Microbial Single Cell Genomics

National Facility


Microbial Single Cell Genomics


Recent user publications

The publications in this database are the result of research conducted at the units of SciLifeLab – both in user projects and technology development.


Henrik Gezelius, Acting Head of Unit

Claudia Bergin, Scientist

Anna-Maria Divne, Scientist


Johan Ankarklev, Plattform Scientific Director

Fabien Burki, Plattform Scientific Director


Stefan Bertilsson, Co-founder

Thijs Ettema, Co-founder

Microbial Single Cell Genomics

Single-cell genomics and transcriptomics are rapidly advancing fields, which enable the microbial research community to gain novel insight into organismal discovery linked to microbial diversity, evolution as well as infection biology, including host-pathogen interaction. 

The Microbial Single Cell Genomics unit provides customized, low to high-throughput experimental services for Swedish and international researchers working with prokaryotic and eukaryotic microbes. The unit also capacitates work with live microbial pathogens and host-pathogen complexes (up to and including biosafety-level 3, BSL3), and can thereby serve a broad variety of research areas.

  • Evolution and diversity of microbes in nature
  • De novo sequencing of uncultured microbial dark matter
  • Asses metabolic potential at the single cell level
  • Characterize cell fate, differentiation and developmental stages
  • Explore host-pathogen interactions
  • Study the effect of perturbations on microbial gene expression profiles


  • Customized project implementation
  • FACS-based single cell sorting of pro- and eukaryotic cells, up to Bio Safety Level 3
  • Micromanipulation for sorting of eukaryotic cells
  • Single cell DNA sequencing of pro- and eukaryotic microbes
  • Single cell RNA sequencing of eukaryotic microbes and host-microbe complexes
  • Bioinformatics; We refer to NBIS for project specific computational analyses


  • Single Cell RNA-sequencing:
    • Smart-seq2, full-length RNA-sequencing
    • 10x Genomics, 3’ gene expression, SC3’
  • Single Cell DNA-sequencing:
    • Whole genome amplification using Multiple Displacement Amplification (MDA)
  • Single Cell ATAC-sequencing:
    • 10x Genomics


  • Cleanrooms customized for minimizing contamination of single cell genomic workflow
    of microbes, including microbial pathogens up to BSL 3
  • Beckman Coulter MoFlo AstriosEQ (with biosafety cabinet for pathogens up to BSL 3)
    Lasers: 355nm, 405 nm, 488 nm, 532 nm, 640 nm
  • 10XGenomics Chromium Controller (with biosafety cabinet for pathogens up to BSL 3)
  • TTP Labtech Mosquito HV Liquid Handler
  • Formulatrix MANTIS® Liquid Handler
  • Beckman Coulter Biomek NxP Liquid Handler with 96 and 384 head
  • BMG Fluostar Omega Plate Reader coupled to plate stacker
  • Leica DMi8 inverted fluorescence microscope with automated stage
  • Eppendorf TransferMan NK2 Roche LC480, Biorad CFX384 real-time qPCR machines

Using the unit

If you are interested in our services, please email to: seq@medsci.uu.se

Add “MSCG” in the email subject.

Mailing Address

Uppsala University,
SciLifeLab, BMC
Microbial Single Cell Genomics
Box 596
751 23 Uppsala

Visiting Address/Deliveries

Uppsala University,
SciLifeLab, BMC
Microbial Single Cell Genomics
Husargatan 3
751 23 Uppsala

Last updated: 2023-05-21

Content Responsible: Anna-Maria Divne(anna-maria.divne@icm.uu.se)