Top-down and Bottom-up Microbiome Engineering Approaches to Enable Biomanufacturing from Waste Biomass

Overview

Journal J Ind Microbiol Biotechnol

Publisher Oxford University Press

Specialty Biotechnology

Date 2024 Jul 13

PMID 39003244

Authors

Xuejiao Lyu

Mujaheed Nuhu

Pieter Candry

Jenna Wolfanger

Michael Betenbaugh

Alexis Saldivar

Cristal Zuniga

Ying Wang

Shilva Shrestha

Affiliations

Soon will be listed here.

Abstract

One-sentence Summary: This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.

References

Jenior M, Glass E, Papin J . Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling. Bioinformatics. 2023; 39(6). PMC: 10275916. DOI: 10.1093/bioinformatics/btad367. View

Shrestha S, Xue S, Raskin L . Competitive Reactions during Ethanol Chain Elongation Were Temporarily Suppressed by Increasing Hydrogen Partial Pressure through Methanogenesis Inhibition. Environ Sci Technol. 2023; 57(8):3369-3379. PMC: 9979639. DOI: 10.1021/acs.est.2c09014. View

Karlsen E, Schulz C, Almaas E . Automated generation of genome-scale metabolic draft reconstructions based on KEGG. BMC Bioinformatics. 2018; 19(1):467. PMC: 6280343. DOI: 10.1186/s12859-018-2472-z. View

Karp P, Paley S, Krummenacker M, Kothari A, Wannemuehler M, Phillips G . Pathway Tools Management of Pathway/Genome Data for Microbial Communities. Front Bioinform. 2022; 2:869150. PMC: 9580912. DOI: 10.3389/fbinf.2022.869150. View

de Raad M, Li Y, Kuehl J, Andeer P, Kosina S, Hendrickson A . A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria. Front Microbiol. 2022; 13:855331. PMC: 9174792. DOI: 10.3389/fmicb.2022.855331. View

Grootscholten T, Steinbusch K, Hamelers H, Buisman C . Chain elongation of acetate and ethanol in an upflow anaerobic filter for high rate MCFA production. Bioresour Technol. 2012; 135:440-5. DOI: 10.1016/j.biortech.2012.10.165. View

Heinken A, Magnusdottir S, Fleming R, Thiele I . DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations. Bioinformatics. 2021; 37(21):3974-3975. PMC: 8570805. DOI: 10.1093/bioinformatics/btab622. View

Zuniga C, Tibocha-Bonilla J, Betenbaugh M . Kinetic, metabolic, and statistical analytics: addressing metabolic transport limitations among organelles and microbial communities. Curr Opin Biotechnol. 2021; 71:91-97. DOI: 10.1016/j.copbio.2021.06.024. View

Lawson C, Harcombe W, Hatzenpichler R, Lindemann S, Loffler F, OMalley M . Common principles and best practices for engineering microbiomes. Nat Rev Microbiol. 2019; 17(12):725-741. PMC: 8323346. DOI: 10.1038/s41579-019-0255-9. View

10.

Parvin F, Tareq S . Impact of landfill leachate contamination on surface and groundwater of Bangladesh: a systematic review and possible public health risks assessment. Appl Water Sci. 2021; 11(6):100. PMC: 8164486. DOI: 10.1007/s13201-021-01431-3. View

11.

Phua Z, Giannis A, Dong Z, Lisak G, Ng W . Characteristics of incineration ash for sustainable treatment and reutilization. Environ Sci Pollut Res Int. 2019; 26(17):16974-16997. DOI: 10.1007/s11356-019-05217-8. View

12.

Mee M, Collins J, Church G, Wang H . Syntrophic exchange in synthetic microbial communities. Proc Natl Acad Sci U S A. 2014; 111(20):E2149-56. PMC: 4034247. DOI: 10.1073/pnas.1405641111. View

13.

Li B, Godfrey B, Redcorn R, Candry P, Abrahamson B, Wang Z . Mainstream nitrogen removal from low temperature and low ammonium strength municipal wastewater using hydrogel-encapsulated comammox and anammox. Water Res. 2023; 242:120303. DOI: 10.1016/j.watres.2023.120303. View

14.

Lin L . Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion. Biotechnol Biofuels Bioprod. 2022; 15(1):14. PMC: 8822760. DOI: 10.1186/s13068-022-02113-1. View

15.

Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted C . Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. ChemSusChem. 2024; 17(16):e202301460. DOI: 10.1002/cssc.202301460. View

16.

Rhee S, Pack M . Effect of environmental pH on fermentation balance of Lactobacillus bulgaricus. J Bacteriol. 1980; 144(1):217-21. PMC: 294626. DOI: 10.1128/jb.144.1.217-221.1980. View

17.

Zelezniak A, Andrejev S, Ponomarova O, Mende D, Bork P, Patil K . Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc Natl Acad Sci U S A. 2015; 112(20):6449-54. PMC: 4443341. DOI: 10.1073/pnas.1421834112. View

18.

Seviour T, Pijuan M, Nicholson T, Keller J, Yuan Z . Understanding the properties of aerobic sludge granules as hydrogels. Biotechnol Bioeng. 2008; 102(5):1483-93. DOI: 10.1002/bit.22164. View

19.

Hu H, Wang M, Huang Y, Xu Z, Xu P, Nie Y . Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use. mLife. 2024; 1(4):382-398. PMC: 10989833. DOI: 10.1002/mlf2.12043. View

20.

Cai J, Tan T, Chan S . Predicting Nash equilibria for microbial metabolic interactions. Bioinformatics. 2020; 36(24):5649-5655. DOI: 10.1093/bioinformatics/btaa1014. View