ArticleIntegrative biology : quantitative biosciences from nano to macro2020
Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'.
Article in Integrative biology : quantitative biosciences from nano to macro, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 26 citations in OpenAlex.
- A digital plating platform for robust and versatile microbial detection and analysis.Scientific reports · 2025Article
- Fragmented micro-growth habitats present opportunities for alternative competitive outcomes.Nature communications · 2024Article
- Meta-omics assisted microbial gene and strain resources mining in contaminant environment.Engineering in life sciences · 2024Review
- Article
- Research progress in isolation and identification of rumen probiotics.Frontiers in cellular and infection microbiology · 2024Review
- [Application of Droplet-Based Microfluidics in Microbial Research].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2023Review
- Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature.ISME communications · 2022Article
- Systematic characterization of effect of flow rates and buffer compositions on double emulsion droplet volumes and stability.Lab on a chip · 2022Article
- Emerging microfluidic technologies for microbiome research.Frontiers in microbiology · 2022Review
- The effect of droplet size on syntrophic dynamics in droplet-enabled microbial co-cultivation.PloS one · 2022Article
- Predicting Microbiome Metabolism and Interactions through Integrating Multidisciplinary Principles.mSystems · 2021Article
- Droplet Microfluidics for Food and Nutrition Applications.Micromachines · 2021Review
- Microdroplet-based system for culturing of environmental microorganisms using FNAP-sort.Scientific reports · 2021Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
While the 'unculturable' majority of the bacterial world is accessible with culture-independent tools, the inability to study these bacteria using culture-dependent approaches has severely limited our understanding of their ecological roles and interactions. To circumvent cultivation barriers, we utilize microfluidic droplets as localized, nanoliter-size bioreactors to co-cultivate subsets of microbial communities. This co-localization can support ecological interactions between a reduced number of encapsulated cells. We demonstrated the utility of this approach in the encapsulation and co-cultivation of droplet sub-communities from a fecal sample collected from a healthy human subject. With the whole genome amplification and metagenomic shotgun sequencing of co-cultivated sub-communities from 22 droplets, we observed that this approach provides accessibility to uncharacterized gut commensals for study. The recovery of metagenome-assembled genomes from one droplet sub-community demonstrated the capability to dissect the sub-communities with high-genomic resolution. In particular, genomic characterization of one novel member of the family Neisseriaceae revealed implications regarding its participation in fatty acid degradation and production of atherogenic intermediates in the human gut. The demonstrated genomic resolution and accessibility to the microbial 'dark matter' with this methodology can be applied to study the interactions of rare or previously uncultivated members of microbial communities.
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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.