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Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities

  • Microbial Systematics and Evolutionary Microbiology
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Abstract

The study of the human gut microbiome is essential in microbiology and infectious diseases as specific alterations in the gut microbiome might be associated with various pathologies, such as chronic inflammatory disease, intestinal infection and colorectal cancer. To identify such dysregulations, several strategies are being used to create a repertoire of the microorganisms composing the human gut microbiome. In this study, we used the “microscomics” approach, which consists of creating an ultrastructural repertoire of all the cell-like objects composing stool samples from healthy donors using transmission electron microscopy (TEM). We used TEM to screen ultrathin sections of 8 resin-embedded stool samples. After exploring hundreds of micrographs, we managed to elaborate ultrastructural categories based on morphological criteria or features. This approach explained many inconsistencies observed with other techniques, such as metagenomics and culturomics. We highlighted the value of our culture-independent approach by comparing our microscopic images to those of cultured bacteria and those reported in the literature. This study helped to detect “minimicrobes” Candidate Phyla Radiation (CPR) for the first time in human stool samples. This “microscomics” approach is non-exhaustive but complements already existing approaches and adds important data to the puzzle of the microbiota.

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Acknowledgments

This work has benefited from the French State support, managed by the ‘Agence Nationale pour la Recherche’, including the “Programme d’Investissement d’avenir” under the reference Méditerranée Infection 10-IAHU-03.

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Authors and Affiliations

  1. IRD, AP-HM, MEPHI, VITROME, IHU Méditerranée Infection, Aix Marseille Univ., Marseille, France

    Edmond Kuete Yimagou, Jean-Pierre Baudoin, Rita Abou Abdallah, Fabrizio Di Pinto & Didier Raoult

  2. Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France

    Jacques Yaacoub Bou Khalil

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  1. Edmond Kuete Yimagou
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  2. Jean-Pierre Baudoin
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  3. Rita Abou Abdallah
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  4. Fabrizio Di Pinto
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  5. Jacques Yaacoub Bou Khalil
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  6. Didier Raoult
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Contributions

Study concept and design: EK, JPB, JB. Acquisition of data: EK, JPB, FDP, CV. Analysis and interpretation of data: JPB, EK, RAA. Drafting of the manuscript: EK, JPB, JB. Critical revision of the manuscript for important intellectual content: JPB, JB, DR. All authors read and approved the final manuscript.

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Correspondence to Jacques Yaacoub Bou Khalil or Didier Raoult.

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The authors declare that they have no competing interests.

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Yimagou, E.K., Baudoin, JP., Abdallah, R.A. et al. Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities. J Microbiol. 58, 377–386 (2020). https://doi.org/10.1007/s12275-020-9365-3

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