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Media type:
E-Article
Title:
Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions
Contributor:
Bellais, Samuel;
Nehlich, Mélanie;
Ania, Maryne;
Duquenoy, Aurore;
Mazier, Wilfrid;
van den Engh, Ger;
Baijer, Jan;
Treichel, Nicole Simone;
Clavel, Thomas;
Belotserkovsky, Ilia;
Thomas, Vincent
imprint:
Springer Science and Business Media LLC, 2022
Published in:Microbiome
Language:
English
DOI:
10.1186/s40168-021-01206-7
ISSN:
2049-2618
Origination:
Footnote:
Description:
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>There is a growing interest in using gut commensal bacteria as “next generation” probiotics. However, this approach is still hampered by the fact that there are few or no strains available for specific species that are difficult to cultivate. Our objective was to adapt flow cytometry and cell sorting to be able to detect, separate, isolate, and cultivate new strains of commensal species from fecal material. We focused on the extremely oxygen sensitive (EOS) species<jats:italic>Faecalibacterium prausnitzii</jats:italic>and the under-represented, health-associated keystone species<jats:italic>Christensenella minuta</jats:italic>as proof-of-concept.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>A BD Influx® cell sorter was equipped with a glovebox that covered the sorting area. This box was flushed with nitrogen to deplete oxygen in the enclosure. Anaerobic conditions were maintained during the whole process, resulting in only minor viability loss during sorting and culture of unstained<jats:italic>F. prausnitzii</jats:italic>strains ATCC 27766, ATCC 27768, and DSM 17677. We then generated polyclonal antibodies against target species by immunizing rabbits with heat-inactivated bacteria. Two polyclonal antibodies were directed against<jats:italic>F. prausnitzii</jats:italic>type strains that belong to different phylogroups, whereas one was directed against<jats:italic>C. minuta</jats:italic>strain DSM 22607. The specificity of the antibodies was demonstrated by sorting and sequencing the stained bacterial fractions from fecal material. In addition, staining solutions including LIVE/DEAD™ BacLight™ Bacterial Viability staining and polyclonal antibodies did not severely impact bacterial viability while allowing discrimination between groups of strains. Finally, we combined these staining strategies as well as additional criteria based on bacterial shape for<jats:italic>C. minuta</jats:italic>and were able to detect, isolate, and cultivate new<jats:italic>F. prausnitzii</jats:italic>and<jats:italic>C. minuta</jats:italic>strains from healthy volunteer’s fecal samples.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Targeted cell-sorting under anaerobic conditions is a promising tool for the study of fecal microbiota. It gives the opportunity to quickly analyze microbial populations, and can be used to sort EOS and/or under-represented strains of interest using specific antibodies, thus opening new avenues for culture experiments.</jats:p></jats:sec>