Isolation of microbes: access to the entire microbiota’s diversity


Biomillenia has unique expertise in isolating microorganisms, including rare and previously uncultured species. Our robust microfluidic workflows have been already validated with source materials such as animal feces (wild, domestic and farmed species), human samples (feces, skin, mouth…), agriculture (soil, leaves, roots…) and environmental materials.

After extraction, microorganisms are isolated in monoclonal cultures using tens of millions of microscopic bioreactors. This allows parallelization of bacterial growth between individually isolated microorganisms in extremely small volumes. These cultures can be generated and maintained under aerobic or anaerobic conditions. Other culturomic factors such as incubation time, choice of medium or temperature are also adjusted to achieve optimal growth. This unique culture environment significantly improves the diversity of the cultured microbiota compared to traditional culture methods, resulting in strain collections containing a wide range of bacterial strains from the original sample.


Our approach not only shortens the overall duration of strain bank operation, but also allows us to deliver high-quality cell libraries with:

Guaranteed monoclonality of cultures
Flexible strain identification:
hypervariable regions (e.g. V4), full-length 16SrRNA sequencing, whole genome sequencing
Traceability from sample to microorganism
Delivery of “Master cell bank ready” cryotubes or MTP
All our collections come with a free one month strain-bank backup
so, if anything happens during shipment, the cell bank will not be lost!

Read our white paper.

Contact us for a customized evaluation of your project!


Real case studies


To enable the discovery of new natural small molecules from the human microbiome, Design Pharmaceuticals needed to access new gut strains grown under stringent anaerobic conditions. The unique strains captured in our microfluidic system showed interesting GPCR activation profiles.

Grain plant
An AgTech* startup looking to develop novel biofertilizers and biocontrol agents needed a culture collection representing the microbiota associated to a specific industrial crop worldwide. Working with Biomillenia, fresh samples from around the world were processed and a master strain bank of 100,000 isolates was created. *[undisclosed for confidentiality reasons]
Dogs running around in a footpath

A major international player* in animal care needed to isolate bacterial strains from different breeds of pets to identify next-generation probiotic strains for animal care. Samples from pets living in different environments were processed with traceability from isolate to original sample to better understand differences between pets living in urban and rural environment.

*[undisclosed for confidentiality reasons]

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