Lab fix removes hidden contamination from microbe-sorting experiments
Goethals V, Vanwinsen N, Mermans F, De Gand S, Boon N
Soil Health
The soil microbes that help your tomatoes fight disease or your compost break down faster are studied using exactly this kind of sorting technology, so a cleaner method means more reliable science behind the soil amendments and biofertilizers that eventually reach garden shelves.
Researchers use a machine called a flow cytometer to pick out individual microbes from samples like soil or water, then sequence their DNA to figure out who's there. The problem: the fluid the machine uses to sort cells was sneaking in its own contaminating DNA, skewing the results. The team figured out how to detect and digitally remove that contamination, plus found the best way to store samples so the microbes stay intact for accurate sorting.
Key Findings
Sheath fluid used during cell sorting introduced contaminating DNA (termed the 'FACSome') that distorted microbial community profiles
A new in silico decontamination method successfully removed this contamination across soil, water, feces, saliva, and gut reactor samples using PacBio and Illumina sequencing
Sorting depleted 97% of 'relic' (leftover, non-living) DNA, and fecal samples stored at -80°C without glycerol cryoprotectant best preserved intact cells for accurate sorting
chevron_right Technical Summary
Scientists found that a popular lab technique for sorting individual microbes from soil, water, or gut samples was accidentally contaminating the results with stray DNA from its own equipment. They built a fix that filters out this contamination, making it possible to trust results when studying which specific microbes are active in an environment.
Abstract Preview
Original paper
An optimized flow cytometry sorting-sequencing workflow reduces storage, sorting, and extraction bias in sorted microbial communities.
Fluorescence-activated cell sorting (FACS) followed by metataxonomics is commonly used to probe the composition of microbial subpopulations with a functionality of interest. Metataxonomic analysis ...
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Microbiome methods encompass the laboratory and computational techniques used to characterize the complex communities of bacteria, fungi, and other microorganisms that inhabit plant tissues, roots, and the surrounding soil. Understanding these microbial communities is critical for plant science
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