Evidence map›Paper›PMID 39003244›Full record

ReviewJournal of industrial microbiology & biotechnology2024

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

Xuejiao Lyu, Mujaheed Nuhu, Pieter Candry, Jenna Wolfanger, Michael Betenbaugh, Alexis Saldivar, Cristal Zuniga, Ying Wang, Shilva Shrestha

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Journal of industrial microbiology & biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Xuejiao LyuDepartment of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Mujaheed NuhuDepartment of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Pieter CandryLaboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands.ORCID 0000-0002-7784-3650
Jenna WolfangerDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Michael BetenbaughDepartment of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
Alexis SaldivarDepartment of Biology, San Diego State University, San Diego, CA 92182-4614, USA.
Cristal ZunigaDepartment of Biology, San Diego State University, San Diego, CA 92182-4614, USA.
Ying WangDepartment of Soil and Crop Sciences, Texas A&M University, TX 77843, USA.
Shilva ShresthaDepartment of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0001-5062-3634

Funding

Johns Hopkins University
6 · The paper itself

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.

Indexed as

BiomassMicrobial ConsortiaBacteriaBiotechnologyMetabolic EngineeringMetabolic Networks and PathwaysMicrobiotaBiomanufacturingBiomassMicrobial communitySynthetic microbial consortiaValue-added products

Identifiers

PMID39003244
PMCPMC11287213

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.