KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

Area of Science:

• Microbiology
• Environmental Science
• Genomics

Background:

• Analyzing low-biomass microbiomes is challenging due to contamination and low throughput.
• Existing methods often yield inaccurate results from minimal microbial samples.
• Technical constraints limit the study of microbial communities in various environments.

Purpose of the Study:

• To develop and validate KatharoSeq, a high-throughput automated protocol for low-biomass microbiome analysis.
• To assess the protocol's performance in detecting and identifying microbial communities from minimal cell inputs.
• To demonstrate the utility of KatharoSeq in diverse low-biomass environments.

Main Methods:

• Development of KatharoSeq, an automated protocol incorporating positive and negative controls.
• Application of 16S rRNA amplicon and shotgun metagenome sequencing.
• Analysis of samples from a spacecraft assembly facility (SAF), neonatal intensive care unit (NICU), and abalone-rearing facility.

Main Results:

• KatharoSeq outperforms single-tube extractions, processing samples five times faster.
• The protocol accurately identifies bacterial communities from as few as 50 cells.
• Spatially resolved microbiomes were obtained from hundreds of samples across diverse environments, revealing unique community compositions and contaminant sources.

Conclusions:

• KatharoSeq enables feasible and reliable large-scale, low-biomass metagenomic analyses.
• The protocol successfully differentiates true microbial signals from contamination in challenging samples.
• This method opens new avenues for studying under-sampled environments.