Abstract
Microbial metabolism analysis is of great significance to the biosynthesis industries and the diagnosis and treatment of infectious diseases caused by microorganisms. However, it remains a grand challenge to offer deep insight into microbial metabolism due to the particularly complex and dynamic processes. Analytical methods are recognized as the critical bottleneck that constrains the in-depth understanding of microbial metabolism. Specific and real-time analytical tools for microbial metabolic processes have currently drawn increasing attention. Here, we summarized the major advances over the past 5 years focusing on the following three aspects including real-time and dynamic analysis of metabolic molecules, selective analysis of specific metabolic pathways and quantitative analysis of the microbial metabolism. Finally, the remaining challenges and perspectives on microbial analysis are discussed and outlooked.
Similar content being viewed by others
References
Salazar G, Sunagawa S. Curr Biol, 2017, 27: R489–R494
Niehaus L, Boland I, Liu M, Chen K, Fu D, Henckel C, Chaung K, Miranda SE, Dyckman S, Crum M, Dedrick S, Shou W, Momeni B. Nat Commun, 2019, 10: 2052
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Science, 2009, 326: 1694–1697
Pamer EG. Science, 2016, 352: 535–538
Belkaid Y, Hand TW. Cell, 2014, 157: 121–141
Tabish SA. J Public Health Res, 2020, 9: jphr.2020.1786
Bos KI, Schuenemann VJ, Golding GB, Burbano HA, Waglechner N, Coombes BK, McPhee JB, DeWitte SN, Meyer M, Schmedes S, Wood J, Earn DJD, Herring DA, Bauer P, Poinar HN, Krause J. Nature, 2011, 478: 506–510
Chen N, Du N, Wang W, Liu T, Yuan Q, Yang Y. Angew Chem Int Ed, 2022, 61: e202115572
Tan GY, Liu T. Metab Eng, 2017, 39: 228–236
Liu Y, Xu P. Curr Opin Biotechnol, 2022, 76: 102754
Gill A. Front Microbiol, 2017, 8: 777
Valeix N, Costa D, Basmaciyan L, Valot S, Vincent A, Razakandrainibe R, Robert-Gangneux F, Nourrisson C, Pereira B, Fréalle E, Poirier P, Favennec L, Dalle F. Microorganisms, 2020, 8: 1450
Huang J, Pu K. Angew Chem Int Ed, 2020, 59: 11717–11731
Shi H, Wang Y, Zheng J, Ning L, Huang Y, Sheng A, Chen T, Xiang Y, Zhu X, Li G. ACS Nano, 2019, 13: 12840–12850
Gonçalves MST. Chem Rev, 2009, 109: 190–212
Benson S, de Moliner F, Tipping W, Vendrell M. Angew Chem Int Ed, 2022, 61: e202204788
Mendive-Tapia L, Mendive-Tapia D, Zhao C, Gordon D, Benson S, Bromley MJ, Wang W, Wu J, Kopp A, Ackermann L, Vendrell M. Angew Chem Int Ed, 2022, 61: e202117218
Benson S, de Moliner F, Fernandez A, Kuru E, Asiimwe NL, Lee JS, Hamilton L, Sieger D, Bravo IR, Elliot AM, Feng Y, Vendrell M. Nat Commun, 2021, 12: 2369
Wang W, Yang Q, Du Y, Zhou X, Du X, Wu Q, Lin L, Song Y, Li F, Yang C, Tan W. Angew Chem Int Ed, 2020, 59: 2628–2633
Wang W, Lin L, Du Y, Song Y, Peng X, Chen X, Yang CJ. Nat Commun, 2019, 10: 1317
Luo Y, Li L, Feng Y, Li R, Yang J, Peijnenburg WJGM, Tu C. Nat Nanotechnol, 2022, 17: 424–431
Brennecke B, Wang Q, Zhang Q, Hu H-, Nazaré M. Angew Chem Int Ed, 2020, 59: 8512–8516
Ni Q, Mehta S, Zhang J. FEBS J, 2018, 285: 203–219
Wang M, Da Y, Tian Y. Chem Soc Rev, 2023, 52: 1189–1214
Zou Y, Wang A, Huang L, Zhu X, Hu Q, Zhang Y, Chen X, Li F, Wang Q, Wang H, Liu R, Zuo F, Li T, Yao J, Qian Y, Shi M, Yue X, Chen W, Zhang Z, Wang C, Zhou Y, Zhu L, Ju Z, Loscalzo J, Yang Y, Zhao Y. Dev Cell, 2020, 53: 240–252.e7
Liu X, Qin L, Yu J, Sun W, Xu J, Li C. Biosens Bioelectron, 2023, 222: 114988
Torello Pianale L, Rugbjerg P, Olsson L. Front Microbiol, 2021, 12: 802169
Crawford JM, Portmann C, Zhang X, Roeffaers MBJ, Clardy J. Proc Natl Acad Sci USA, 2012, 109: 10821–10826
Jin N, Paraskevaidi M, Semple KT, Martin FL, Zhang D. Anal Chem, 2017, 89: 9814–9821
Uniyal S, Sharma RK. Biosens Bioelectron, 2018, 116: 37–50
Terrell JL, Tschirhart T, Jahnke JP, Stephens K, Liu Y, Dong H, Hurley MM, Pozo M, McKay R, Tsao CY, Wu HC, Vora G, Payne GF, Stratis-Cullum DN, Bentley WE. Nat Nanotechnol, 2021, 16: 688–697
Simoska O, Sans M, Fitzpatrick MD, Crittenden CM, Eberlin LS, Shear JB, Stevenson KJ. ACS Sens, 2019, 4: 170–179
Chen D, Guo J, Li A, Sun C, Lin H, Lin H, Yang C, Wang W, Gao J. Sci Adv, 2023, 9: eabg6808
Bourdeau RW, Lee-Gosselin A, Lakshmanan A, Farhadi A, Kumar SR, Nety SP, Shapiro MG. Nature, 2018, 553: 86–90
Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. Chem Rev, 2018, 118: 4–72
Hedges JB, Ryan KS. Angew Chem Int Ed, 2019, 58: 11647–11651
Ban YH, Song MC, Hwang J, Shin H, Kim HJ, Hong SK, Lee NJ, Park JW, Cha SS, Liu H, Yoon YJ. Nat Chem Biol, 2019, 15: 295–303
Wang J, Chen N, Wang W, Li Z, Huang B, Yang Y, Yuan Q. CCS Chem, 2023, 5: 164–175
Jang C, Chen L, Rabinowitz JD. Cell, 2018, 173: 822–837
Dong W, Rawat ES, Stephanopoulos G, Abu-Remaileh M. Curr Opin Biotechnol, 2022, 76: 102739
Miller TL, Wolin MJ. Appl Environ Microbiol, 1996, 62: 1589–1592
Fernández-García J, Altea-Manzano P, Pranzini E, Fendt SM. Trends Biochem Sci, 2020, 45: 185–201
Yu H, Leadbetter JR. Nature, 2020, 583: 453–458
Zhou Z, Zhang C, Liu P, Fu L, Laso-Pérez R, Yang L, Bai L, Li J, Yang M, Lin J, Wang W, Wegener G, Li M, Cheng L. Nature, 2022, 601: 257–262
Steffens L, Pettinato E, Steiner TM, Mall A, König S, Eisenreich W, Berg IA. Nature, 2021, 592: 784–788
Kim S, Lindner SN, Aslan S, Yishai O, Wenk S, Schann K, Bar-Even A. Nat Chem Biol, 2020, 16: 538–545
Lin L, Song J, Du Y, Wu Q, Gao J, Song Y, Yang C, Wang W. Angew Chem Int Ed, 2020, 59: 11923–11926
Vieira-Silva S, Sabino J, Valles-Colomer M, Falony G, Kathagen G, Caenepeel C, Cleynen I, van der Merwe S, Vermeire S, Raes J. Nat Microbiol, 2019, 4: 1826–1831
Gao P, Xu G. Anal Bioanal Chem, 2015, 407: 669–680
Zhao L, Ni Y, Su M, Li H, Dong F, Chen W, Wei R, Zhang L, Guiraud SP, Martin FP, Rajani C, Xie G, Jia W. Anal Chem, 2017, 89: 5565–5577
Han S, Van Treuren W, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, Higginbottom SK, Guthrie L, Fall LA, Dodd D, Fischbach MA, Sonnenburg JL. Nature, 2020, 595: 415–420
Chen N, Cheng D, He T, Yuan Q. Chin J Chem, 2023, 41: 1836–1840
D’Souza G, Shitut S, Preussger D, Yousif G, Waschina S, Kost C. Nat Prod Rep, 2018, 35: 455–488
Feng D, Li H, Xu T, Zheng F, Hu C, Shi X, Xu G. Anal Chim Acta, 2022, 1221: 340116
Acknowledgements
This work was supported by the National Natural Science Foundation of China (21925401, 21904033), the National Key R&D Program of China (2017YFA0208000, 2021YFA1202400), the Fundamental Research Funds for the Central Universities (2042022rc0004), the New Cornerstone Science Foundation through the XPLORER PRIZE and the interdisciplinary innovative talents foundation from Renmin Hospital of Wuhan University.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest The authors declare no conflict of interest.
Rights and permissions
About this article
Cite this article
Chen, N., Zhang, X., Xi, J. et al. Recent advances of microbial metabolism analysis: from metabolic molecules to environments. Sci. China Chem. 66, 2941–2950 (2023). https://doi.org/10.1007/s11426-023-1660-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11426-023-1660-x