Table 4.

Engineered Microbial Hosts, In Vitro Systems and Metabolites Produced

Host/System	Engineering/elicitation strategy	Key metabolites produced	Highlights	Reference
E. coli	Overexpression of (−)-patchoulol synthase (PTS) and exogenous mevalonate (MVA) pathway; fermentation optimisation; solid − liquid phase partitioning	(−)-Patchoulol, α-Bulnesene, trans-β-Caryophyllene	First (−)-patchoulol production in E. coli with SLPPC; 5-fold titre increase; 99.65% recovery using Diaion HP20	Aguilar et al. 2020
E. coli	Expression of flavone/flavonol biosynthesis genes; RBS tuning; tyrosine pathway enhancement; cerulenin addition	Apigenin, Kaempferol, Chrysin, Luteolin	Highest apigenin (128 mg/L) and kaempferol (151 mg/L) titres in E. coli; enabled flavonoid biosynthesis without exogenous tyrosine	Yiakoumetti et al. 2023
E. coli and S. venezuelae cocultivation	E. coli expressing phenylpropanoid backbones + S. venezuelae expressing SaOMT2 for O-methylation	Tri-methylated stilbenes, Di-/Tri-methylated flavanones/flavones	First high-yield microbial production of trimethoxystilbene and derivatives; S. venezuelae-expressed SaOMT2 showed high regiospecificity	Cui et al. 2019
E. coli	Genome engineering to overproduce pinocembrin and derivatives; enzyme screening; glycerol as carbon source	Pinocembrin, Chrysin, Pinostrobin, Pinobanksin, Galangin	Produced 353 mg/L pinocembrin; 153 mg/L pinostrobin; highest reported titres for several flavonoids	Hanko et al. 2024
E. coli	Directed evolution of CHS; thioesterase knockout; co-expression of CHIL	Naringenin, CTAL, Naringenin chalcone	Highest naringenin titre (1082 mg/L); minimized byproduct CTAL; improved enzyme specificity	Xiang et al. 2024
E. coli	CRISPRi-based fine-tuning of central carbon metabolism; malonyl-CoA redirection; flavonoid pathway construction	(2S)-Naringenin, Malonyl-CoA	421.6 mg/L naringenin titre (7.4 × increase); malonyl-CoA increased by 433%; first CRISPRi system for flux tuning in flavonoid biosynthesis	Wu et al. 2015
E. coli	Codon-optimized longifolene synthase expression; mevalonate pathway integration; two-phase fed-batch fermentation	Longifolene, FPP, IPP, Mevalonate	382 mg/L longifolene; first microbial system for longifolene production; enhanced FPP flux using E. coli IspA	Cao et al. 2019
E. coli	Transient expression of 7 enzymes; heterologous enzyme expression in E. coli and yeast; comparative omics in Apiaceae	Prim-O-glucosylcimifugin (POG), 5-O-methylvisamminoside (5-O-MVG)	First complete furochromone pathway; 5-O-MVG biosynthesis (17.48 μg/g DW); discovery of lineage-specific enzymes (SdPCS, SdPC)	Zou et al. 2025
S. cerevisiae	Integration of isopentenol utilisation pathway (IUP); knockout of ERG13; enzyme engineering; pathway flux redirection	IPP, DMAPP, Limonene, β-Carotene, Amorphadiene, Taxadiene, Lycopene	IUP simplified terpenoid synthesis; 695-fold increase in squalene; 20-fold increase in limonene; universal yeast platform for terpenoids	Li et al. 2024a
S. cerevisiae	Diauxie-inducible expression; ERG20M & GGPP synthase integration; IUP and MVA pathway coordination	Limonene, Amorphadiene, Lycopene, β-Amyrin, Taxadiene	IUP boosted GGPP by 374-fold; up to 4.3-fold improvement in terpene titres; versatile and controllable yeast platform	Ma et al. 2022
S. cerevisiae	Overexpression of 8 mevalonate pathway genes; terpene synthase screening	δ-Guaiene, α-Humulene, β-Eudesmol	ERG9 repression, enzyme fusion enhanced yield; first β-eudesmol biosynthesis	Promdonkoy et al. 2022
E. coli	Expression of terpene synthase genes (TPS9, TPS12, AmDG2)	α-Humulene, β-Caryophyllene, Cedrol, Nerolidol, γ-Eudesmol	Functional validation of cloned enzymes from Aquilaria spp.	Kurosaki et al. 2016; Sundaraj et al. 2023; Yu et al. 2023
Chlamydomonas reinhardtii	Genetic engineering: CO₂-fed photobioreactor; in situ extraction and oxidation	9 Sesquiterpenoid skeletons, Oxygenated STPs	Green bioprocess, solvent recycling, CO₂ fixation, continuous production	Gutiérrez et al. 2024
Aquilaria (callus or shoot culture)	Methyl jasmonate and F. solani crude extract elicitation	Sesquiterpenes, Chromone derivative, Aromatic compounds	MeJA induced agarwood-like metabolites; fungal elicitor modulated profile	Faizal et al. 2021; Kumeta & Ito 2010
A. crassna (callus culture)	Exposure to various Metal-Organic Frameworks (MOFs), e.g. ZIF-67	Secondary metabolites with fragrance potential	ZIF-67 elicited highest metabolite yield; metal-ligand specificity observed	Overmans et al. 2025