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Flow Cytometry

Flow Cytometry

The development of flow cytometry techniques began in 1934 with initial attempts by Andrew Moldavan, a bacteriologist who counted the cells in a flowing capillary system. Moldavan pumped cells through a capillary tube focused under a microscope for visualization. The invention of photometry allowed the measurement of differentially-stained cells, and Louis Kamentsky developed the first multiparameter flow cytometer in 1965 to identify and count the cancer cells in cervical tissue specimens.
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Updated: Jan 16, 2026

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Published on: July 12, 2018

Single-cell quantification of the microbiota by flow cytometry: MicFLY.

Christine M Tin^1,2,3, Bianca Cordazzo Vargas⁴, Darryl A Abbott^1,2,3

¹Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA.

Biorxiv : the Preprint Server for Biology

|September 26, 2025

Summary

A new technology, Microbiota Flow Cytometry (MicFLY), enables precise, single-cell measurement of gut bacteria. This innovation links specific bacterial interactions, like unbound E. coli, to infant necrotizing enterocolitis development.

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Single-cell Analysis of Bacillus subtilis Biofilms Using Fluorescence Microscopy and Flow Cytometry

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Area of Science:

Microbiology
Immunology
Bioengineering

Background:

The intestinal microbiota is crucial for host health, influencing digestion and immune system development.
Current technologies primarily measure relative bacterial abundance, limiting a deep understanding of microbiota shifts.
Absolute abundance and single-cell measurements are needed to understand microbiota composition changes.

Purpose of the Study:

To develop a novel single-cell technology for quantifying and characterizing gut bacteria with species-level resolution.
To enable detailed analysis of bacterial absolute abundance, viability, gene expression, and host immune molecule binding.
To investigate the relationship between specific bacterial features and necrotizing enterocolitis in preterm infants.

Main Methods:

Development and application of Microbiota Flow Cytometry (MicFLY), a single-cell technology.
Quantification of total bacterial abundances at the species level.
Discrimination of live vs. dead bacteria and measurement of bacterial mRNA expression.
Concurrent quantification of Immunoglobulin (Ig) A and G binding to intestinal bacteria.

Main Results:

MicFLY successfully quantifies and characterizes total bacterial abundances with species-level resolution.
The technology allows for live/dead discrimination, single-cell mRNA expression analysis, and Ig binding quantification.
Longitudinal analysis revealed that E. coli unbound by IgG and IgA is associated with necrotizing enterocolitis in preterm infants.

Conclusions:

MicFLY provides unprecedented single-cell resolution for quantitative microbiota analysis.
This technology offers deeper mechanistic insights into microbiota compositional changes and host-microbe interactions.
MicFLY application identified a specific bacterial-immune association linked to necrotizing enterocolitis, paving the way for improved diagnostics and therapeutics.