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Cited by 53Microbial Metabolic Engineering and BioproductionMicrobial bioremediation and biosurfactantsMicrobial Fuel Cells and Bioremediation

Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass

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Lyu, Xuejiao, Nuhu, Mujaheed, Candry, Pieter, Wolfanger, Jenna, Betenbaugh, Michael, Saldivar, Alexis, Zuniga, Cristal, Wang, Ying +1 more·2024·Journal of Industrial Microbiology and Biotechnology
DOI 10.1093/jimb/kuae025PMC PMC11287213
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Abstract

Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted. 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.

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Authors
Lyu, X., Nuhu, M., Candry, P., Wolfanger, J., Betenbaugh, M., Saldivar, A., Zuniga, C., Wang, Y., & Shrestha, S.
Affiliations
  • Johns Hopkins University (US)
  • Wageningen University & Research (NL)
  • San Diego State University (US)
  • Department of Biology, San Diego State University , San Diego, CA 92182-4614,
  • Texas A&M University (US)
Corresponding author
Shrestha, Shilva
ORCID
Venue
Journal of Industrial Microbiology and Biotechnology
Publisher
Oxford University Press (OUP)
Published
2024
Volume
51
ISSN
  • 1367-5435 (ISSN-L)
  • 1476-5535
DOI
10.1093/jimb/kuae025
PMC
PMC11287213
OpenAlex
W4400612253
Cited by
53
References
5
Citations by year
2026: 38 · 2025: 14 · 2024: 1
FWCI
2.08
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Industrial Microbiology & Biotechnology (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
  • Socio-Environmental Systems Modeling (submittedVersion, cc-by-nc-nd)
Funders
Johns Hopkins University
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
  • Physical Sciences › Environmental Science › Pollution › Microbial bioremediation and biosurfactants
  • Physical Sciences › Environmental Science › Environmental Engineering › Microbial Fuel Cells and Bioremediation
Keywords
microbiome engineering, microbial consortia, waste valorization, synthetic microbial consortia, metabolic engineering, metabolic modeling, ecological engineering, circular economy, resource recovery
MeSH terms
Bacteria, Biotechnology, Biomass, Metabolic Networks and Pathways, Microbial Consortia, Metabolic Engineering, Microbiota

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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