Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes
| Title: | Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes |
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| Authors: | William J Watterson, Melikhan Tanyeri, Andrea R Watson, Candace M Cham, Yue Shan, Eugene B Chang, A Murat Eren, Savaş Tay |
| Source: | eLife, Vol 9 (2020) |
| Publisher Information: | eLife Sciences Publications Ltd, 2020. |
| Publication Year: | 2020 |
| Collection: | LCC:Medicine LCC:Science LCC:Biology (General) |
| Subject Terms: | droplet microfluidics, high-throughput cultivation, fecal microbial transplantation, rare bacteria, antibiotic resistance screening, Medicine, Science, Biology (General), QH301-705.5 |
| More Details: | Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivation experiments. Here we describe a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts them based on colony density to enhance slow-growing organisms. We applied our strategy to a fecal microbiota transplant (FMT) donor stool using multiple growth media, and found significant increase in taxonomic richness and larger representation of rare and clinically relevant taxa among droplet-grown cells compared to conventional plates. Furthermore, screening the FMT donor stool for antibiotic resistance revealed 21 populations that evaded detection in plate-based assessment of antibiotic resistance. Our method improves cultivation-based surveys of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles. |
| Document Type: | article |
| File Description: | electronic resource |
| Language: | English |
| ISSN: | 2050-084X |
| Relation: | https://elifesciences.org/articles/56998; https://doaj.org/toc/2050-084X |
| DOI: | 10.7554/eLife.56998 |
| Access URL: | https://doaj.org/article/ef8cd5832d59451aac795414adbdc03b |
| Accession Number: | edsdoj.f8cd5832d59451aac795414adbdc03b |
| Database: | Directory of Open Access Journals |
| ISSN: | 2050084X |
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| DOI: | 10.7554/eLife.56998 |
| Published in: | eLife |
| Language: | English |