Microbiome Research

Isolate single cells from complex microbiome samples and accelerate the culturing of unknown species.

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What is Microbiome Research?

Microbiome research investigates the diverse microbial communities found in environments such as the human gut, soil, oceans, and wastewater. To understand the role of individual microorganisms, researchers must isolate single microbial cells and generate pure cultures—a process that is often challenging using traditional colony isolation techniques.

The B.SIGHT streamlines microbial isolation by combining automated single-cell dispensing with high-resolution microscopy. Capable of detecting and isolating even the smallest bacteria in real time, it enables researchers to recover difficult-to-culture microorganisms, increase isolation throughput, and gain deeper insights into complex microbial communities.

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Research Workflows

Single-Cell Genomics of Uncultivated Bacteria

1. Sample Preparation

Prepare microbial samples based on cell density and whether un-biased or enriched population is required.

2. Single-Cell Isolation

Accurately isolate and dispense individual microbial cells into PCR wells for downstream whole-genome amplification.

Solution: B.SIGHT

3. Miniaturized WGA & PCR

Precisely dispense low-volume reagents for cell lysis, whole-genome amplification, and PCR while reducing reaction volumes.

Solution: I.DOT

4. Whole Genome or 16S rRNA Sequencing

Analyze isolated microbial cells using whole-genome or 16S rRNA sequencing to identify and characterize uncultivated bacteria.

Sample Preparation Explained

Prepare microbiota samples, such as stool, by suspending them in supplemented anaerobic PBS, diluting under oxygen-free conditions, and filtering to remove debris. After preparation, B.SIGHT enables single-cell isolation directly into liquid culture media or onto solid agar, including within an anaerobic chamber.

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Anaerobic Isolation and Cultivation of Microbiota Samples

Traditional cultivation can take up to 21 days to produce pure isolates. B.SIGHT accelerates this process with high-throughput, label-free single-cell isolation, enabling efficient sorting and cultivation of diverse microbiota, including anaerobic microorganisms.

B.SIGHT also enables isolation of novel strains not observed with streak-plating alone.

Single-Cell Genomics of Uncultivated Bacteria

Most microbial organisms remain unexplored. B.SIGHT enables precise single-cell isolation directly into PCR wells for whole-genome amplification. Combined with I.DOT for low-volume liquid handling, the workflow supports efficient sequencing and genetic characterization of individual microbes without the need for cultivation.

 

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Application Notes

Explore our application notes to learn how automated single-cell isolation and cultivation technologies are helping researchers overcome the challenges of microbiome research, enabling the discovery and characterization of microorganisms from even the most complex microbial communities.

APPLICATION NOTE

B.SIGHT™ – Accelerating bacteria transformation and cloning workflows using microbial single-cell isolation

Understand the B.SIGHT's ability to dispense single bacteria with image confirmation, furthering colony picking and growth processes.

 

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APPLICATION NOTE

B.SIGHT™ – High-throughput Cultivation Workflow for Isolation of Anaerobic Gut Bacteria

The B.SIGHT enables a high-throughput workflow for isolating anaerobic gut bacteria by dispensing image-confirmed single cells into 96- or 384-well plates.

 

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More Resources

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Applications and Advances in Bacterial and Yeast Strain Development

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Featured Products

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B.SIGHT

Optimized for single-cell sorting of microbial cells.

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I.DOT

High-precision drop-on-demand dispensing for fast, tip-free nanoliter transfers.

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Frequently Asked Questions

Is there a single-cell dispenser for bacteria and anaerobes?

Yes — B.SIGHT is CYTENA's single-cell dispenser for microbiology and the first with full anaerobic compatibility. It moves in and out of a glove box or anaerobic chamber, isolating microbial cells up to 20 µm, label-free or GFP-tagged, under the conditions they need.

How does single-cell isolation help culture "unculturable" microbes?

By giving each cell its own well — a competition-free microenvironment with no fast-growing neighbours or antagonistic metabolites — B.SIGHT lets rare and fastidious organisms establish. Isolation is deterministic, reaching taxa below 0.1% relative abundance that bulk culture in plates or liquid culture never surfaces.

Can B.SIGHT be used for microbial strain development, probiotics or LBPs?

Yes. B.SIGHT isolates thousands of clonal starting points in parallel, so you can screen producers and variants, develop novel growth media, and raise the odds of finding the low-frequency, high-value strains behind fermentation, probiotics and live biotherapeutic products (LBPs).

What sample types can B.SIGHT process?

Complex microbiome samples including fecal matter, soil, water, fermented foods and bioengineered microbial cultures have all been processed with B.SIGHT, with exceptional recovery of the microbial diversity, and image-based verification of single-cell isolation for every well.