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Wu M, Wang H. Re-considering and designing microbiomes for future waste biorefinery. Microb Biotechnol 2024; 17:e14395. [PMID: 38206186 PMCID: PMC10835331 DOI: 10.1111/1751-7915.14395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
It is an increasingly promising research direction using microbiomes to produce various chemicals in order to support people's growing need for sustainability. Currently, bottom-up constructed defined microbiomes and top-down constructed undefined microbiomes play an essential role in the fields of synthetic biology and environmental engineering, respectively. However, if we are goal-oriented and want to align scientific principles with technology and engineering in future waste biorefinery, we need to reconsider and design microbiomes interdisciplinarily. In this editorial, we briefly review the latest applications of two approaches to microbiome design (bottom-up and top-down) and the dilemmas faced in using complex waste. Consequently, we introduce the concept of 'sustainable synthetic microbiomics' to apply combined bottom-up and top-down constructed microbiomes to provide products for human needs from low-value waste. Furthermore, we outline the relatively comprehensive research contents and expected prospects based on the pressing problems. Finally, burning questions on key research contents are proposed for specific cases, hoping to provide valuable views for future microbiome biorefinery.
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Affiliation(s)
- Menghan Wu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Hui Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
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Altamira-Algarra B, Rueda E, Lage A, San León D, Martínez-Blanch JF, Nogales J, García J, Gonzalez-Flo E. New strategy for bioplastic and exopolysaccharides production: Enrichment of field microbiomes with cyanobacteria. N Biotechnol 2023; 78:141-149. [PMID: 37852438 DOI: 10.1016/j.nbt.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 09/29/2023] [Accepted: 10/14/2023] [Indexed: 10/20/2023]
Abstract
Seven photosynthethic microbiomes were collected from field environmental samples to test their potential in polyhydroxybutyrate (PHB) and exopolysaccharides (EPS) production, both alternatives to chemical-based polymers. Microscope observations together with microbial sequence analysis revealed the microbiome enrichment in cyanobacteria after culture growth under phosphorus limitation. PHB and EPS production were studied under three culture factors (phototrophy, mixotrophy and heterotrophy) by evaluating and optimizing the effect of three parameters (organic and inorganic carbon and days under light:dark cycles) by Box-Behnken design. Results showed that optimal conditions for both biopolymers synthesis were microbiome-dependent; however, the addition of organic carbon boosted PHB production in all the tested microbiomes, producing up to 14 %dcw PHB with the addition of 1.2 g acetate·L-1 and seven days under light:dark photoperiods. The highest EPS production was 59 mg·L-1 with the addition of 1.2 g acetate·L-1 and four days under light:dark photoperiods. The methodology used is suitable for enriching microbiomes in cyanobacteria, and for testing the best conditions for bioproduct synthesis for further scale up.
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Affiliation(s)
- Beatriz Altamira-Algarra
- GEMMA-Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya-BarcelonaTech, Av. Eduard Maristany 16, Building C5.1, E-08019 Barcelona, Spain
| | - Estel Rueda
- GEMMA-Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya-BarcelonaTech, Av. Eduard Maristany 16, Building C5.1, E-08019 Barcelona, Spain
| | - Artai Lage
- GEMMA-Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya-BarcelonaTech, Av. Eduard Maristany 16, Building C5.1, E-08019 Barcelona, Spain
| | - David San León
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Juan F Martínez-Blanch
- Department of preventive medicine, public health, food sciences, toxicology and forensic medicine, Universitat de Valencia, Valencia, Spain; Biopolis S.L., ADM, Parc Cientifc Universidad De Valencia, Edif. 2, C/ Catedrático Agustín Escardino Benlloch, 9, 46980 Paterna, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Joan García
- GEMMA-Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya-BarcelonaTech, c/ Jordi Girona 1-3, Building D1, E-08034 Barcelona, Spain
| | - Eva Gonzalez-Flo
- GEMMA-Group of Environmental Engineering and Microbiology, Department of Civil and Environmental Engineering, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya-BarcelonaTech, Av. Eduard Maristany 16, Building C5.1, E-08019 Barcelona, Spain.
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Walters KA, Mohan G, Myers KS, Ingle AT, Donohue TJ, Noguera DR. A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate. Front Bioeng Biotechnol 2023; 11:1173656. [PMID: 37324413 PMCID: PMC10263058 DOI: 10.3389/fbioe.2023.1173656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to determine the genomic features of community members that are characteristic to the accumulation of different products. To address this knowledge gap, we performed a 282-day bioreactor experiment with a microbial community that was fed ultra-filtered milk permeate, a low-value coproduct from the dairy industry. The bioreactor was inoculated with a microbial community from an acid-phase digester. A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. This analysis led us to propose that, in this reactor, members of the Actinobacteriota phylum are important in the degradation of lactose, via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, and succinic acids. In addition, members of the Firmicutes phylum contribute to the chain-elongation-mediated production of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, ethanol, or lactic acid as the growth substrate. We conclude that genes encoding carbohydrate utilization pathways, and genes encoding lactic acid transport into the cell, electron confurcating lactate dehydrogenase, and its associated electron transfer flavoproteins, are genomic features whose presence in Firmicutes needs to be established to infer the growth substrate used for chain elongation.
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Affiliation(s)
- Kevin A. Walters
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Geethaanjali Mohan
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Kevin S. Myers
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Abel T. Ingle
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Timothy J. Donohue
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Daniel R. Noguera
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, United States
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