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Review

State of the Art in the Culture of the Human Microbiota: New Interests and Strategies

Maryam Tidjani Alou, Sabrina Naud, Saber Khelaifia, Marion Bonnet, Jean-Christophe Lagier, Didier Raoult
Maryam Tidjani Alou
aAix-Marseille Université, IRD, MEPHI, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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Sabrina Naud
aAix-Marseille Université, IRD, MEPHI, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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Saber Khelaifia
aAix-Marseille Université, IRD, MEPHI, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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Marion Bonnet
aAix-Marseille Université, IRD, MEPHI, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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Jean-Christophe Lagier
aAix-Marseille Université, IRD, MEPHI, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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Didier Raoult
aAix-Marseille Université, IRD, MEPHI, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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  • ORCID record for Didier Raoult
DOI: 10.1128/CMR.00129-19
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SUMMARY

The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization–time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.

FOOTNOTES

    • Published 28 October 2020.
  • Supplemental material is available online only.

  • Copyright © 2020 American Society for Microbiology.

All Rights Reserved.

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State of the Art in the Culture of the Human Microbiota: New Interests and Strategies
Maryam Tidjani Alou, Sabrina Naud, Saber Khelaifia, Marion Bonnet, Jean-Christophe Lagier, Didier Raoult
Clinical Microbiology Reviews Oct 2020, 34 (1) e00129-19; DOI: 10.1128/CMR.00129-19

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State of the Art in the Culture of the Human Microbiota: New Interests and Strategies
Maryam Tidjani Alou, Sabrina Naud, Saber Khelaifia, Marion Bonnet, Jean-Christophe Lagier, Didier Raoult
Clinical Microbiology Reviews Oct 2020, 34 (1) e00129-19; DOI: 10.1128/CMR.00129-19
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  • Top
  • Article
    • SUMMARY
    • INTRODUCTION
    • NEW STRATEGIES TO ISOLATE BACTERIA FROM HUMAN MICROBIOTA
    • NEW STRATEGIES TO ISOLATE ARCHAEA FROM HUMAN MICROBIOTA
    • NEW STRATEGIES TO CULTURE EUKARYOTES FROM HUMAN MICROBIOTA
    • BACTERIOTHERAPY APPLIED TO THE TREATMENT OF CERTAIN PATHOLOGIES
    • PERSPECTIVES
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
    • Author Bios
  • Figures & Data
  • Info & Metrics
  • PDF

KEYWORDS

culture strategies
human microbiota
bacteria
archaea
Fungi
culturomics

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