Spatial Omics Solutions for Microbiology

Spatial Omics Solutions for Microbiology

Microbial populations display heterogeneous gene expression profiles resulting in phenotypic differences between individual bacteria. This diversity allows populations to survive under uncertain and fluctuating conditions, such as sudden antibiotic exposure and enables interactions between different phenotypes. The large-scale application of sequencing technologies has enabled researchers to conduct new studies of biological mechanisms, evolutionary relationships, and intercellular communication networks. Massively parallel sequencing has paved the way for the integration of high-throughput analysis, including the study of gene expression, protein expression, and microbial community mapping.

How we can interpret microbiological aspects through spatial omics technologies

Capturing heterogeneous phenotypes of microbial populations at relevant spatial and temporal scales is very challenging. CD Genomics offers a spatial transcriptomic imaging approach to record gene expression and spatial context within microscale assemblies at single-cell and molecular resolution. We can perform an integrated analysis of transcriptome and proteome in the same tissue section. to identify the many transcriptional states associated with specific physiological processes that emerge dynamically during growth, as well as spatially resolved metabolic heterogeneity.

Microbial biogeography can be measured through a diverse range of technologies.Figure 1. Microbial biogeography can be measured through a diverse range of technologies. (Hao, S., et al., 2021)

What our customers can get

  • Detection of rare cell populations that retain spatial resolution while increasing insight into the larger biological environment.
  • Capture the gene expression profiles of individual bacteria while preserving their physical environment in a spatially structured setting.
  • Gene expression is recorded, capturing cell biological parameters such as cell size, and can be further combined with specific dyes to measure features such as chromosome copies in the same cell.
  • Revealing the biological location context of cell states provides new insights into the spatial expression of various genes.

Technical features and advantages

  • Generate highly complex multi-omics characterization of tissues in a high-throughput manner while exhibiting low technical variation.
  • Define the microscopic heterogeneity of microbial life. This plays an important role in community organization and function, including antibiotic resistance and virulence.
  • In combination with LCM, spatially localized measurements (resolution ~10µm) can be achieved to locate DNA elements in complex samples and reveal microscale changes in the microbiome.
  • Multiple bacterial taxa can be detected simultaneously, increasing the number of identifiable species and revealing the complexity of microbial organization in complex systems.
  • Use seqFISH to map mRNA molecules spatially and resolve gene expression spatially. Mapping transcriptional heterogeneity in complex microbial communities.
  • The complex dynamics of microbial populations can be resolved and is a new approach to studying them at high resolution.

We do it better

CD Genomics can obtain microscopic phenotypic variation and metabolic heterogeneity of microbial populations by spatial transcriptome addition with image capture. This multiplexed and spatially resolved approach provides a versatile tool for studying populations on spatial and temporal scales directly in their native environment. Future applications in natural and clinical samples will provide insights into the conditions experienced by microorganisms in complex environments and the metabolic events that occur sequentially and reshape coordinated physiological responses to them.


  1. Hao, S., et al., (2021). "Recent advances in tools to map the microbiome." Current Opinion in Biomedical Engineering. 19, 100289.
For research use only, not intended for any clinical use.

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