with fermented food. While different types of CDTs had generally distinct bacterial structures, the two types of brick teas produced from adjacent regions displayed strong similarity in bacterial composition, suggesting that the producing environment and processing condition perhaps together influence bacterial succession in CDTs. The global characterization of bacterial communities in CDTs is an essential first step for us to understand their function in fermentation and their potential impact on human health. Such knowledge will be important guidance for improving the production of CDTs with higher quality and elevated health benefits.

What's Inside That Seed We Brew? A New Approach To Mining the Coffee Microbiome

Coffee is a critically important agricultural commodity for many tropical states and is a beverage enjoyed by millions of people worldwide. Recent concerns over the sustainability of coffee production have prompted investigations of the coffee microbiome as a tool to improve crop health and bean quality. This review synthesizes literature informing our knowledge of the coffee microbiome, with an emphasis on applications of fruit- and seed-associated microbes in coffee production and processing. A comprehensive inventory of microbial species cited in association with coffee fruits and seeds is presented as reference tool for researchers investigating coffee-microbe associations. It concludes with a discussion of the approaches and techniques that provide a path forward to improve our understanding of the coffee microbiome and its utility, as a whole and as individual components, to help ensure the future sustainability of coffee production.