Reversible fixation of microbial cells for targeted genomics
- 1School of Environment and Life Sciences, University of Portsmouth, Portsmouth, United Kingdom.
Abstract
Phylogeny- or activity-based fluorescent labelling of microorganisms coupled with fluorescence activated cell sorting (FACS) is a powerful approach to rapidly isolate cells of interest from complex communities for targeted genomics. However, the method has not been widely adopted because standard paraformaldehyde or ethanol fixation procedures hamper nucleic acid recovery and/or long-term sample storage. Here, we present dithiobis(succinimidyl propionate) (DSP) as a reversible fixative for microbial cells that enables fluorescence imaging and DNA extraction and amplification for sequencing. DSP fixation is compatible with widely used fluorescence in situ hybridization (FISH) approaches and bioorthogonal non-canonical amino acid tagging, and can be applied to diverse sample types, where it consistently performed as well as paraformaldehyde. Furthermore, high-quality genomes were obtained from individual and multiple bacterial cells selectively extracted from complex samples using FISH-FACS. Thus, DSP is a dual-use fixative for microbiome imaging and sequencing, improving targeted microbial genomics.
Related
- A Taxonomy-Informed Sparse DNA Foundation Model for Microbial Genomics
- Systematic Comparison of 10X Genomics and Parse Single Cell RNA Technologies across PBMC and CD8+ TEMRA Cells
- House Dust Mite Induces Distinct Cellular and Extracellular Vesicle-Associated miRNA Signatures in BEAS-2B Cells: Targeted Analysis of IL-4 Responses
- AAV-DJ Enables Targeted Gene Modulation in Human Ovarian Cells
- CD8+ tissue-resident memory T cells are expanded in primary Sjögren's disease and can be therapeutically targeted by CD103 blockade
BibTeX
@misc{engelberts2026reversible,
title = {{Reversible fixation of microbial cells for targeted genomics}},
author = {J. P. Engelberts and K. Wasmund and M. Mussmann and N. Solntseva and F. C. Pereira and C. Rinke and A. Prabhu and J. G. Volmer and B. T. Hanson and B. Hausmann and J. Osvatic and G. W. Tyson and S. J. McIlroy and A. Loy},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.12.758561},
url = {https://www.biorxiv.org/content/10.64898/2026.10.12.758561v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Reversible fixation of microbial cells for targeted genomics
AU - J. P. Engelberts
AU - K. Wasmund
AU - M. Mussmann
AU - N. Solntseva
AU - F. C. Pereira
AU - C. Rinke
AU - A. Prabhu
AU - J. G. Volmer
AU - B. T. Hanson
AU - B. Hausmann
AU - J. Osvatic
AU - G. W. Tyson
AU - S. J. McIlroy
AU - A. Loy
PY - 2026
DA - 2026/10/12
PB - bioRxiv
DO - 10.64898/2026.10.12.758561
UR - https://www.biorxiv.org/content/10.64898/2026.10.12.758561v1
AB - Phylogeny- or activity-based fluorescent labelling of microorganisms coupled with fluorescence activated cell sorting (FACS) is a powerful approach to rapidly isolate cells of interest from complex communities for targeted genomics. However, the method has not been widely adopted because standard paraformaldehyde or ethanol fixation procedures hamper nucleic acid recovery and/or long-term sample storage. Here, we present dithiobis(succinimidyl propionate) (DSP) as a reversible fixative for microbial cells that enables fluorescence imaging and DNA extraction and amplification for sequencing. DSP fixation is compatible with widely used fluorescence in situ hybridization (FISH) approaches and bioorthogonal non-canonical amino acid tagging, and can be applied to diverse sample types, where it consistently performed as well as paraformaldehyde. Furthermore, high-quality genomes were obtained from individual and multiple bacterial cells selectively extracted from complex samples using FISH-FACS. Thus, DSP is a dual-use fixative for microbiome imaging and sequencing, improving targeted microbial genomics.
ER -