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Abstract Background The marine environment boasts distinctive physical, chemical, and biological characteristics. While numerous studies have delved into the microbial ecology and biological potential of the marine environment, exploration of genetically encoded, deep-sea sourced secondary metabolites remains scarce. This study endeavors to investigate marine bioproducts derived from deep-sea water samples at a depth of 1,000 m in the Java Trench, Indonesia, utilizing both culture-dependent and whole-genome sequencing methods. Results Our efforts led to the successful isolation and cultivation of a bacterium Priestia flexa JT4 from the water samples, followed by comprehensive genome sequencing. The resultant high-quality draft genome, approximately 4 Mb, harbored 5185 coding sequences (CDSs). Notably, 61.97% of these CDSs were inadequately characterized, presenting potential novel CDSs. This study is the first to identify the "open-type" (α

Abstract Virgibacillus salarius 19.PP.SC1.6 is a coral symbiont isolated from Indonesia's North Java Sea; it has the ability to produce secondary metabolites that provide survival advantages and biological functions, such as ectoine, which is synthesized by an ectoine gene cluster. Apart from being an osmoprotectant for bacteria, ectoine is also known as a chemical chaperone with numerous biological activities such as maintaining protein stability, which makes ectoine in high demand in the market industry and makes it beneficial to investigate V. salarius ectoine. However, there has been no research on genome-based secondary metabolite and ectoine gene cluster characterization from Indonesian marine V. salarius. In this study, we performed a genomic analysis and ectoine identification of V. salarius. A high-quality draft genome with total size of 4.45 Mb and 4426 coding sequence (CDS) was characterized and then mapped into the Cluster of Orthologous Groups (COG) category. The genus Virgibacillus has an "open" pangenome type with total of 18 genomic islands inside the V. salarius 19.PP.SC1.6 genome. There were seven clusters of secondary metabolite-producing genes found, with a total of 80 genes classified as NRPS, PKS (type III), terpenes, and ectoine biosynthetic related genes. The ectoine gene cluster forms one operon consists of ectABC gene with 2190 bp gene cluster length, and is successfully characterized. The presence of ectoine in V. salarius was confirmed using UPLC-MS/MS operated in Multiple Reaction Monitoring (MRM) mode, which indicates that V. salarius has an intact ectoine gene clusters and is capable of producing ectoine as compatible solutes.

Rutin, a well-known bioflavonoid, was found abundantly in cassava leaves. In the present study, extraction techniques including maceration, boiling, reflux, ultrasound-assisted extraction (UAE), and microwave-assisted extraction (MAE) were optimised to increase the yield of rutin. Extraction parameters such as solvents, solid-liquid ratio, temperature, and time were optimised to give better extraction yields for each method. HPLC analysis showed a high content of rutin which is up to 2.4% per dry weight of cassava leaves. The extraction yields under optimised condition were found to be 16.00 ± 0.21, 20.38 ± 0.66, 22.33 ± 2.3, 24.49 ± 0.41, and 23.37 ± 1.00 g rutin per kg dry weight for maceration, boiling, reflux, UAE and MAE methods, respectively. Specifically, UAE reduced the extraction time to 90 min, using only 40–60% of aqueous ethanol. Meanwhile, MAE completed the extraction under 5 min and no significant differences in output was observed between the use of water and aqueous ethanol. Accordingly, with the extraction efficiency of up to 99 and 94%, respectively, both processes provided better results. The subsequent green purification using chilling method produced a typical cassava bioflavonoid containing 82% of rutin and 17% of nicotiflorin. This study informs a new abundant source of rutin and provides the optimum condition of extraction methods for high yield of rutin from cassava leaves.

Ursodeoxycholic acid (UDCA), a secondary bile acid (BA), has been used as a drug to treat various liver diseases. UDCA is synthesised from cholic or chenodeoxycholic acid (CA/CDCA), two primary BAs frequently used as the starting materials. Nowadays, swine, cattle, and poultry bile are the main sources of those BAs. However, other commercial animals could be promising sources as well. We identified two livestock, two poultries, and eight fishes that are commercially cultivated in Indonesia. Four free BAs including CA, CDCA, deoxycholic acid (DCA), and lithocholic acid (LA) were identified for their occurrences using thin-layer chromatography and high-performance liquid chromatography. CA was detected in cow, duck, red tilapia, gourami, the common carp, and grouper, whereas CDCA was only detected in two poultries and the common carp. The occurrence of DCA was common and abundant in most tested animals. In contrast, the presence of LA was found to be very low in all samples. The biliary bile of tilapia has been found to contain a high abundance of free CA (43% of the total bile). A simple extraction was able to purify CA from biliary bile of tilapia. This is a new promising and competitive source of CA.