How does Flow-FISH differ from traditional plate counting?

Plate counting relies on colony growth on agar, which can take 48–72 hours and may miss viable-but-non-culturable (VBNC) cells. Flow-FISH directly detects live cells by targeting ribosomal RNA and using a viability dye, providing results in 3–4 hours and counting cells that are alive even if they cannot form colonies on standard media.

Can this method detect VBNC (viable but non-culturable) bacteria?

Yes, because Flow-FISH enumerates cells based on rRNA content and membrane integrity rather than colony formation. Bacteria in the VBNC state retain sufficient rRNA to be detected by fluorescent probes and are counted as viable if they exclude the viability dye.

What types of probiotic products can be tested?

We accept lyophilized powders, capsules, tablets, fermented dairy products, fruit preparations, and other complex matrices. The sample is homogenized and filtered if needed to ensure single-cell suspension before staining.

Is the method compatible with any flow cytometer?

Our protocol is validated on commonly used benchtop flow cytometers with at least two fluorescence channels. We adjust optical configurations and compensation as needed to match your instrument. Please consult about specific cytometer models during project scoping.

How many strains can be differentiated in a single test?

Using spectrally distinct probes, we can simultaneously enumerate up to four target species or strains per sample. Larger panels are possible but must be evaluated for spectral overlap and sensitivity case by case.

What sample volume or mass is required?

Typical sample requirements are 1 g of powder or 1 mL of liquid per strain being tested. Larger volumes may be needed for low-titer samples or when multiple technical replicates are required. Exact requirements are confirmed during consultation.

Do you provide controls to confirm probe specificity?

Yes. Every project includes a positive control strain (the target), a negative control (a closely related non-target strain), and a no-probe background control to assess autofluorescence. These controls ensure that reported counts are specific and not due to non-specific binding or sample background.

How soon will I receive the results?

Turnaround time is scoped per project during consultation, as it depends on sample quantity, number of targets, and any additional validation steps requested. Our workflow is designed to provide results rapidly once the project plan is agreed.

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Probiotic Strain Identification & Viability Testing

Probiotic Quality Control

Using Flow-FISH technology, we deliver species- or strain-level identification and accurate live-cell enumeration directly in complex.

Species- and strain-specific fluorescent probes target ribosomal RNA of viable cells
Viability dye discrimination excludes dead or damaged cells from the count
Results in hours instead of days, with no need for selective agar or anaerobic incubation
Suitable for lyophilizates, powders, capsules, fermented products, and multi-strain blends

Verify Your Strains

Fast, Specific Live-Cell Enumeration

Flow-FISH combines fluorescence in situ hybridization with flow cytometry to count only living probiotic cells in complex samples, providing a realistic picture of product potency.

Detects viable cells — not DNA from dead cells or colony-forming aggregates
Identifies target bacteria at genus, species, or subspecies level
Compatible with standard flow cytometers and routine laboratory workflows

Fast

Live-Only

Technology & Workflow

How Flow-FISH Delivers Accurate Viable Counts

Our service is built on a validated Flow-FISH protocol that is modular, probe-based, and tailored to your probiotic product. The method is designed for both pure preparations and complex multi-strain formulations.

Core Flow-FISH Pipeline

From sample receipt to final count, each step is optimized for probiotic matrices to ensure specificity and reproducibility.

Sample homogenization and optional filtration to remove particulates
Fixation and permeabilization to allow probe access to ribosomal RNA
Hybridization with species/strain-specific fluorescent probes and viability dye

Multi-Strain Differentiation

When your product contains multiple probiotic strains, we use probe panels that distinguish each target population by fluorescence signal.

Parallel labeling with spectrally distinct probes for up to several targets
Gating strategy that separates live target populations from background
Reporting of viable cell count per gram or per dose for each target strain

Quality Control

Each run includes positive and negative control strains, replicate measurements, and instrument calibration to maintain data integrity.

Statistical Rigor

Counts are derived from thousands of events per sample, enabling robust statistical comparisons and confidence intervals for product release.

Biological Interpretability

The viability assessment directly measures rRNA content, which correlates with metabolic activity, giving you a functionally relevant estimate of shelf-life stability.

What You Receive

Data Deliverables & Reporting

Every project yields a comprehensive data package that supports label claims, regulatory submissions, and internal QC documentation.

Data Deliverables

Raw flow cytometry data files (FCS format) for audit traceability
Gating scheme documentation showing live/dead and probe-positive gates
Viable cell enumeration results in CFU-equivalent per gram or per dose
Species or strain identity confirmation via probe specificity

Reporting & Support

Certificate of Analysis with method description and results summary
Graphical report including histograms, dot plots, and summary statistics
Optional comparison to conventional plate counts on request
Consultation on data interpretation and follow-up stability study design

Service Scope

Project Parameters and Customization

Because probiotic products vary widely in matrix, strain composition, and intended use, each project is scoped case by case during consultation.

Parameter	Typical Project Scope
Sample Matrix	Lyophilizates, powders, capsules, fermented dairy, fruit preparations, or other complex matrices
Target Strains	Up to 4 target species/strains per panel (expanded panel scoped per project)
Probe Design	Custom fluorescent probes designed against 16S or 23S rRNA sequences; validation on reference strains included
Technical Replicates	Minimum 2 technical replicates per sample; additional replicates scoped as needed
Quality Controls	Positive control (target strain), negative control (non-target), and no-probe background control
Data Reporting Format	PDF Certificate of Analysis; FCS files; summary spreadsheet (Excel) with counts and statistics
Documentation	Method description with probe sequences, gating strategy, and instrument settings

Process

End-to-End Service Workflow

From sample arrival to final report, the Flow-FISH enumeration process is completed in a matter of hours, providing actionable results for quality decisions.

Sample Homogenization

The probiotic product (powder, capsule, or liquid) is suspended and homogenized to release bacterial cells. If necessary, coarse filtration removes insoluble matrix components that could clog the cytometer.

Fixation and Permeabilization

Cells are fixed with paraformaldehyde to preserve RNA integrity, then permeabilized to allow fluorescent probes and viability dye to enter the cell.

Hybridization with Probes and Viability Dye

Species- or strain-specific fluorescently labeled probes are hybridized to ribosomal RNA at optimized temperature. A viability dye (e.g., propidium iodide) is added simultaneously to mark membrane-compromised cells.

Flow Cytometry Acquisition and Gating

The stained sample is run on a calibrated flow cytometer. Events are gated on forward/side scatter to select bacterial-sized particles, then on fluorescence channels: viability dye-negative (live) and probe-positive (target).

Data Analysis and Enumeration

The number of live, probe-positive events is converted to viable cells per gram or per dose using a known counting bead concentration. Results are compiled into a Certificate of Analysis with statistical confidence intervals.

Applications

Where This Service Fits Your Workflow

Our Flow-FISH enumeration service supports quality assurance across the probiotic product lifecycle, from raw material verification to finished product release and stability monitoring.

Verify Incoming Probiotic Strains

Confirm that starter cultures and bulk ingredients contain the correct viable strain at the declared titer before manufacturing.

Rapid identity confirmation of received cultures
Viable count as received vs. certificate of analysis

Support Label Claims and Regulatory Compliance

Obtain an independent, culture-independent viable count for the final packaged product to substantiate potency claims.

Enumeration of each target strain in multi-strain blends
Direct comparison to product label specifications

Monitor Viability Over Shelf Life

Track the viable cell count of your probiotic product at multiple time points under defined storage conditions.

Time-point sampling (e.g., 0, 6, 12, 24 months)
Viable count trends and shelf-life determination

Differentiate Multiple Probiotics in One Sample

Simultaneously enumerate up to four target species or strains within a single test, ideal for commercial blends.

Probe panels with spectrally distinct fluorophores
Separate viable counts for each target population

Common Questions

Flow-FISH Probiotic Enumeration FAQs

Answers to the most frequent questions about our Flow-FISH-based viable count service.

Plate counting relies on colony growth on agar, which can take 48–72 hours and may miss viable-but-non-culturable (VBNC) cells. Flow-FISH directly detects live cells by targeting ribosomal RNA and using a viability dye, providing results in 3–4 hours and counting cells that are alive even if they cannot form colonies on standard media.
Yes, because Flow-FISH enumerates cells based on rRNA content and membrane integrity rather than colony formation. Bacteria in the VBNC state retain sufficient rRNA to be detected by fluorescent probes and are counted as viable if they exclude the viability dye.
We accept lyophilized powders, capsules, tablets, fermented dairy products, fruit preparations, and other complex matrices. The sample is homogenized and filtered if needed to ensure single-cell suspension before staining.
Our protocol is validated on commonly used benchtop flow cytometers with at least two fluorescence channels. We adjust optical configurations and compensation as needed to match your instrument. Please consult about specific cytometer models during project scoping.
Using spectrally distinct probes, we can simultaneously enumerate up to four target species or strains per sample. Larger panels are possible but must be evaluated for spectral overlap and sensitivity case by case.
Typical sample requirements are 1 g of powder or 1 mL of liquid per strain being tested. Larger volumes may be needed for low-titer samples or when multiple technical replicates are required. Exact requirements are confirmed during consultation.
Yes. Every project includes a positive control strain (the target), a negative control (a closely related non-target strain), and a no-probe background control to assess autofluorescence. These controls ensure that reported counts are specific and not due to non-specific binding or sample background.
Turnaround time is scoped per project during consultation, as it depends on sample quantity, number of targets, and any additional validation steps requested. Our workflow is designed to provide results rapidly once the project plan is agreed.

Scientific Literature

References

Warzée JP, Elli M, Fall A, et al. Supranational Assessment of the Quality of Probiotics: Collaborative Initiative between Independent Accredited Testing Laboratories. Microorganisms. 2021;9(7). View on PubMed
Guimarães GM, Soares LA, Silva TNL, et al. Cocoa Pulp as Alternative Food Matrix for Probiotic Delivery. Recent patents on food, nutrition & agriculture. 2020;11(1):82-90. View on PubMed
Afrin S, Akter S, Begum S, et al. The Prospects of Lactobacillus oris as a Potential Probiotic With Cholesterol-Reducing Property From Mother's Milk. Frontiers in nutrition. 2021;8:619506. View on PubMed
Zawistowska-Rojek A, Zaręba T, Tyski S. Microbiological Testing of Probiotic Preparations. International journal of environmental research and public health. 2022;19(9). View on PubMed
Farahmand N, Ouoba LII, Naghizadeh Raeisi S, et al. Probiotic Lactobacilli in Fermented Dairy Products: Selective Detection, Enumeration and Identification Scheme. Microorganisms. 2021;9(8). View on PubMed
Arellano K, Lim J, Bucheli JEV, et al. Identification of safe putative probiotics from various food products. Folia microbiologica. 2024;69(5):1053-1068. View on PubMed

Please kindly note that our products and services are for research use only.