Single-cell detection and quantification of the microbiota by MicFLY.

MicFLY enables precise single-cell quantification of intestinal microbiota at species-level resolution, revealing key immune interactions and disease associations in preterm infants.

• Why it matters: Current microbiome studies mainly measure relative abundance, limiting understanding of actual bacterial dynamics and their role in health and disease. Accurate, absolute measurements are needed to uncover mechanisms behind microbiota shifts and related conditions like necrotizing enterocolitis (NEC).
• What they did: The team developed MicFLY, a flow cytometry-based method that quantifies individual bacterial cells, distinguishes live/dead bacteria, measures mRNA expression, and detects immunoglobulin binding, applied to a cohort of preterm infants.
• The result: Findings show that increases in IgA- and IgG-unbound bacteria from Enterobacteriaceae are linked to NEC development, demonstrating MicFLY’s potential to advance mechanistic insights and improve disease prediction.