Gas chromatography/mass spectrometry-based metabolite profiling of coffee beans obtained from different altitudes and origins with various postharvest processing.

INTRODUCTION: Coffee is a popular beverage because of its pleasant aroma and distinctive flavor. The flavor of coffee results from chemical transformations influenced by various intrinsic and extrinsic factors, including altitude, geographical origin, and postharvest processing. Despite is the importance of grading coffee quality, there is no report on the dominant factor that influences the metabolomic profile of green coffee beans and the correlated metabolites for each factor. OBJECTIVE: This study investigated the total metabolite profile of coffees from different altitudes and coffees subjected to different postharvest processing. METHOD: Arabica green coffee beans obtained from different geographical origins and different altitudes (400 and 800 m) and produced by different postharvest processes (dry, honey, and washed process) were used in this study. Coffee samples obtained from altitudes of 400-1600 m above sea level from various origins that were produced by the washed method were used for further study with regard to altitudes. Samples were subjected to gas chromatography/mass spectrometry (GC/MS) analysis and visualized using principal component analysis (PCA) and orthogonal partial least squares (OPLS) regression analysis. RESULTS: The PCA results showed sample separation based on postharvest processing in PC1 and sample separation based on altitude in PC2. A clear separation between samples from different altitudes was observed if the samples were subjected to the same postharvest processing method, and the samples were of the same origin. Based on this result, OPLS analysis was conducted using coffee samples obtained from various altitudes with the same postharvest processing. An OPLS model using altitude as a response variable and 79 metabolites annotated from the GC/MS analysis as an explanatory variable was constructed with good R2 and Q2 values. CONCLUSION: Postharvest processing was found to be the dominant factor affecting coffee metabolite composition; this was followed by geographical origin and altitude. The metabolites glutamic acid and galactinol were associated with the washed and honey process, while glycine, lysine, sorbose, fructose, glyceric acid, and glycolic acid were associated with the dry process. Two metabolites with high variable influence on projection scores in the OPLS model for altitude were inositol and serotonin, which showed positive and negative correlations, respectively. This is the first study to report characteristic coffee metabolites obtained from different altitudes.

GC/MS-based metabolic profiling for the evaluation of solid state fermentation to improve quality of Arabica coffee beans.

INTRODUCTION: Coffee fermentation has been reported as one key process in aroma and flavor development of coffee. However, natural fermentation often results in inconsistent quality of coffee. In this study, second fermentation using isolates from feces of civet (Luwak) and Cilembu sweet potato were used to improve the quality of Arabica green coffee beans. OBJECTIVES: The aim of this research was to improve the quality of various Arabica coffee from different origins in Indonesia by controlled-second fermentation. METHOD: The Arabica coffee beans used in this study were from three origins in Indonesia: Kintamani-Bali (I), Aceh-Gayo (II) and Nagarawangi-Sumedang (III). The second fermentation was done using three bacterial isolates coded as BF5C(2); UciSp14; and AF7E which belong to Bacillus genus. Quality assessment of fermented coffee was performed by cupping test following Specialty Coffee Association of America (SCAA) protocol by licensed Q graders, GC/MS metabolite profiling, and total polyphenol content measurement. RESULTS: The controlled-second fermentation for 4-8 h was successful to increase total polyphenol content well as to improve the complexity of coffee taste and coffee quality (cupping score > 84). Comparative GC/MS analysis showed that fermentation of coffee beans resulted in alteration of metabolite profiles of coffee beans compared with control, while still maintaining the characteristics of coffee based on each origin. CONCLUSION: The controlled-second fermentation was effective to increase the quality of coffee and alter metabolite composition of coffee that were associated with changes in taste profile of coffee. This report may serve as basis for producing coffee with better taste quality with higher polyphenols content through standardized fermentation production in industrial scale.

Metabolite profiling of whiteleg shrimp Litopenaeus vannamei from super-intensive culture in closed aquaculture systems: a recirculating aquaculture system and a hybrid zero water discharge-recirculating aquaculture system.

INTRODUCTION: The production of the whiteleg shrimp Litopenaeus vannamei now accounts for approximately 75% of the total shrimp production in Indonesia. The techniques used to produce whiteleg shrimp in Indonesia are still dominated by conventional rearing strategies using open-pond systems, which often contribute to unpredictable culture performance and weak sustainability. Alternative production strategies of closed aquaculture systems, including the recirculating aquaculture system (RAS) and hybrid zero water discharge-recirculating aquaculture system (hybrid system), have been developed and implemented for higher productivity, stability and sustainability of whiteleg shrimp grow-out production in Indonesia. Despite the positive aspects of the application of closed aquaculture systems in shrimp aquaculture, the differences in the characteristics of shrimp grown in closed RAS and hybrid systems compared to open-pond systems remain unclear. OBJECTIVE: This study aims to investigate the differences in the metabolite profiles of shrimp grown in intensive closed aquaculture systems, including an RAS and hybrid system, compared to those of shrimp grown in a semi-intensive, open, earthen pond system by means of non-targeted GC-MS metabolite profiling. METHODS: Shrimp cultured in the closed systems (RAS and hybrid system) and an open system (pond) were harvested and subjected to GC-MS non-targeted metabolomics analysis. A total of 112 metabolites were annotated from shrimp samples and subjected to principal component analysis (PCA). RESULTS: The metabolites annotated from GC-MS mainly included organic compounds, proteinogenic and non-proteinogenic amino acids, sugars, nucleosides and fatty acids. The results of principal component analysis showed several metabolites with high variable importance in projection (VIP) scores, including shikimic acid, ß-alanine, uric acid, hypoxanthine, inosine, homocysteine, methionine, phenylalanine, tryptophan and lysine, as the main metabolites differentiating the shrimp grown in the three production systems. CONCLUSION: Our findings showed that shrimp cultured in different aquaculture systems exhibited distinct metabolite profiles, and the metabolites showing high VIP scores, including shikimic acid, ß-alanine, uric acid, hypoxanthine, inosine, homocysteine, methionine, phenylalanine, tryptophan and lysine, may serve as candidate markers to indicate the differences in shrimp from different production systems.

Metabolite Changes in Indonesian Tempe Production from Raw Soybeans to Over-Fermented Tempe.

Tempe is fermented soybean from Java, Indonesia, that can serve as a functional food due to its high nutritional content and positive impact on health. Although the tempe fermentation process is known to affect its nutrient content, changes in the metabolite profile during tempe production have not been comprehensively examined. Thus, this research applied a metabolomics approach to investigate the metabolite profile in each step of tempe production, from soybean soaking to over-fermentation. Fourteen samples of raw soybeans, i.e., soaked soybeans (24 h), steamed soybeans, fungal fermented soybeans, and over-fermented soybeans (up to 72 h), were collected. Untargeted metabolomics by gas chromatography/mass spectrometry (GC-MS) was used to determine soybean transformations from various fermentation times and identify disparity-related metabolites. The results showed that soybeans samples clustered together on the basis of the different fermentation steps. The results also showed that sugar, sugar alcohol, organic acids, and amino acids, as well as fermentation time, contributed to the soybean metabolite profile transformations. During the fermentation of tempe, sugars and sugar alcohols accumulated at the beginning of the process before gradually decreasing as fermentation progressed. Specifically, at the beginning of the fermentation, gentiobiose, galactinol, and glucarate were accumulated, and several metabolites such as glutamine, 4-hydroxyphenylacetic acid, and homocysteine increased along with the progression of fermentation. In addition, notable isoflavones daidzein and genistein increased from 24 h of fermentation until 72 h. This is the first report that provides a complete description of the metabolic profile of the tempe production from soybean soaking to over-fermentation. Through this study, the dynamic changes at each step of tempe production were revealed. This information can be beneficial to the tempe industry for the improvement of product quality based on metabolite profiling.

Dynamic Changes in the Bacterial Community and Metabolic Profile during Fermentation of Low-Salt Shrimp Paste (Terasi).

Low-salt shrimp paste, or terasi, is an Indonesian fermented food made from planktonic shrimp mixed with a low concentration of salt. Since high daily intake of sodium is deemed unhealthy, reduction of salt content in shrimp paste production is desired. Until now, there is no reported investigation on the bacterial population and metabolite composition of terasi during fermentation. In this study, the bacterial community of terasi was assessed using high-throughput sequencing of the 16S rRNA V3-V4 region. From this analysis, Tetragenococcus, Aloicoccus, Alkalibacillus, Atopostipes, and Alkalibacterium were found to be the dominant bacterial genus in low-salt shrimp paste. GC/MS-based metabolite profiling was also conducted to monitor the metabolite changes during shrimp paste fermentation. Results showed that acetylated amino acids increased, while glutamine levels decreased, during the fermentation of low-salt shrimp paste. At the start of shrimp paste fermentation, Tetragenococcus predominated with histamine and cadaverine accumulation. At the end of fermentation, there was an increase in 4-hydroxyphenyl acetic acid and indole-3-acetic acid levels, as well as the predominance of Atopostipes. Moreover, we found that aspartic acid increased during fermentation. Based on our findings, we recommend that fermentation of low-salt shrimp paste be done for 7 to 21 days, in order to produce shrimp paste that has high nutritional content and reduced health risk.

Gas chromatography coupled with mass spectrometry-based metabolomics for the classification of tempe from different regions and production processes in Indonesia.

Tempe, a fermented soybean originally from Indonesia, is an excellent protein source with high nutritional quality. Differences in the production process and unique fermentation condition in different regions result in varieties of tempe. Despite its high cultural and economic values, there are very few studies on the characterization of tempe based on the differences of production process and geographical origin. Metabolomics is a powerful tool assessing food quality, food safety, and determination of origin and varietal differences. In this study, metabolomics is applied for the study of Indonesian tempe obtained from various regions and different production processes. Seventeen samples were collected from 6 different cities in Java Island, which were produced by local tempe crafters (traditional), semi-modern industry and modern industry. Untargeted metabolomics by gas chromatography coupled with mass spectrometry (GC/MS) was implemented to discriminate various kinds of tempe and identify metabolites that are associated with these differences. Results showed that tempe produced in different places clustered together according to the cities and their production category. Sugars and amino acids groups were found to be primary compounds that contributed to this result. This is the first report that address the metabolic differences between different varieties of tempe from different regions and production processes. The knowledge from this study is important for future development of tempe production.

Complete Genome Sequence of Bordetella pertussis Pelita III, the Production Strain for an Indonesian Whole-Cell Pertussis Vaccine.

PT Bio Farma, the sole World Health Organization-approved Indonesian vaccine producer, manufactures a whole-cell whooping cough vaccine (wP) that, as part of a pentavalent diphtheria-tetanus-pertussis/hepatitis B/Haemophilus influenzae b (DTP/HB/Hib) vaccine, is used in Indonesia and many other countries. We report here the whole-genome sequence for Bordetella pertussis Pelita III, PT Bio Farma's wP production strain.

Microbial diversity of acidic hot spring (kawah hujan B) in geothermal field of kamojang area, west java-indonesia.

Microbial communities in an acidic hot spring, namely Kawah Hujan B, at Kamojang geothermal field, West Java-Indonesia was examined using culture dependent and culture independent strategies. Chemical analysis of the hot spring water showed a characteristic of acidic-sulfate geothermal activity that contained high sulfate concentrations and low pH values (pH 1.8 to 1.9). Microbial community present in the spring was characterized by 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) analysis. The majority of the sequences recovered from culture-independent method were closely related to Crenarchaeota and Proteobacteria phyla. However, detail comparison among the member of Crenarchaeota showing some sequences variation compared to that the published data especially on the hypervariable and variable regions. In addition, the sequences did not belong to certain genus. Meanwhile, the 16S Rdna sequences from culture-dependent samples revealed mostly close to Firmicute and gamma Proteobacteria.

Simple enrichment and independent cultures to expand bacterial community analysis from Gedongsongo hot spring.

Denaturing gradient gel electrophoresis was used to identify bacterial communities from Gedongsongo hot spring, Indonesia, by culture-independent and -dependent procedures. Predominant species were found to be closely related to beta-proteobacteria, particularly from genus Ralstonia and Delftia. Other species present include alpha- and gamma-proteobacteria and Thermus groups. Some of the strains showed unique 16S rDNA sequences.