Analysis of bacterial community composition in fermented mustard green through amplicon sequencing / Sen Yung Jie

Faculty of Industrial Sciences and Technology

Final Year Report (Bachelor of Applied Science in Industrial Biotechnology) -- Universiti Malaysia Pahang Al-Sultan Abdullah - 2025

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This study provides a comprehensive examination of fermented mustard greens by simultaneously analyzing their liquid and solid fractions to elucidate microbial diversity, community composition, and functional attributes. DNA was extracted via the QIAamp PowerFecal Pro Kit, amplified with 16S rRNA primers targeting the V3 region, and subjected to high-throughput sequencing and QIIME2-based taxonomic classification. Alpha-diversity metrics (e.g., Chao1, ACE) revealed only modest, statistically non-significant differences between the brine and the leafy fractions, indicating that both harbors comparably rich microbial communities. Beta-diversity analyses (Bray–Curtis PCoA) showed moderate compositional distinctions (ANOSIM R ≈ 0.55, p < 0.1), suggesting that with a larger sample size, these differences might become more pronounced. Taxonomic profiling underscored the dominance of beneficial bacterial phyla—most notably Actinobacteriota, Proteobacteria, and Firmicutes—reinforced by multiple probiotic genera such as Bifidobacterium, Weissella, Ligilactobacillus, Faecalibacterium, and Brevibacterium. Although low levels of potentially pathogenic species (e.g., Cutibacterium acnes, Streptococcus dysgalactiae, Clostridium perfringens) were detected, their relative abundances were negligible, posing minimal health risk. Functional analyses, validated by statistical significance (p < 0.05) and robust effect sizes, pinpointed key metabolic pathways—including L-Methionine Biosynthesis III, S-Adenosyl-LMethionine Biosynthesis, Pantothenate and Coenzyme A Biosynthesis, Taxadiene Biosynthesis, and Glucose/Xylose Degradation—that collectively bolster antioxidant defense, energy metabolism, and microbial stability. Enzymatic profiling further illuminated crucial enzymes (e.g., fructose-bisphosphatase, ribokinase, shikimate dehydrogenase) that aid in carbohydrate breakdown, foster beneficial microbial proliferation, and generate short-chain fatty acids vital to gut health. Overall, the findings confirm that both fractions of fermented mustard greens contribute to a resilient and functionally diverse microbiome, underscoring the potential of this food product as a probiotic-rich, metabolically active, and health-promoting option for personalized nutrition and improved gut health management