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Ma P, Amemiya HM, He LL, Gandhi SJ, Nicol R, Bhattacharyya RP, Smillie CS, Hung DT. Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states. Cell 2023; 186:877-891.e14. [PMID: 36708705 PMCID: PMC10014032 DOI: 10.1016/j.cell.2023.01.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/15/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023]
Abstract
We introduce BacDrop, a highly scalable technology for bacterial single-cell RNA sequencing that has overcome many challenges hindering the development of scRNA-seq in bacteria. BacDrop can be applied to thousands to millions of cells from both gram-negative and gram-positive species. It features universal ribosomal RNA depletion and combinatorial barcodes that enable multiplexing and massively parallel sequencing. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and to elucidate their heterogeneous responses to antibiotic stress. In an unperturbed population presumed to be homogeneous, we found within-population heterogeneity largely driven by the expression of mobile genetic elements that promote the evolution of antibiotic resistance. Under antibiotic perturbation, BacDrop revealed transcriptionally distinct subpopulations associated with different phenotypic outcomes including antibiotic persistence. BacDrop thus can capture cellular states that cannot be detected by bulk RNA-seq, which will unlock new microbiological insights into bacterial responses to perturbations and larger bacterial communities such as the microbiome.
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Affiliation(s)
- Peijun Ma
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Haley M Amemiya
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lorrie L He
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shivam J Gandhi
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Robert Nicol
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Roby P Bhattacharyya
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher S Smillie
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Deborah T Hung
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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Moltzau Anderson J, Lachnit T, Lipinski S, Falk-Paulsen M, Rosenstiel P. Impact of antibiotic perturbation on fecal viral communities in mice. G3 (Bethesda) 2022; 13:6839982. [PMID: 36413074 PMCID: PMC9836353 DOI: 10.1093/g3journal/jkac293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022]
Abstract
Viruses and bacteriophages have a strong impact on intestinal barrier function and the composition and functional properties of commensal bacterial communities. Shifts of the fecal virome might be involved in human diseases, including inflammatory bowel disease (IBD). Loss-of-function variants in the nucleotide-binding oligomerization domain-containing protein 2 (NOD2) gene are associated with an increased risk of developing Crohn's disease, a subtype of human chronic IBD, where specific changes in fecal viral communities have also been described. To improve our understanding of the dynamics of the enteric virome, we longitudinally characterized the virome in fecal samples from wild-type C57BL/6J and NOD2 knock-out mice in response to an antibiotic perturbation. Sequencing of virus-like particles demonstrated both a high diversity and high interindividual variation of the murine fecal virome composed of eukaryotic viruses and bacteriophages. Antibiotics had a significant impact on the fecal murine virome. Viral community composition only partially recovered in the observation period (10 weeks after cessation of antibiotics) irrespective of genotype. However, compositional shifts in the virome and bacteriome were highly correlated, suggesting that the loss of specific phages may contribute to prolonged dysregulation of the bacterial community composition. We suggest that therapeutic interference with the fecal virome may represent a novel approach in microbiota-targeted therapies.
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Affiliation(s)
- Jacqueline Moltzau Anderson
- Present address for Jacqueline Moltzau Anderson: Department of Medicine, University of California San Francisco, 94117 San Francisco, CA, USA
| | | | - Simone Lipinski
- Present address for Simone Lipinski: University Cancer Center Schleswig-Holstein, University Medical Center Campus Kiel, 24105 Kiel, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, 24098 Kiel, Germany
| | - Philip Rosenstiel
- Corresponding author: Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University (CAU) Kiel, Rosalind-Franklin-Str. 12, Kiel 24105, Germany.
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