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ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Microbiotechnology
Volume 15 - 2024 |
doi: 10.3389/fmicb.2024.1516656
High throughput Single Cell Metagenomic Sequencing with Semi-Permeable Capsule: Unraveling Microbial Diversity at the Single-Cell Level in Sewage and Feces Microbiomes
Provisionally accepted- 1 Technical University of Denmark, Kongens Lyngby, Denmark
- 2 University of Copenhagen, Copenhagen, Capital Region of Denmark, Denmark
- 3 atrandi, Vilnius, Lithuania
- 4 Imperial College London, London, England, United Kingdom
Single-cell sequencing may serve as a powerful complementary technique to shotgun metagenomics to study microbiomes. This emerging technology allows the separation of complex microbial communities into individual bacterial cells, enabling high-throughput sequencing of genetic material from thousands of singular bacterial cells in parallel. Here, we validated the use of microfluidics and semi-permeable capsule (SPC) technology (Atrandi) to isolate individual bacterial cells from sewage and pig fecal samples. Our method involves extracting and amplifying single bacterial DNA within individual SPCs, followed by combinatorial split-and-pool single-amplified genome (SAG) barcoding and short-read sequencing. We tested two different sequencing approaches with different numbers of SPCs from the same sample for each sequencing run. Using a deep sequencing approach, we detected 1,796 and 1,220 SAGs, of which 576 and 599 were used for further analysis from onefor sewage and one fecal samples, respectively. In shallow sequencing data, we aimed for 10-times more cells and detected 12,731 and 17,909 SAGs, of which we used 2,456 and 1,599 for further analysis for sewage and fecal samples, respectively. Additionally, we identified the top 10 antimicrobial resistance genes (ARGs) in both sewage and feces samples and linked them to their individual host bacterial species.
Keywords: Single cell sequencing, Metagenomics, Microbial Diversity, Sewage, Antimicrobial resistance (AMR), Pig feces
Received: 24 Oct 2024; Accepted: 24 Dec 2024.
Copyright: © 2024 Ling, Szarvas, Kurmauskaitė, Kiseliovas, Žilionis, Avot, Munk, Otani and Aarestrup. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Saria Otani, Technical University of Denmark, Kongens Lyngby, Denmark
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