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Caveat fermentor

The microbiome field gets four doses of self-reflection

Four papers published this quarter have called out caveats in translational microbiome research, and proposed solutions to improve experimental design in the field. The papers identified hurdles in characterizing microbiome-phenotype relationships, quantifying microbiotic load, choosing the right diet in animal studies and reproducing microbial analyses.

The collective push for more causative, quantitative, standardized and reproducible microbiome analyses is good news for a sprawling field trying to create therapies based on a new modality that has little precedent in drug development and an unknown set of rules.

The most recent study, published last week in Nature, highlighted the limitations of typical approaches that use correlations to link gut microbes to disease, and proposed a method to triangulate microbe-phenotype relationships.

A second Nature study, published in November, argued that to link microbial analyses to other quantitative measurements, the field should switch from monitoring ratios of bacterial species to absolute counts, and described a method involving both amplicon

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