Biological detoxification of coffee husk by filamentous fungi using a solid state fermentation system

Microbial metabolism of caffeine and potential applications in bioremediation

With increasing global consumption of caffeine-rich products, such as coffee, tea, and energy drinks, there is also an increase in urban and processing waste full of residual caffeine with limited disposal options. This waste caffeine has been found to leach into the surrounding environment where it poses a threat to microorganisms, insects, small animals, and entire ecosystems. Growing interest in harnessing this environmental contaminant has led to the discovery of 79 bacterial strains, eight yeast strains, and 32 fungal strains capable of metabolizing caffeine by N-demethylation and/or C-8 oxidation. Recently observed promiscuity of caffeine-degrading enzymes in vivo has opened up the possibility of engineering bacterial strains capable of producing a wide variety of caffeine derivatives from a renewable resource. These engineered strains can be used to reduce the negative environmental impact of leached caffeine-rich waste through bioremediation efforts supplemented by our increasing understanding of new techniques such as cell immobilization. Here, we compile all of the known caffeine-degrading microbial strains, discuss their metabolism and related enzymology, and investigate their potential application in bioremediation.

Caffeine Synthesis and Its Mechanism and Application by Microbial Degradation, A Review

Caffeine is a metabolite derived from purine nucleotides, typically accounting for 2-5% of the dry weight of tea and 1-2% of the dry weight of coffee. In the tea and coffee plants, the main synthesis pathway of caffeine is a four-step sequence consisting of three methylation reactions and one nucleosidase reaction using xanthine as a precursor. In bacteria, caffeine degradation occurs mainly through the pathways of N-demethylation and C-8 oxidation. However, a study fully and systematically summarizing the metabolism and application of caffeine in microorganisms has not been established elsewhere. In the present study, we provide a review of the biosynthesis, microbial degradation, gene expression, and application of caffeine microbial degradation. The present review aims to further elaborate the mechanism of caffeine metabolism by microorganisms and explore the development prospects in this field.

Valorization of cocoa, tea and coffee processing by-products-wastes

The growing threat of food insecurity together with some challenges in demography, health, malnutrition, and income instability around the globe has led researchers to take sustainable solutions to ensure secure production and distribution of food. The last decades have been remarkable in the agri-food supply chain for many food industries. However, vast quantities of food by-products and wastes are generated each year. These products are generally disposed in the environment, which could have remarkable adverse effects on the environment and biodiversity. However, they contain significant quantities of bioactive, nutritional, antioxidative, and aroma compounds. Their sustainable use could meet the increased demand for value-added pharmaceutical, nutraceutical, and food products. The amount of agri-food wastes and their disposal in the environment are predicted to double in the next decade. The valorization of these by-products could effectively contribute to the manufacture of cheaper functional food ingredients and supplements while improving regional economy and food security and mitigating environmental pollution. The main aim of this chapter is to present an understanding of the valorization of the wastes and by-products from cacao, coffee and tea processing with a focus on their bioactive, nutritional, and antioxidant capacity.

Valorization of agro-industrial wastes into animal feed through microbial fermentation: A review of the global and Ghanaian case

Agricultural and industrial activities around the world lead to the production of large quantities of agro-industrial wastes (e.g., peels of cassava, pineapple, plantain, banana, and yam, as well as rice husks, rice bran , corn husks, corn cobs, palm kernel cake, soybean meal, wheat bran, etc.). These agro-industrial wastes are discarded indiscriminately, thereby polluting the environment and becoming hazardous to human and animal health. Solid-state fermentation (SSF), a microbial fermentation process, is a viable, efficient approach that transforms discarded agro-industrial wastes into a plethora of useful value-added bioproducts. There is growing interest in the application of SSF in valorizing agro-industrial wastes for the production of fermented, protein-rich animal feed within the livestock industry. SSF reduces anti-nutritional factors whose presence hinders the digestibility and bioavailability of nutrients in agro-industrial wastes. Thus, the application of SSF improves the nutrient contents and quality of valorized agro-industrial wastes as animal feed. Fermented animal feed production may be safer, cheaper and enhance the overall growth performance and health of animals. SSF, therefore, as a strategic approach in a circular bioeconomy, presents economic and practical advantages that guarantee efficient recycling and valorization of agro-industrial wastes that ameliorate environmental pollution. This paper reviews the status of global and local Ghanaian biotransformation and valorization of agro-industrial wastes through SSF for the production of nutrient-rich animal feed.

Coffee by-products: An underexplored source of prebiotic ingredients

Consumers' demand for foods with high nutritional value and health benefits has fueled the development of prebiotic foods. In coffee industry, cherries transformation into roasted beans generates a large amount of waste/by-products (pulp/husks, mucilage, parchment, defective beans, silverskin and spent coffee grounds) that usually end up in landfills. The possibility to use coffee by-products as relevant sources of prebiotic ingredients is herein ascertained. As a prelude to this discussion, an overview of pertinent literature on prebiotic action was conducted, including on biotransformation of prebiotics, gut microbiota, and metabolites. Existing research indicates that coffee by-products contain significant levels of dietary fiber and other components that can improve gut health by stimulating beneficial bacteria in the colon, making them excellent candidates for prebiotic ingredients. Oligosaccharides from coffee by-products have lower digestibility than inulin and can be fermented by gut microbiota into functional metabolites, such as short-chain fatty acids. Depending on the concentration, melanoidins and chlorogenic acids may also have prebiotic action. Nevertheless, there is still a lack of in vivo studies to validate such findings in vitro. This review shows how coffee by-products can be interesting for the development of functional foods, contributing to sustainability, circular economy, food security, and health.

Physico-chemical characterization study of coffee husk for feasibility assessment in fluidized bed gasification process

The biomasses like post-harvest agricultural residues are usually disposed of as landfills and used as cattle fodder and manure. Large quantities of such wastes are often set to open firing. The open firing of such waste biomasses leads to particulate matter emission and air pollution. Kerala, the second-largest producer of coffee in India, produces around 65,925 metric tonnes of coffee. Almost 30-50% of waste is produced during coffee processing, out of which coffee husk has a significant contribution. The thermochemical process like gasification helps in bio-energy extraction and proper disposal of coffee husk. In the present study, the physico-chemical characteristics of coffee husk are studied in detail to investigate its feasibility as a biomass feedstock for thermochemical applications. The thermal degradation of coffee husk at higher temperatures (up to 1000 °C) is investigated using thermogravimetric (TG) analysis. The higher heating value is determined using a bomb calorimeter and is found to be 19.67 MJ/kg. The selected sample has a volatile matter content of 66.85% and fixed carbon content of 14%. The elemental composition is also determined to identify the presence of inorganic elements in the sample. The presence of inorganic elements like potassium and sodium in the feedstock often leads to defluidization when used in fluidized bed gasifiers. The physical and chemical properties analysed would enable in apt handling and treating coffee husk prior to thermochemical processing.

Valorization of Spent Coffee Grounds as a Natural Source of Bioactive Compounds for Several Industrial Applications-A Volatilomic Approach

Coffee is one of the most popular beverages worldwide, whose production and consumption result in large amounts of waste, namely spent coffee grounds, constituting an important source of compounds for several industrial applications. This work focused on the establishment of the volatile fingerprint of five spent coffee grounds from different geographical origins using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS), as a strategy to identify volatile organic metabolites (VOMs) with potential application in the food industry as antioxidant, anti-inflammatory, and antiproliferative agents. One hundred eleven VOMs belonging to different chemical families were identified, of which 60 were found in all spent coffee grounds analyzed. Furanic compounds (34%), nitrogen compounds (30%), and esters (19%) contributed significant to the total volatile fingerprint. The data obtained suggest that spent coffee grounds have great potential to be used as raw material for different approaches in the food industry towards the development of new food ingredients or products for human consumption, in addition to pharmaceutical and cosmetic applications, namely as antioxidant (e.g., limonene, carvacrol), antimicrobial (e.g., pyrrole-2-carboxaldehyde, β-myrcene) and anti-inflammatory (e.g., furfural, 2-furanmethanol) agents, promoting their integral valorization within the circular bioeconomy concept.

Application of solid-state fermentation by microbial biotechnology for bioprocessing of agro-industrial wastes from 1970 to 2020: A review and bibliometric analysis

This paper reviews the pertinent literature from 1970 to 2020 and presents a bibliometric analysis of research trends in the application of solid-state fermentation in the bioprocessing of agro-industrial wastes. A total 5630 publications of studies on solid-state fermentation that comprised of 5208 articles (92.50%), 340 book chapters (6.04%), 39 preprints (0.69%), 32 proceedings (0.56%), 8 edited books (0.14%) and 3 monographs (0.05%) were retrieved from Dimensions database. A review of the literature indicated that (i) fermentation of solid substrates is variously defined in the literature over the past 50 years, where "solid-state fermentation" is the most dominant research term used, and (ii) key products derived from the valorization of agro-industrial wastes through solid-state fermentation include, among others, enzymes, antioxidants, animal feed, biofuel, organic acids, biosurfactants, etc. Bibliometric analyses with VOSviewer revealed an astronomic increase in publications between 2000 and 2020, and further elucidated the most frequently explored core research topics, the most highly cited publications and authors, and countries/regions with the highest number of citations. The most cited publication between 2010 and 2020 had 382 citations compared to 725 citations for the most cited publication from 1970 to 2020. Ashok Pandey from India was the most published and cited author with 123 publications and 8,613 citations respectively; whereas Bioresource Technology was the most published and cited journal with 233 publications and 12,394 citations. Countries with the most publications and citations are Brazil, France, India, and Mexico. These findings suggest that research in the application of solid-state fermentation for bioprocessing of agro-industrial wastes has gained prominence over the past 50 years. Future perspectives and implications are discussed.

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.

3-Methylxanthine production through biodegradation of theobromine by Aspergillus sydowii PT-2

Background

Methylxanthines, including caffeine, theobromine and theophylline, are natural and synthetic compounds in tea, which could be metabolized by certain kinds of bacteria and fungi. Previous studies confirmed that several microbial isolates from Pu-erh tea could degrade and convert caffeine and theophylline. We speculated that these candidate isolates also could degrade and convert theobromine through N-demethylation and oxidation. In this study, seven tea-derived fungal strains were inoculated into various theobromine agar medias and theobromine liquid mediums to assess their capacity in theobromine utilization. Related metabolites with theobromine degradation were detected by using HPLC in the liquid culture to investigate their potential application in the production of 3-methylxanthine.

Results

Based on theobromine utilization capacity, Aspergillus niger PT-1, Aspergillus sydowii PT-2, Aspergillus ustus PT-6 and Aspergillus tamarii PT-7 have demonstrated the potential for theobromine biodegradation. Particularly, A. sydowii PT-2 and A. tamarii PT-7 could degrade theobromine significantly (p < 0.05) in all given liquid mediums. 3,7-Dimethyluric acid, 3-methylxanthine, 7-methylxanthine, 3-methyluric acid, xanthine, and uric acid were detected in A. sydowii PT-2 and A. tamarii PT-7 culture, respectively, which confirmed the existence of N-demethylation and oxidation in theobromine catabolism. 3-Methylxanthine was common and main demethylated metabolite of theobromine in the liquid culture. 3-Methylxanthine in A. sydowii PT-2 culture showed a linear relation with initial theobromine concentrations that 177.12 ± 14.06 mg/L 3-methylxanthine was accumulated in TLM-S with 300 mg/L theobromine. Additionally, pH at 5 and metal ion of Fe²⁺ promoted 3-methylxanthine production significantly (p < 0.05).

Conclusions

This study is the first to confirm that A. sydowii PT-2 and A. tamarii PT-7 degrade theobromine through N-demethylation and oxidation, respectively. A. sydowii PT-2 showed the potential application in 3-methylxanthine production with theobromine as feedstock through the N-demethylation at N-7 position.

Use of coffee pulp and sorghum mixtures in the production of n-demethylases by solid-state fermentation

One of the compounds generally found in the residues of the coffee and tea industries is caffeine, which in high concentration is toxic to various organisms, making it necessary to find an adequate treatment for these residues. Biotechnological treatments using enzymes can be an alternative to valorize and detoxify these residues. However, mixtures of substrates have not been evaluated to improve production. Therefore, the present investigation aimed to study the effect of different proportions of sorghum-coffee pulp mixtures as a substrate in solid-state fermentation with the fungus Rhizopus oryzae (MUCL 28168) for the production of n-demethylases. To evaluate the synergistic and antagonistic effects of coffee pulp and sorghum mixtures on n-demethylase enzyme production, a simplex-centroid design, using four levels: 1 (100%), 1/4 (25%), 1/2 (50%), 3/4 (75%). Results obtained were favorable, achieving a caffeine demethylase activity of 18.762 U/g, and reducing the caffeine content in the coffee pulp.

The Application of Fermentation Technology in Traditional Chinese Medicine: A Review

In Chinese medicine, fermentation is a highly important processing technology whereby medicinal herbs are fermented under appropriate temperature, humidity, and moisture conditions by means of the action of microorganisms to enhance their original characteristics and/or produce new effects. This expands the scope of such medicines and helps them to meet the stringent demands of clinical application. Since ancient times, Chinese medicine has been made into Yaoqu to reduce its toxicity and increase its efficiency. Modern fermentation technologies have been developed on the basis of traditional fermentation techniques and modern biological technology, and they can be divided into solid fermentation, liquid fermentation, and two-way fermentation technologies according to the fermentation form employed. This review serves as an introduction to traditional fermentation technology and its related products, modern fermentation technologies, and the application of fermentation technology in the field of Chinese medicine. Several problems and challenges facing the field are also briefly discussed.

Modeling Dark Fermentation of Coffee Mucilage Wastes for Hydrogen Production: Artificial Neural Network Model vs. Fuzzy Logic Model

This study presents the analysis and estimation of the hydrogen production from coffee mucilage mixed with organic wastes by dark anaerobic fermentation in a co-digestion system using an artificial neural network and fuzzy logic model. Different ratios of organic wastes (vegetal and fruit garbage) were added and combined with coffee mucilage, which led to an increase of the total hydrogen yield by providing proper sources of carbon, nitrogen, mineral, and other nutrients. A two-level factorial experiment was designed and conducted with independent variables of mucilage/organic wastes ratio, chemical oxygen demand (COD), acidification time, pH, and temperature in a 20-L bioreactor in order to demonstrate the predictive capability of two analytical modeling approaches. An artificial neural network configuration of three layers with 5-10-1 neurons was developed. The trapezoidal fuzzy functions and an inference system in the IF-THEN format were applied for the fuzzy logic model. The quality fit between experimental hydrogen productions and analytical predictions exhibited a predictive performance on the accumulative hydrogen yield with the correlation coefficient (R2) for the artificial neural network (> 0.7866) and fuzzy logic model (> 0.8485), respectively. Further tests of anaerobic dark fermentation with predefined factors at given experimental conditions showed that fuzzy logic model predictions had a higher quality of fit (R2 > 0.9508) than those from the artificial neural network model (R2 > 0.8369). The findings of this study confirm that coffee mucilage is a potential resource as the renewable energy carrier, and the fuzzy-logic-based model is able to predict hydrogen production with a satisfactory correlation coefficient, which is more sensitive than the predictive capacity of the artificial neural network model.

Isolation, characterization and application of theophylline-degrading Aspergillus fungi

Background

Caffeine, theobromine and theophylline are main purine alkaloid in tea. Theophylline is the downstream metabolite and it remains at a very low level in Camellia sinensis. In our previous study, Aspergillus sydowii could convert caffeine into theophylline in solid-state fermentation of pu-erh tea through N-demethylation. In this study, tea-derived fungi caused theophylline degradation in the solid-state fermentation. The purpose of this study is identify and isolate theophylline-degrading fungi and investigate their application in production of methylxanthines with theophylline as feedstock through microbial conversion.

Results

Seven tea-derived fungi were collected and identified by ITS, β-tubulin and calmodulin gene sequences, Aspergillus ustus, Aspergillus tamarii, Aspergillus niger and A. sydowii associated with solid-state fermentation of pu-erh tea have shown ability to degrade theophylline in liquid culture. Particularly, A. ustus and A. tamarii could degrade theophylline highly significantly (p < 0.01). 1,3-dimethyluric acid, 3-methylxanthine, 3-methyluric acid, xanthine and uric acid were detected consecutively by HPLC in A. ustus and A. tamarii, respectively. The data from absolute quantification analysis suggested that 3-methylxanthine and xanthine were the main degraded metabolites in A. ustus and A. tamarii, respectively. 129.48 ± 5.81 mg/L of 3-methylxanthine and 159.11 ± 10.8 mg/L of xanthine were produced by A. ustus and A. tamarii in 300 mg/L of theophylline liquid medium, respectively.

Conclusions

For the first time, we confirmed that isolated A. ustus, A. tamarii degrade theophylline through N-demethylation and oxidation. We were able to biologically produce 3-methylxanthine and xanthine efficiently from theophylline through a new microbial synthesis platform with A. ustus and A. tamarii as appropriate starter strains.

Chemical composition and health properties of coffee and coffee by-products

Coffee can be an ally in the fight against diseases such as type 2 diabetes, cancer, hepatic injury, cirrhosis, depression, suicidal behavior, and neurological and cardiovascular disorders. The properties of coffee also favor gastrointestinal tract and gut microbiota establishment. Coffee bioactive components include phenolic compounds (chlorogenic acids, cafestol and kahweol), alkaloids (caffeine and trigonelin), diterpenes (cafestol and kahweol) and other secondary metabolites. The image of coffee as a super functional food has helped to increase coffee consumption across the globe. This chapter addresses the main health promotion mechanisms associated with coffee consumption. Related topics on coffee production chain, world consumption and reuse of coffee by-products in the production of high-value-adding molecules with potential applications in the food industry are addressed and discussed.

LC-MS/MS-based metabolomic analysis of caffeine-degrading fungus Aspergillus sydowii during tea fermentation

Natural microorganisms involved in solid-state fermentation (SSF) of Pu-erh tea have a significant impact on its chemical components. Aspergillus sydowii is a fungus with a high caffeine-degrading capacity. In this work, A. sydowii was inoculated into sun-dried green tea leaves for SSF. Metabolomic analysis was carried out by using UPLC-QTOF-MS method, and caffeine and related demethylated products were determined by HPLC. The results showed that A. sydowii had a significant (P < 0.05) impact on amino acids, carbohydrates, flavonoids, and caffeine metabolism. Moreover, A. sydowii could promote the production of ketoprofen, baclofen, and tolbutamide. Along with caffeine degradation, theophylline, 3-methylxanthine, 1,7-dimethylxanthine, 1-methylxanthine, and 7-methylxanthine were increased significantly (P < 0.05) during inoculated fermentation, which showed that demethylation was the main pathway of caffeine degradation in A. sydowii secondary metabolism. The absolute quantification analysis showed that caffeine could be demethylated and converted to theophylline and 3-methylxanthine. Particularly, about 93.24% of degraded caffeine was converted to theophylline, 27.92 mg/g of theophylline was produced after fermentation. PRACTICAL APPLICATION: Aspergillus sydowii could cause caffeine degradation in Pu-erh tea solid-state fermentation and produce theophylline through the demethylation route. Using a starter strain to ferment tea leaves offers a more controllable, reproducible, and highly productive alternative for the biosynthesis of theophylline.

Caffeine Content and Related Gene Expression: Novel Insight into Caffeine Metabolism in Camellia Plants Containing Low, Normal, and High Caffeine Concentrations

Caffeine is a crucial secondary metabolic product in tea plants. Although the presence of caffeine in tea plants has been identified, the molecular mechanisms regulating relevant caffeine metabolism remain unclear. For the elucidation of the caffeine biosynthesis and catabolism in Camellia plants, fresh, germinated leaves from four Camellia plants with low (2), normal (1), and high (1) caffeine concentrations, namely, low-caffeine tea 1 (LCT1, Camellia crassicolumna), low-caffeine tea 2 (LCT2, C. crassicolumna), Shuchazao (SCZ, C. sinensis), and Yunkang 43 (YK43, C. sinensis) were used in this research. Transcriptome and purine alkaloids analyses of these Camellia leaves were performed using RNA-Seq and liquid chromatography-mass spectrometry (LC-MS). Moreover, ¹⁵N-caffeine tracing was performed to determine the metabolic fate of caffeine in leaves of these plants. Caffeine content was correlated with related gene expression levels, and a quantitative real-time (qRT) PCR analysis of specific genes showed a consistent tendency with the obtained transcriptomic analysis. On the basis of the results of stable isotope-labeled tracer experiments, we discovered a degradation pathway of caffeine to theobromine. These findings could assist researchers in understanding the caffeine-related mechanisms in Camellia plants containing low, normal, and high caffeine content and be applied to caffeine regulation and breeding improvement in future research.

Effects of partial dietary substitution of groundnut meal by defatted, Aspergillus niger-fermented and heated Jatropha curcas kernel meal on feed intake and growth performance of broiler chicks

This study was conducted to determine intake and growth performance of broiler chicks fed with Jatropha curcas kernel meal physico-chemically and biologically processed. The feed experiment lasted for 7 days with 20-day-old Ross 308 strain unsexed broiler chicks. Two dietary treatments were given each to ten animals, according to a complete randomized design. Kernels, manually obtained from J. curcas seed, were defatted, heated, and fermented with a strain of Aspergillus niger and oven-dried, in order to obtain the treated jatropha kernel meal. This latter was used to replace one third of a groundnut meal premix which was then incorporated in a commercial diet to warrant iso-nitrogenous and iso-caloric characteristics of the diets. Data collected were analyzed according to ANOVA procedure. The results revealed that the animals that received the diet incorporating jatropha kernel meal had numerically higher live weight (156.1 vs. 152.7 g/animal) (P > 0.05) and average daily weight gain (12.3 vs. 11.7 g/day/animal) (P > 0.05) than the control ones, at the end of experiment. The average daily feed intake was the same for the two groups of animals (23.2 g/day/animal) (P > 0.05) with a similar feed conversion ratio (2.0 vs. 2.1 respectively for the jatropha group and the control group). The survival rate, at the end of the experiment, was 100% for the two groups of animals. Physico-chemically and biologically processed Jatropha curcas kernel could be an interesting by-product for poultry feeding.

Hydrogen Production from Coffee Mucilage in Dark Fermentation with Organic Wastes

One of primary issues in the coffee manufacturing industry is the production of large amounts of undesirable residues, which include the pericarp (outer skin), pulp (outer mesocarp), parchment (endocarp), silver-skin (epidermis) and mucilage (inner mesocarp) that cause environmental problems due to toxic molecules contained therein. This study evaluated the optimal hydrogen production from coffee mucilage combined with organic wastes (wholesale market garbage) in a dark fermentation process. The supplementation of organic wastes offered appropriate carbon and nitrogen sources with further nutrients; it was positively effective in achieving cumulative hydrogen production. Three different ratios of coffee mucilage and organic wastes (8:2, 5:5, and 2:8) were tested in 30 L bioreactors using two-level factorial design experiments. The highest cumulative hydrogen volume of 25.9 L was gained for an 8:2 ratio (coffee mucilage: organic wastes) after 72 h, which corresponded to 1.295 L hydrogen/L substrates (0.248 mol hydrogen/mol hexose). Biochemical identification of microorganisms found that seven microorganisms were involved in the hydrogen metabolism. Further studies of anaerobic fermentative digestion with each isolated pure bacterium under similar experimental conditions reached a lower final hydrogen yield (up to 9.3 L) than the result from the non-isolated sample (25.9 L). Interestingly, however, co-cultivation of two identified microorganisms (Kocuria kristinae and Brevibacillus laterosporus), who were relatively highly associated with hydrogen production, gave a higher yield (14.7 L) than single bacterium inoculum but lower than that of the non-isolated tests. This work confirms that the re-utilization of coffee mucilage combined with organic wastes is practical for hydrogen fermentation in anaerobic conditions, and it would be influenced by the bacterial consortium involved.

Enzymatic dynamics into the Eisenia fetida (Savigny, 1826) gut during vermicomposting of coffee husk and market waste in a tropical environment

Epigeic worms modify microbial communities through their digestive processes, thereby influencing the decomposition of organic matter in vermicomposting systems. Nevertheless, the enzyme dynamics within the gut of tropically adapted earthworms is unknown, and the enzymes involved have not been simultaneously studied. The activities of 19 hydrolytic enzymes within three different sections of the intestine of Eisenia fetida were determined over a fasting period and at 24 h and 30, 60, and 90 days of vermicomposting, and data were evaluated by multivariate analyses. There were found positive correlations between the maximal activity of glycosyl hydrolases and one esterase with the anterior intestine (coincident with the reduction of hemicellulose in the substrate) and the activity of the protease α-chymotrypsin with posterior intestine. The results suggest that activities of enzymes change in a coordinated manner within each gut section, probably influenced by selective microbial enzyme enrichment and by the availability of nutrients throughout vermicomposting.

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.

Genetic characterization of caffeine degradation by bacteria and its potential applications

The ability of bacteria to grow on caffeine as sole carbon and nitrogen source has been known for over 40 years. Extensive research into this subject has revealed two distinct pathways, N-demethylation and C-8 oxidation, for bacterial caffeine degradation. However, the enzymological and genetic basis for bacterial caffeine degradation has only recently been discovered. This review article discusses the recent discoveries of the genes responsible for both N-demethylation and C-8 oxidation. All of the genes for the N-demethylation pathway, encoding enzymes in the Rieske oxygenase family, reside on 13.2-kb genomic DNA fragment found in Pseudomonas putida CBB5. A nearly identical DNA fragment, with homologous genes in similar orientation, is found in Pseudomonas sp. CES. Similarly, genes for C-8 oxidation of caffeine have been located on a 25.2-kb genomic DNA fragment of Pseudomonas sp. CBB1. The C-8 oxidation genes encode enzymes similar to those found in the uric acid metabolic pathway of Klebsiella pneumoniae. Various biotechnological applications of these genes responsible for bacterial caffeine degradation, including bio-decaffeination, remediation of caffeine-contaminated environments, production of chemical and fuels and development of diagnostic tests have also been demonstrated.

New genetic insights to consider coffee waste as feedstock for fuel, feed, and chemicals

Caffeine is a natural plant product found in many drinks, including coffee, tea, soft and energy drinks. Due to caffeine’s presence in the environment, microorganisms have evolved two different mechanisms to live on caffeine. The genetic maps of the caffeine N-demethylation pathway and C-8 oxidation pathway have been discovered in Pseudomonas putida CBB5 and Pseudomonas sp. CBB1, respectively. These genes are the only characterized bacterial caffeine-degrading genes, and may be of great value in producing fine chemicals, biofuels, and animal feed from coffee and tea waste. Here, we present preliminary results for production of theobromine and 7-methylxanthine from caffeine and theobromine, respectively, by two strains of metabolically engineered E. coli. We also demonstrate complete decaffeination of tea extract by an immobilized mixed culture of Klebsiella and Rhodococcus cells. These processes provide a first level demonstration of biotechnological utilization of coffee and tea waste.

Solid-state fermentation of Jatropha seed cake for optimization of lipase, protease and detoxification of anti-nutrients in Jatropha seed cake using Aspergillus versicolor CJS-98

This study focused on the solid-state fermentation of Jatropha seed cake (JSC), a byproduct generated after biodiesel production. Presence of anti-nutritional compounds and toxins restricts its application in livestock feed. The disposal of the JSC is a major environmental problem in the future, due to the generation of huge quantity of JSC after biodiesel extraction. Hence the JSC was assessed for its suitability as substrate for production and optimization of lipase and protease from Aspergillus versicolor CJS-98 by solid-state fermentation (SSF). The present study was also focused on the biodetoxification of anti-nutrients and toxins in JSC. The SSF parameters were optimized for maximum production of lipase and protease. Under the optimized conditions, the JSC supplemented with maltose and peptone (2%), adjusted to pH 7.0, moisture content 40%, inoculated with 1 × 10(7) spores per 5 g cake and incubated at 25°C, produced maximum lipase, 1288 U/g and protease, 3366 U/g at 96 h. The anti-nutrients like phytic acid (6.08%), tannins (0.37%), trypsin inhibitors (697.5 TIU/g), cyanogenic glucosides (692.5 μg/100 g), and lectins (0.309 mg/ml), were reduced to 1.70%, 0.23%, 12.5 TIU/g, 560.6 μg/100 g and 0.034 mg/ml respectively. The main toxic compound phorbol esters content in the JSC was reduced from 0.083% to 0.015% after SSF. Our results indicate that viability of SSF to utilize the huge amount of seed cake generated after extraction of biodiesel, for production of industrial enzymes and biodetoxification of anti-nutrients, toxins.

Delineation of the caffeine C-8 oxidation pathway in Pseudomonas sp. strain CBB1 via characterization of a new trimethyluric acid monooxygenase and genes involved in trimethyluric acid metabolism

The molecular basis of the ability of bacteria to live on caffeine via the C-8 oxidation pathway is unknown. The first step of this pathway, caffeine to trimethyluric acid (TMU), has been attributed to poorly characterized caffeine oxidases and a novel quinone-dependent caffeine dehydrogenase. Here, we report the detailed characterization of the second enzyme, a novel NADH-dependent trimethyluric acid monooxygenase (TmuM), a flavoprotein that catalyzes the conversion of TMU to 1,3,7-trimethyl-5-hydroxyisourate (TM-HIU). This product spontaneously decomposes to racemic 3,6,8-trimethylallantoin (TMA). TmuM prefers trimethyluric acids and, to a lesser extent, dimethyluric acids as substrates, but it exhibits no activity on uric acid. Homology models of TmuM against uric acid oxidase HpxO (which catalyzes uric acid to 5-hydroxyisourate) reveal a much bigger and hydrophobic cavity to accommodate the larger substrates. Genes involved in the caffeine C-8 oxidation pathway are located in a 25.2-kb genomic DNA fragment of CBB1, including cdhABC (coding for caffeine dehydrogenase) and tmuM (coding for TmuM). Comparison of this gene cluster to the uric acid-metabolizing gene cluster and pathway of Klebsiella pneumoniae revealed two major open reading frames coding for the conversion of TM-HIU to S-(+)-trimethylallantoin [S-(+)-TMA]. The first one, designated tmuH, codes for a putative TM-HIU hydrolase, which catalyzes the conversion of TM-HIU to 3,6,8-trimethyl-2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (TM-OHCU). The second one, designated tmuD, codes for a putative TM-OHCU decarboxylase which catalyzes the conversion of TM-OHCU to S-(+)-TMA. Based on a combination of enzymology and gene-analysis, a new degradative pathway for caffeine has been proposed via TMU, TM-HIU, TM-OHCU to S-(+)-TMA.

Physiology, biochemistry and possible applications of microbial caffeine degradation

Caffeine, a purine alkaloid is a constituent of widely consumed beverages. The scientific evidence which has proved the harm of this alkaloid has paved the way for innumerable research in the area of caffeine degradation. In addition to this, the fact that the by-products of the coffee and tea industry pollute the environment has called for the need of decaffeinating coffee and tea industry's by-products. Though physical and chemical methods for decaffeination are available, the lack of specificity for removal of caffeine in these techniques and their non-eco-friendly nature has opened the area of microbial and enzymatic degradation of caffeine. Another important application of microbial caffeine degradation apart from its advantages like specificity, eco-friendliness and cost-effectiveness is the fact that this process will enable the production of industrially and medically useful components of the caffeine degradation pathway like theobromine and theophylline. This is a comprehensive review which mainly focuses on caffeine degradation, large-scale degradation of the same and its applications in the industrial world.