Synthetic Biology Journal ›› 2023, Vol. 4 ›› Issue (6): 1082-1121.DOI: 10.12211/2096-8280.2023-047
• Invited Review • Previous Articles Next Articles
Xiongying YAN, Zhen WANG, Jiyun LOU, Haoyu ZHANG, Xingyu HUANG, Xia WANG, Shihui YANG
Received:
2023-07-02
Revised:
2023-08-30
Online:
2024-01-19
Published:
2023-12-31
Contact:
Xia WANG, Shihui YANG
晏雄鹰, 王振, 娄吉芸, 张皓瑜, 黄星宇, 王霞, 杨世辉
通讯作者:
王霞,杨世辉
作者简介:
基金资助:
CLC Number:
Xiongying YAN, Zhen WANG, Jiyun LOU, Haoyu ZHANG, Xingyu HUANG, Xia WANG, Shihui YANG. Progress in the construction of microbial cell factories for efficient biofuel production[J]. Synthetic Biology Journal, 2023, 4(6): 1082-1121.
晏雄鹰, 王振, 娄吉芸, 张皓瑜, 黄星宇, 王霞, 杨世辉. 生物燃料高效生产微生物细胞工厂构建研究进展[J]. 合成生物学, 2023, 4(6): 1082-1121.
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URL: https://synbioj.cip.com.cn/EN/10.12211/2096-8280.2023-047
产物 Product | 价格 Price /(元/t) | 宿主 Host | 发酵方式 Fermentation | 原料 Substrate | 滴度 Titer /(g/L) | 参考文献 Reference |
---|---|---|---|---|---|---|
Propanol | 7000~7400 | E. coli | Fed-batch | Glucose or glycerol | 10.3 | [ |
E. coli | Shake flask | Glucose | 3.5 | [ | ||
Isopropanol | 6500~7500 | E. coli | Fed-batch with gas stripping | Glucose | 143 | [ |
E. coli | Shake flask | Glucose | 13.6 | [ | ||
1-Butanol | 8550 | C. acetobutylicum | Bioreactor | Glucose | 20.3 | [ |
E. coli | Bioreactor with gas stripping | Glucose | 30 | [ | ||
C. tyrobutyricum | Bioreactor | Mannitol | 20.5 | [ | ||
Isobutanol | 8100 | E. coli | Capped flask | Glucose | 22 | [ |
E. coli | Bioreactor | Glucose | 56 | [ | ||
Z. mobilis | Shake flask | Glucose | 4 | [ | ||
C. thermocellum | Consolidated bioprocessing | Cellulose | 5.4 | [ | ||
C. glutamicum | Shake flask | Glucose | 20.8 | [ | ||
S. cerevisiae | NA | Glucose | 5.8 | [ | ||
2,3-Butanediol | 10 000 | S. marcescens | Shake flask | Glucose | 42.5 | [ |
S. marcescens | Fed-batch | Sucrose | 152 | [ | ||
Z. mobilis | Shake flask | Glucose | 13.3 | [ | ||
2-Methy-1-butanol | 15 500 | B. flavum | Shake flash | Glucose; duckweed | 19.5/17.5 | [ |
E. coli | Shake flask | Glucose | 1.25 | [ | ||
C. crenatum | Shake flask | Glucose | 5.26 | [ | ||
3-Methy-1-butanol | 22 000 | E. coli | Shake flask; two-phase fermentation | Glucose | 9.5 | [ |
B. flavum | Shake flask | Glucose; duckweed | 0.79/0.78 | [ | ||
C. crenatum | Shake flask | Glucose | 3.78 | [ |
Table 1 Summary of microbial production of higher carbon chain alcohols
产物 Product | 价格 Price /(元/t) | 宿主 Host | 发酵方式 Fermentation | 原料 Substrate | 滴度 Titer /(g/L) | 参考文献 Reference |
---|---|---|---|---|---|---|
Propanol | 7000~7400 | E. coli | Fed-batch | Glucose or glycerol | 10.3 | [ |
E. coli | Shake flask | Glucose | 3.5 | [ | ||
Isopropanol | 6500~7500 | E. coli | Fed-batch with gas stripping | Glucose | 143 | [ |
E. coli | Shake flask | Glucose | 13.6 | [ | ||
1-Butanol | 8550 | C. acetobutylicum | Bioreactor | Glucose | 20.3 | [ |
E. coli | Bioreactor with gas stripping | Glucose | 30 | [ | ||
C. tyrobutyricum | Bioreactor | Mannitol | 20.5 | [ | ||
Isobutanol | 8100 | E. coli | Capped flask | Glucose | 22 | [ |
E. coli | Bioreactor | Glucose | 56 | [ | ||
Z. mobilis | Shake flask | Glucose | 4 | [ | ||
C. thermocellum | Consolidated bioprocessing | Cellulose | 5.4 | [ | ||
C. glutamicum | Shake flask | Glucose | 20.8 | [ | ||
S. cerevisiae | NA | Glucose | 5.8 | [ | ||
2,3-Butanediol | 10 000 | S. marcescens | Shake flask | Glucose | 42.5 | [ |
S. marcescens | Fed-batch | Sucrose | 152 | [ | ||
Z. mobilis | Shake flask | Glucose | 13.3 | [ | ||
2-Methy-1-butanol | 15 500 | B. flavum | Shake flash | Glucose; duckweed | 19.5/17.5 | [ |
E. coli | Shake flask | Glucose | 1.25 | [ | ||
C. crenatum | Shake flask | Glucose | 5.26 | [ | ||
3-Methy-1-butanol | 22 000 | E. coli | Shake flask; two-phase fermentation | Glucose | 9.5 | [ |
B. flavum | Shake flask | Glucose; duckweed | 0.79/0.78 | [ | ||
C. crenatum | Shake flask | Glucose | 3.78 | [ |
类别 Class | 产物 Product | 宿主 Host | 发酵方式 Fermentation | 底物 Substrate | 产量 Titer/(g/L) | 参考文献 Reference |
---|---|---|---|---|---|---|
Fatty acids | Lipid | Y. lipolytica | 3-L bioreactor | Glucose | 90.00 | [ |
Shake flask | Fructose | 5.51 | [ | |||
Shake flask | Sucrose | 9.15 | [ | |||
2-L bioreactor | Galactose | 3.22 | [ | |||
3-L, fed-batch | Hydrolysate | 16.50 | [ | |||
E. coli | 0.45-L, fed-batch | Glucose | 21.50 | [ | ||
L. starkeyi | Shake flask | Glucose and xylose | 12.60 | [ | ||
Thraustochytrid T18 | 7-L, fed-batch | Glucose and xylose | 87.00 | [ | ||
Fatty acid | S. cerevisiae | 1-L bioreactor, fed-batch | Glucose | 33.40 | [ | |
R. opacus | 6.6-L, fed-batch | Glucose | 50.20 | [ | ||
C. glutamicum | Shake flask | Glucose | 1.07 | [ | ||
Fatty acid ethyl esters | Y. lipolytica | Shake flash | Glucose | 0.137 | [ | |
R. toruloides | 1-L, fed-batch | Glucose | 9.97 | [ | ||
Wax ester | A. baylyi | Shake flask | Glucose | 1.82 | [ | |
Methyl ketone | E. coli | 2-L, fed-batch | Glucose | 3.40 | [ | |
P. putida | Test tube | Glucose | 1.10 | [ | ||
Heavy oils | A. melanogenum | 10-L bioreactor | Glucose | 43.00 | [ | |
Alkanes | Short chain alkane (C2~C5) | E. coli | Bioreactor | Glycerol | 0.11~0.14 | [ |
Medium chain alkane (C6~C12) | Synechocystis sp. PCC6803 | Bioreactor | CO2 | 0.026 | [ | |
E. coli | 5-L, fed-batch | Glucose | 1.01 | [ | ||
6.6-L, fed-batch | Glucose | 0.58 | [ | |||
5-L, fed-batch | Glucose | 2.5 | [ | |||
Shake flask | Glucose | 0.26 | [ | |||
Long chain alkane (C13~C22) | R. opacus | 6.6-L, fed-batch | Glucose | 5.2 | [ | |
A. melanogenum | 10-L bioreactor | Glucose | 32.5 | [ | ||
S. cerevisiae | NA | Glucose | 86 μg/g | [ |
Table 2 Summary of microbial production of fatty acids and alkanes
类别 Class | 产物 Product | 宿主 Host | 发酵方式 Fermentation | 底物 Substrate | 产量 Titer/(g/L) | 参考文献 Reference |
---|---|---|---|---|---|---|
Fatty acids | Lipid | Y. lipolytica | 3-L bioreactor | Glucose | 90.00 | [ |
Shake flask | Fructose | 5.51 | [ | |||
Shake flask | Sucrose | 9.15 | [ | |||
2-L bioreactor | Galactose | 3.22 | [ | |||
3-L, fed-batch | Hydrolysate | 16.50 | [ | |||
E. coli | 0.45-L, fed-batch | Glucose | 21.50 | [ | ||
L. starkeyi | Shake flask | Glucose and xylose | 12.60 | [ | ||
Thraustochytrid T18 | 7-L, fed-batch | Glucose and xylose | 87.00 | [ | ||
Fatty acid | S. cerevisiae | 1-L bioreactor, fed-batch | Glucose | 33.40 | [ | |
R. opacus | 6.6-L, fed-batch | Glucose | 50.20 | [ | ||
C. glutamicum | Shake flask | Glucose | 1.07 | [ | ||
Fatty acid ethyl esters | Y. lipolytica | Shake flash | Glucose | 0.137 | [ | |
R. toruloides | 1-L, fed-batch | Glucose | 9.97 | [ | ||
Wax ester | A. baylyi | Shake flask | Glucose | 1.82 | [ | |
Methyl ketone | E. coli | 2-L, fed-batch | Glucose | 3.40 | [ | |
P. putida | Test tube | Glucose | 1.10 | [ | ||
Heavy oils | A. melanogenum | 10-L bioreactor | Glucose | 43.00 | [ | |
Alkanes | Short chain alkane (C2~C5) | E. coli | Bioreactor | Glycerol | 0.11~0.14 | [ |
Medium chain alkane (C6~C12) | Synechocystis sp. PCC6803 | Bioreactor | CO2 | 0.026 | [ | |
E. coli | 5-L, fed-batch | Glucose | 1.01 | [ | ||
6.6-L, fed-batch | Glucose | 0.58 | [ | |||
5-L, fed-batch | Glucose | 2.5 | [ | |||
Shake flask | Glucose | 0.26 | [ | |||
Long chain alkane (C13~C22) | R. opacus | 6.6-L, fed-batch | Glucose | 5.2 | [ | |
A. melanogenum | 10-L bioreactor | Glucose | 32.5 | [ | ||
S. cerevisiae | NA | Glucose | 86 μg/g | [ |
产物 Product | 宿主 Host | 发酵方式 Fermentation | 底物 Substrate | 产量 Titer/(g/L) | 参考文献 Reference |
---|---|---|---|---|---|
Pinene | E. coli | Shake flask | Glucose | 0.14 | [ |
Y. lipolytica | Shake flask | Hydrolysate | 0.036 | [ | |
C. glutamicum | Shake flask | Glucose | 27 μg/g | [ | |
R. sphaeroides | Shake flask | CO2 | 0.54 mg/L | [ | |
Sabinene | E. coli | 5-L bioreactor | Glycerol | 2.65 | [ |
S. cerevisiae | Shake flask | Glucose | 0.018 | [ | |
Limonene | E. coli | Shake flask | Glucose | 1.29 | [ |
3.1-L,two-phase | Glycerol | 3.6 | [ | ||
Y. lipolytica | 1.5-L;fed-batch | Glycerol | 0.17 | [ | |
S. cerevisiae | Shake flask | Glucose | 0.92 | [ | |
Farnesene | E. coli | Shake flask | Glycerol | 8.74 | [ |
S. cerevisiae | NA | NA | 104.3 | Amyris | |
P. pastoris | Shake flask | Oleic acid; sorbitol | 2.56 | [ | |
Y. lipolytica | 1-L;fed-batch | Glucose | 2.56 | [ | |
200 t;fed-batch | Cane syrup | 130 | [ | ||
Bisabolene | E. coli | Shake flask | Glucose | 0.91 | [ |
S. cerevisiae | Shake flask | Mannose; glucose | 0.99 | [ | |
R. capsulatus | Shake flask | Glucose | 1.08 | [ |
Table 3 Summary of microbial production of isoprenoid-derived fuels
产物 Product | 宿主 Host | 发酵方式 Fermentation | 底物 Substrate | 产量 Titer/(g/L) | 参考文献 Reference |
---|---|---|---|---|---|
Pinene | E. coli | Shake flask | Glucose | 0.14 | [ |
Y. lipolytica | Shake flask | Hydrolysate | 0.036 | [ | |
C. glutamicum | Shake flask | Glucose | 27 μg/g | [ | |
R. sphaeroides | Shake flask | CO2 | 0.54 mg/L | [ | |
Sabinene | E. coli | 5-L bioreactor | Glycerol | 2.65 | [ |
S. cerevisiae | Shake flask | Glucose | 0.018 | [ | |
Limonene | E. coli | Shake flask | Glucose | 1.29 | [ |
3.1-L,two-phase | Glycerol | 3.6 | [ | ||
Y. lipolytica | 1.5-L;fed-batch | Glycerol | 0.17 | [ | |
S. cerevisiae | Shake flask | Glucose | 0.92 | [ | |
Farnesene | E. coli | Shake flask | Glycerol | 8.74 | [ |
S. cerevisiae | NA | NA | 104.3 | Amyris | |
P. pastoris | Shake flask | Oleic acid; sorbitol | 2.56 | [ | |
Y. lipolytica | 1-L;fed-batch | Glucose | 2.56 | [ | |
200 t;fed-batch | Cane syrup | 130 | [ | ||
Bisabolene | E. coli | Shake flask | Glucose | 0.91 | [ |
S. cerevisiae | Shake flask | Mannose; glucose | 0.99 | [ | |
R. capsulatus | Shake flask | Glucose | 1.08 | [ |
类别 Class | 菌株 Strain | 生长条件 Growth condition | 安全性 Safety status | 基因组大小 Genome size /Mb | 底物 Substrates | 基因组修饰工具 Genome manipulation tools | 产物 Products |
---|---|---|---|---|---|---|---|
Model microbes | E. coli | Facultative aerobic | Not GRAS | 4.64 | Pentose, hexose, glycerol, starch | Various tools | Alcohols, fatty acids and terpenoids |
S. cerevisiae | Facultative aerobic | GRAS | 11.8 16 chromosomes | Starch, sucrose, hexose | Various tools | Terpenoids, nature products | |
C. glutamicum | Facultative aerobic | GRAS | 3.28 | Sugars, alcohols, organic acid | HR, CRISPR-Cas9 CRISPR-Cpf1/dCpf1 | Alcohols, aminol acid | |
Non-model microbes | Y. lipolytica | Facultative aerobic | GRAS | 20.5 6 chromosomes | Glucose, glycerol, sucrose, starch, inulin, cellobiose | NHEJ, ZFN, TALEN CRISPR-Cas9 (CRISPRi/CRISPRa) | Lipid, FAAE, terpenoids, Alkanes |
Z. mobilis | Facultative anaerobic | GRAS | 2.2 4 plasmids | Glucose, sucrose, fructose | HR, CRISPR-Cas9, CRISPR-Cas 12a, Endogenous Type-Ⅰ-F CRISPR-Cas system | Ethanol, isobutanol, 2,3-butanediol, PHB | |
C. thermocellum | Strictly anaerobic | Not GRAS | 3.56 | Hydrolysate | Endogenous Ⅰ-B CRISPR system; Heterologous Ⅱ CRISPR system | Ethanol, isobutanol | |
C. acetobutylicum | Strictly anaerobic | Not GRAS | 4.1 | Glucose | CRISPR-Cas9/dCas9 | Acetone, ethanol, butanol |
Table 4 Characteristics of partial model and non-model microbial chassis cell
类别 Class | 菌株 Strain | 生长条件 Growth condition | 安全性 Safety status | 基因组大小 Genome size /Mb | 底物 Substrates | 基因组修饰工具 Genome manipulation tools | 产物 Products |
---|---|---|---|---|---|---|---|
Model microbes | E. coli | Facultative aerobic | Not GRAS | 4.64 | Pentose, hexose, glycerol, starch | Various tools | Alcohols, fatty acids and terpenoids |
S. cerevisiae | Facultative aerobic | GRAS | 11.8 16 chromosomes | Starch, sucrose, hexose | Various tools | Terpenoids, nature products | |
C. glutamicum | Facultative aerobic | GRAS | 3.28 | Sugars, alcohols, organic acid | HR, CRISPR-Cas9 CRISPR-Cpf1/dCpf1 | Alcohols, aminol acid | |
Non-model microbes | Y. lipolytica | Facultative aerobic | GRAS | 20.5 6 chromosomes | Glucose, glycerol, sucrose, starch, inulin, cellobiose | NHEJ, ZFN, TALEN CRISPR-Cas9 (CRISPRi/CRISPRa) | Lipid, FAAE, terpenoids, Alkanes |
Z. mobilis | Facultative anaerobic | GRAS | 2.2 4 plasmids | Glucose, sucrose, fructose | HR, CRISPR-Cas9, CRISPR-Cas 12a, Endogenous Type-Ⅰ-F CRISPR-Cas system | Ethanol, isobutanol, 2,3-butanediol, PHB | |
C. thermocellum | Strictly anaerobic | Not GRAS | 3.56 | Hydrolysate | Endogenous Ⅰ-B CRISPR system; Heterologous Ⅱ CRISPR system | Ethanol, isobutanol | |
C. acetobutylicum | Strictly anaerobic | Not GRAS | 4.1 | Glucose | CRISPR-Cas9/dCas9 | Acetone, ethanol, butanol |
菌株 Strain | 模型 Model | 基因、反应与代谢物 Genes, reactions and metabolites | 时间 Time | 应用 Applications | 参考文献 Reference |
---|---|---|---|---|---|
E. coli | iJE660 | 660、627、438 | 2000 | NR | [ |
iJR904 | 904、931、625 | 2003 | 1,4-BDO production | [ | |
iAF1260 | 1260、2077、1039 | 2007 | Fatty acid production | [ | |
iJO1366 | 1366、2251、1136 | 2011 | NR | [ | |
iML1515 | 1515、2719、1192 | 2017 | NR | [ | |
B. subtilis | iBsu1103 | 1103、1437、1138 | 2009 | NR | [ |
iBsu1103V2 | 1147、1742、1456 | 2013 | NR | [ | |
iBsu1147 | 1147、1742、1456 | 2013 | Riboflavin, cellulase, 2,3-butanediol and isobutanol production | [ | |
iBsu1144 | 1144、1955、1103 | 2017 | Serine alkaline protease production | [ | |
ec-iY0844 | 844、1020、988 | 2019 | Poly-γ-glutamic acid production | [ | |
C. glutamicum | iCW773 | 773、1207、950 | 2017 | L-lysine and hyaluronic acid production | [ |
iJM658 | 658、1065、984 | 2016 | NR | [ | |
S. cerevisiae | iFF708 | 708、1175、584 | 2003 | Ethanol production | [ |
iND750 | 750、1149、646 | 2004 | NR | [ | |
iLL672 | 672、1038、636 | 2005 | NR | [ | |
iLN800 | 800、1446、1013 | 2008 | NR | [ | |
iMM904 | 904、1412、1228 | 2009 | 2,3-BDO production | [ | |
Yeast1 | 832、962、813 | 2008 | NR | [ | |
Yeast8 | 1133、3949、2680 | 2019 | NR | [ |
Table 5 Summary of typical microbial metabolic network models and their application
菌株 Strain | 模型 Model | 基因、反应与代谢物 Genes, reactions and metabolites | 时间 Time | 应用 Applications | 参考文献 Reference |
---|---|---|---|---|---|
E. coli | iJE660 | 660、627、438 | 2000 | NR | [ |
iJR904 | 904、931、625 | 2003 | 1,4-BDO production | [ | |
iAF1260 | 1260、2077、1039 | 2007 | Fatty acid production | [ | |
iJO1366 | 1366、2251、1136 | 2011 | NR | [ | |
iML1515 | 1515、2719、1192 | 2017 | NR | [ | |
B. subtilis | iBsu1103 | 1103、1437、1138 | 2009 | NR | [ |
iBsu1103V2 | 1147、1742、1456 | 2013 | NR | [ | |
iBsu1147 | 1147、1742、1456 | 2013 | Riboflavin, cellulase, 2,3-butanediol and isobutanol production | [ | |
iBsu1144 | 1144、1955、1103 | 2017 | Serine alkaline protease production | [ | |
ec-iY0844 | 844、1020、988 | 2019 | Poly-γ-glutamic acid production | [ | |
C. glutamicum | iCW773 | 773、1207、950 | 2017 | L-lysine and hyaluronic acid production | [ |
iJM658 | 658、1065、984 | 2016 | NR | [ | |
S. cerevisiae | iFF708 | 708、1175、584 | 2003 | Ethanol production | [ |
iND750 | 750、1149、646 | 2004 | NR | [ | |
iLL672 | 672、1038、636 | 2005 | NR | [ | |
iLN800 | 800、1446、1013 | 2008 | NR | [ | |
iMM904 | 904、1412、1228 | 2009 | 2,3-BDO production | [ | |
Yeast1 | 832、962、813 | 2008 | NR | [ | |
Yeast8 | 1133、3949、2680 | 2019 | NR | [ |
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