ArticlemSystems2020
Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture.
Article in mSystems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Microfluidic-based high-throughput isolation enhances the recovery of novel strains and diversity from Arctic soil microbiome.Applied and environmental microbiology · 2026Article
- Microfluidic enrichment of proteolytic microbial consortia from sewage sludge.Applied and environmental microbiology · 2026Article
- Microfluidic encapsulation of the human gut microbiota-a tool for research and beyond.Microsystems & nanoengineering · 2026Article
- Multiplexing antibiotic screening assay in droplet microfluidics.Scientific reports · 2026Article
- Harnessing the Gut Microbes of Low Abundance With a Bent-Capillary-Centrifugal-Driven (BCCD) Microdroplet Method.MicrobiologyOpen · 2026Article
- Fecal microbiomes from healthy adult consumers of fruits and vegetables exhibit fiber- and donor-specific fermentation: "5 a day" is not enough.Food & function · 2025Article
- A droplet microfluidic strategy for cultivation, investigation, and high-throughput isolation of mouse gut microbiome bacteria.Applied and environmental microbiology · 2025Article
- Exploration of Multi-Source Lignocellulose-Degrading Microbial Resources and Bioaugmentation Strategies: Implications for Rumen Efficiency.Animals : an open access journal from MDPI · 2025Review
- Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.Journal of microbiology and biotechnology · 2025Review
- Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms.Applied and environmental microbiology · 2025Article
- Intratumoral microbiome: implications for immune modulation and innovative therapeutic strategies in cancer.Journal of biomedical science · 2025Review
- Purified fibers in chemically defined synthetic diets destabilize the gut microbiome of an omnivorous insect model.bioRxiv : the preprint server for biology · 2024Article
- A Guide to Biodetection in Droplets.Analytical chemistry · 2024Review
- Interplay between particle size and microbial ecology in the gut microbiome.bioRxiv : the preprint server for biology · 2024Article
- Interplay between particle size and microbial ecology in the gut microbiome.The ISME journal · 2024Article
- Purified fibers in chemically defined synthetic diets destabilize the gut microbiome of an omnivorous insect model.Frontiers in microbiomes · 2024Article
- Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique.ISME communications · 2024Article
- High-throughput microbial culturomics using automation and machine learning.Nature biotechnology · 2023Article
- Gut microbiota in colorectal cancer development and therapy.Nature reviews. Clinical oncology · 2023Review
- [Application of Droplet-Based Microfluidics in Microbial Research].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2023Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Culture and screening of gut bacteria enable testing of microbial function and therapeutic potential. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. Here, we combine advances in droplet microfluidics and high-throughput DNA sequencing to develop a platform for separating and assaying growth of microbiota members in picoliter droplets (MicDrop). MicDrop enabled us to cultivate 2.8 times more bacterial taxa than typical batch culture methods. We then used MicDrop to test whether individuals possess similar abundances of carbohydrate-degrading gut bacteria, using an approach which had previously not been possible due to throughput limitations of traditional bacterial culture techniques. Single MicDrop experiments allowed us to characterize carbohydrate utilization among dozens of gut bacterial taxa from distinct human stool samples. Our aggregate data across nine healthy stool donors revealed that all of the individuals harbored gut bacterial species capable of degrading common dietary polysaccharides. However, the levels of richness and abundance of polysaccharide-degrading species relative to monosaccharide-consuming taxa differed by up to 2.6-fold and 24.7-fold, respectively. Additionally, our unique dataset suggested that gut bacterial taxa may be broadly categorized by whether they can grow on single or multiple polysaccharides, and we found that this lifestyle trait is correlated with how broadly bacterial taxa can be found across individuals. This demonstration shows that it is feasible to measure the function of hundreds of bacterial taxa across multiple fecal samples from different people, which should in turn enable future efforts to design microbiota-directed therapies and yield new insights into microbiota ecology and evolution.
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