High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes
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...
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Frontiers Media S.A.
2025-02-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1516656/full |
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| author | Meilee Ling Judit Szarvas Vaida Kurmauskaitė Vaidotas Kiseliovas Rapolas Žilionis Rapolas Žilionis Baptiste Avot Baptiste Avot Patrick Munk Frank M. Aarestrup |
| author_facet | Meilee Ling Judit Szarvas Vaida Kurmauskaitė Vaidotas Kiseliovas Rapolas Žilionis Rapolas Žilionis Baptiste Avot Baptiste Avot Patrick Munk Frank M. Aarestrup |
| author_sort | Meilee Ling |
| collection | DOAJ |
| description | 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 capsules (SPCs) 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 one sewage and one fecal sample, 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. |
| format | Article |
| id | doaj-art-d7e57a36ffb744d8b22081cfa323a633 |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj-art-d7e57a36ffb744d8b22081cfa323a6332025-02-04T16:37:26ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-02-011510.3389/fmicb.2024.15166561516656High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomesMeilee Ling0Judit Szarvas1Vaida Kurmauskaitė2Vaidotas Kiseliovas3Rapolas Žilionis4Rapolas Žilionis5Baptiste Avot6Baptiste Avot7Patrick Munk8Frank M. Aarestrup9Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, DenmarkResearch Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, DenmarkAtrandi Biosciences, Vilnius, LithuaniaAtrandi Biosciences, Vilnius, LithuaniaAtrandi Biosciences, Vilnius, LithuaniaInstitute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, LithuaniaResearch Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, DenmarkImperial College London, London, United KingdomResearch Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, DenmarkResearch Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, DenmarkSingle-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 capsules (SPCs) 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 one sewage and one fecal sample, 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.https://www.frontiersin.org/articles/10.3389/fmicb.2024.1516656/fullsingle cell sequencingmetagenomicsmicrobial diversitysewageantimicrobial resistance (AMR)pig fecal sample |
| spellingShingle | Meilee Ling Judit Szarvas Vaida Kurmauskaitė Vaidotas Kiseliovas Rapolas Žilionis Rapolas Žilionis Baptiste Avot Baptiste Avot Patrick Munk Frank M. Aarestrup High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes Frontiers in Microbiology single cell sequencing metagenomics microbial diversity sewage antimicrobial resistance (AMR) pig fecal sample |
| title | High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes |
| title_full | High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes |
| title_fullStr | High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes |
| title_full_unstemmed | High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes |
| title_short | High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes |
| title_sort | high throughput single cell metagenomic sequencing with semi permeable capsules unraveling microbial diversity at the single cell level in sewage and fecal microbiomes |
| topic | single cell sequencing metagenomics microbial diversity sewage antimicrobial resistance (AMR) pig fecal sample |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1516656/full |
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