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Microbial Automation and Culturomics Core Facility

A facility for large-scale microbial cultivation, genetics and phenotyping.

Services

The facility offers researchers access, support and training into cutting-edge instrumentation and unique knowhow related to automation for microbial work at scale. Our systems enable modular workflows and allow researchers to combine equipment according to their experimental needs. Our focus is on high-throughput cultivation, genetics and phenotyping of microbes and their communities.

After an initial discussion with the user, MACCF staff advise on suitable instrumentation, program and test the automation according to individual needs, and provides hands-on support in experimental setup, execution and data analysis.  Experienced users can book and use the different machines following SOPs we have established.

High-throughput cultivation

The expertise of the staff combined with the automation enables high- throughput cultivation of different species, strain collections and communities. Our core experience lies on human-associated bacteria (and their viruses) and fungi, but we are open to work together with experienced researchers on microbes of other environments and other unicellular organisms – archaea, protists and algae. 

Growth of microbes & their communities in controlled environments

The facility houses 4 large environmental chambers, connected to customizable gas mixtures to provide precisely controlled atmospheres and temperatures, for the cultivation of a wide range of microbes, from strict anaerobes to microaerophiles, and from psychrophiles to thermophiles. These chambers are routinely used for cultivation and phenotyping of human associated microbiomes.

The facility has 9 further incubators/shakers, where different variables (temperature, light, atmosphere, shaking, humidity) can be controlled to support cultivation of diverse microbes.

Handling of large number of microbial species and complex communities

With 3 automated and 5 semi-automated liquid handlers, the MACCF supports versatile liquid handling protocols on multi-well plates (96-, 384- formats) of different sizes/volumes, for different purposes related to cultivation:

  • propagation, (re)arraying of cryopreserved microbial libraries
  • assembly of complex communities of different compositions
  • handing of phages and large-scale infection assays
  • automated PCR workflows (e.g. for 16S in communities)
  • culturomics approaches –using high-throughput plate assays in different media

Microbial isolation

A main goal in microbial work is to isolate particular species/strains from microbiomes of different complexity. With the colony picker and the single-cell dispenser, housed within controlled environments, the facility supports:

  • HT picking and arraying of large number of colonies
  • Assays to detect (NGS-based or phenotyping-based) targeted species/strains
  • microbial single cell dispensing

High-throughput phenotyping

HT screens

We offer integrated platforms combining stackers/ shakers housed within controlled chambers, and linked to multimode plate readers via robotic arms. We have also high-capacity for liquid handling to assemble assays/screens, and multimodal plate readers that combine even microscopy and single-cell readouts. Within this setup we can support a variety of HTS, from compound screening to large-scale phenotyping of microbes and their interactions:

  • HT compound screening – single compounds and combinations. The facility has 6 compound libraries relative to different aspects of microbial research, all commercially acquired, amounting to in total 7K compounds.
  • quantitative phenotyping (from growth to single-cell readouts) with kinetics in multi-well plates
  • microbial interaction screening – combinatorial (pairwise or higher-order) pooling with liquid handling and measuring compositions

High-throughput assays using high-density agar arrays

Arrayed libraries of microbes (mutants, species collections) can be pinned on high density format on agar (96, 384, 1536, 6144 colonies per plate) and assayed in 100’s of conditions – from media requirements to different chemical stresses or drug libraries. The readouts can include growth (colony morphology), enzyme production (colorimetric), biofilm (colony morphology) or interactions. Plates can be grown on different environments and imaged with a versatile setup we have to allow for epi and trans illumination, fluorescence and luminescence detection. Colony phenotypes are analyzed by in-house software.

Imaging flow analysis

We offer high-throughput imaging flowcytometric analysis, which can be used to monitor live pathogenic cells, count cells and subpopulations within microbiomes, and for fitness competition assays in simple/complex environments. Samples can be used past analysis for other assays, including for sorting.

Microscopy

We support automated live cell assays, from slide scanning to time-lapse combined with a multimode reader. Our setting allows for widefield fluorescence, brightfield and phase contrast microscopy under controlled environments (temperature, CO2, O2-controlled) and for live S2 samples. Single cell parameters, including growth rates and fluorescence signal (reporters) can be quantified on 96/384-well plates.

High-throughput genetics

The facility has extensive knowhow on the generation and manipulation of genetic libraries (mutant, overexpression) in both model and gut bacteria. These libraries can be generated barcoded in pools, where barcode sequencing allows for large-scale fitness-dependent assays. They can also be arrayed so phenotypes can be assessed for each mutant separately (in high-density arrays), allowing for studying processes that are cell-autonomous (extracellular) or fitness-independent. The MACCF can train researchers in the design, construction and use of highly-saturated barcoded transposon mutant libraries in diverse microbes. This comes on top of the numerous available mutant and overexpression libraries available in the MACCF for use in experiments.

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