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Microbial Single Cell Genomics

National facility

The Microbial Single Cell Genomics facility provides single cell genomics services to the scientific community. Single cell genomics is an emerging technology that allows for the exploration of the genome content of individual cells without the need for prior cultivation in the lab. The facility offers streamlined single-cell sorting and lysis, whole-genome amplification and screening of individual cells by targeting 16S/18S rRNA or customer-specified marker genes, as well as whole genome and targeted gene sequencing services to the scientific community in Sweden and beyond.


The Microbial Single Cell facility will arrange a practical and theoretical workshop

on the 4th to 6th of March 2020

Register latest on the 10 th of February at



  • Single-cell sorting. Single-cell sorting in microwell plates using fluorescence-assisted cell sorting (FACS) or the C1 Single-Cell Auto Prep system
  • Lysis and amplification. Lysis and whole-genome amplification (WGA) of individual cells using multiple-strand displacement amplification (MDA)
  • PCR screening. PCR screening of amplified single cell genomes for marker genes (e.g. microbial 16S rRNA, protein-coding genes)
  • Support. Advising in the design of single-cell experiments, whole-genome sequencing, genome assembly and bioinformatics support


  • Assessing the genomic content of a given environmental or medical sample at the individual cell level
  • Studying the phylogenetic distribution of target genes in a microbial population, such as antibiotic resistance genes
  • De novo identification of metabolic networks in microbial communities (‘Who is doing what?’)
  • Studying genomic variability within microbial populations


  • Beckman Coulter MoFlo AstriosEQ with biosafety cabinet for processing samples up to safety level II
  • BD Influx cell sorter
  • Formulatrix MANTIS® Liquid Handler
  • TTP Labtech Mosquito HV® Liquid Handler
  • Fluidigm C1 Single-Cell Auto Prep system
  • Beckman Biomek NxP robotic liquid handler
  • Apricot TPS-24 12-channel pipetting robot
  • BMG Fluostar Omega plate reader coupled to plate stacker
  • Leica DMi8 inverted fluorescence microscope with automated stage
  • Roche LC480 Real-Time qPCR machine
  • Clean-room customized for cell sorting and single-cell DNA amplification including PCR hood and UV-based reagent purification equipment
  • PCR instruments, plate sealer, incubator, and high-speed centrifuge for tubes and microwell plates


Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes.
Troell K, Hallström B, Divne AM, Alsmark C, Arrighi R, Huss M, Beser J, Bertilsson S.
BMC Genomics. 2016 Jun 23;17:471.

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. Alneberg J, Karlsson CMG, Divne AM, Bergin C, Homa F, Lindh MV, Hugerth LW, Ettema TJG, Bertilsson S, Andersson AF, Pinhassi J. Microbiome. 2018 Sep 28;6(1):173.

Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei. Montoliu-Nerin M, Sánchez-García M, Bergin C, Grabherr M, Ellis B, Kutschera VE, Kierczak M, Johannesson H, Rosling A. Sci Rep. 2020 Jan 28;10(1):1303. doi: 10.1038/s41598-020-58025-3.