Human microbiome cultivation expands with AI

An automated system for picking bacterial colonies is used to create a biobank of personalized microbiomes.

Research on microbiomes is driven today by metagenomic sequencing, but microbial cell culture remains indispensable for obtaining reference genomes and for generating mechanistic and functional insights. Traditional methods for culturing microbes are labor intensive and intrinsically difficult to scale to high numbers of samples and high numbers of isolates per sample. A study in Nature Biotechnology by Huang et al.1 describes an automated process to systematically isolate large numbers of different bacterial taxa present in microbiomes through machine learning analyses of colony morphology. The cultivation workflow represents a substantial advance in the toolkit for exploring microbiome diversity. The authors also provide a publicly available culture biobank of 20 human microbiomes and new assemblies of ~1,200 microbial genomes, providing a rich resource for studying the diversity of individual human microbiomes.

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Fig. 1: Summary of the CAMII workflow for automated and targeted high-throughput culturomics from single microbiome samples.

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Authors and Affiliations

Department CIBIO, University of Trento, Trento, Italy

Marta Selma-Royo, Nicola Segata & Liviana Ricci

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Correspondence to
Nicola Segata.

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The authors declare no competing interests.

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Selma-Royo, M., Segata, N. & Ricci, L. Human microbiome cultivation expands with AI.
Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01852-2

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Published: 22 June 2023

DOI: https://doi.org/10.1038/s41587-023-01852-2

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