Sea grape kombucha has been known to exhibit high antioxidant activity due to its elevated total polyphenol content. This study aims to identify and characterize the active microbial community involved in the fermentation of kombucha using sea grapes (C. racemosa) as the primary substrate. Furthermore, it evaluates the effects of different Symbiotic Culture of Bacteria and Yeast (SCOBY) starter concentrations on the physicochemical properties and antioxidant activity of sea grape kombucha. Our results showed that the pH of the kombucha was higher after 7 days of fermentation compared to later time points. The microbial community was composed of 97.08% bacteria and 2.92% eukaryotes, divided into 10 phyla and 69 genera. The dominant genus in all samples was Komagataeibacter. Functional profiling based on 16S rRNA data revealed that metabolic functions accounted for 77.04% of predicted microbial activities during fermentation. The most enriched functional categories were carbohydrate metabolism (15.70%), cofactor and vitamin metabolism (15.54%), and amino acid metabolism (14.24%). At KEGG Level 3, amino acid-associated pathways, particularly alanine, aspartate, and glutamate metabolism (4.24%), were predominant. The fermentation process in sea grape kombucha is primarily driven by carbohydrate and amino acid metabolism, supported by energy-generating and cofactor biosynthesis pathways. Our findings indicate that different metabolic pathways lead to variations in kombucha components, and distinct fermentation stages result in different metabolic reactions. For instance, early fermentation stages (Day 7) are dominated by amino acid metabolism, whereas the late stages (Day 21) show increased activity in carbohydrate and sulfur metabolism. Metabolomic analysis revealed that increasing the SCOBY starter concentration significantly influenced pH, soluble solid content, vitamin C, tannin, and flavonoid content. These variations suggest that fermentation duration and microbial composition significantly influence the spectrum of bioactive metabolites, which synergistically provide functional benefits such as antimicrobial, antioxidant, and metabolic health-promoting activities. For example, sample K1 produced more fatty acids and simple sugar alcohols, sample K2 enriched complex lipid compounds and phytosterols, while sample K3 dominated the production of polyols and terpenoid compounds.

Oyster mushroom ( Pleurotus ostreatus ) is recognized as a functional food due to its bioactive compounds content which have therapeutic potential, particularly in metabolic disorder management. This study aims to explore the bioactive profile of oyster mushroom flour (OMF) using a multi-omics approach to evaluate its antioxidant, antiobesity, and antidiabetic properties. A comprehensive multi-omics approach has been employed, integrating metabolomics and proteomics profiling using LC-HRMS and Orbitrap mass spectrometry. In vitro assays assessed antioxidant capacity through ABTS and superoxide dismutase (SOD) activity, antiobesity potential via lipase inhibition and 3T3-L1 adipocyte assays, and antidiabetic effects via α-glucosidase, α-amylase, and dipeptidyl peptidase-4 (DPP-4) inhibition tests. In silico analysis further mapped molecular interactions and pathways. Metabolomic profiling identified 376 unique compounds and 13 peptides, including antioxidants, and enzyme inhibitors, contributing to antiobesity and antidiabetic effects. Proteomic analysis revealed peptides targeting metabolic pathways associated with oxidative stress and glucose regulation. γ-tocotrienol, estriol, kynurenic acid, and palmitoylcarnitine exhibited strong binding affinities with key metabolic targets, suggesting their potential as natural inhibitors for diabetes and obesity management. In vitro assays confirmed the oyster mushroom radical scavenging activity, lipase inhibition, and enzymatic modulation capabilities, with strong support from in silico analyses mapping molecular targets and pathways. These findings suggest P. ostreatus as a natural resource for managing metabolic disorders and developing evidence-based functional foods. This research bridges the gap between compound discovery and therapeutic application, paving the way for its broader utilization in nutraceuticals and precision nutrition strategies.

Agricultural and agro-industrial byproducts from tropical crops represent abundant sources of structurally bound and freely extractable bioactive compounds. However, variability in feedstock composition, the incomplete characterization of microbial transformations, and limited translation beyond chemical antioxidant assays constrain their development as standardized ingredients. This review critically evaluates metabolomics-guided fermentation as a strategy for converting tropical agricultural byproducts into functional and circular products. It covers fruit-processing residues, coffee and cocoa byproducts, cereal bran, cassava-processing residues, coconut and oilseed materials, and selected medicinal-crop tissues. Solid-state, submerged, lactic-acid-bacterial, yeast, filamentous fungal, Bacillus-based, and mixed-culture fermentations are compared. Particular attention is given to cell-wall deconstruction, phenolic release, flavonoid deglycosylation, phenolic-acid conversion, carotenoid stability, peptide generation, fiber modification, organic-acid production, antinutrient reduction, and undesirable metabolite formation. Analytical strategies based on untargeted and targeted LC-MS, GC-MS, NMR, volatilomics, peptidomics, and multiomics integration are assessed, together with experimental design, quality control, annotation confidence, and statistical validation. A substrate–microorganism–process–metabolite–function framework and a six-level evidence-grading system are proposed to distinguish exploratory chemical findings from mechanistically validated and industrially translatable outcomes. Applications in functional foods, nutraceutical ingredients, natural preservatives, animal feed, active packaging, agricultural inputs, and cascade biorefineries are evaluated alongside microbial safety, mycotoxins, biogenic amines, contaminants, regulatory classification, life-cycle assessment, and techno-economic feasibility. The central conclusion is that fermentation can become a programmable platform for tropical byproduct valorization only when metabolite-resolved characterization, causal validation, process standardization, safety, and sustainability are developed as an integrated pipeline.