ArticleNature communications2024
Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 2 of them syntheses that pooled 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.
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.
Who cites it
77 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Principles for Rigorous Design and Application of Synthetic Microbial Communities.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Pooled it
- PRISMA-based review ofFrontiers in microbiology · 2026Pooled it
- Harnessing synthetic microbial communities for desert vegetation restoration.Synthetic and systems biotechnology · 2027Review
- Gut microbiome and metabolic health: mechanisms and precision interventions.Gut microbes · 2026Review
- Microbiome-based therapeutics forGut microbes · 2026Review
- Top-down/bottom-up consortia achieve robust γ-HCH degradation and reduced methanogenic contribution in wetlands.Applied and environmental microbiology · 2026Article
- Targeting the human gut microbiome: a comparative review of probiotics, prebiotics, synbiotics, and postbiotics.Journal of advanced research · 2026Review
- Hydrogel-encapsulated microalgae-bacteria consortia for resilient saline agriculture.World journal of microbiology & biotechnology · 2026Review
- Article
- Evaluation of the substrate profile of microbial-host-isozyme reveals the role of BvDPP4 in inflammatory bowel disease.Science China. Life sciences · 2026Article
- Breeding for beneficial microbial associations.Nature communications · 2026Review
- Amylase Production From Potato Peels by Bacillus sp. Under Improved Culture Conditions.Biotechnology and applied biochemistry · 2026Article
- Metabolic Modelling Facilitates the Design of Synthetic Communities by Simplifying Natural Microbial Communities.Environmental microbiology · 2026Article
- Impacts of pollution on the soil microbiome.Nature reviews. Microbiology · 2026Review
- Plant-Microbiome Interactions in Medicinal Plants: A Synergistic Partnership for Biomass Production and Secondary Metabolite Accumulation.Microorganisms · 2026Review
- To Biotic or Abiotic: Biohybrid Systems for Artificial Photosynthesis.Chemical reviews · 2026Review
- Synergistic effects of crop straw formulations onMicrobiology spectrum · 2026Article
- Synthetic Microbial Community Biosensors: From Engineered Ecosystems to Modular Detection Platforms with AI-Driven Intelligence.Biosensors · 2026Review
- Biofilm synergy byBiofilm · 2026Article
- Review
17 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.