Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions

Abstract

Background 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 Faecalibacterium prausnitzii and the under-represented, health-associated keystone species Christensenella minuta as proof-of-concept. Results 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 F. prausnitzii 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 F. prausnitzii type strains that belong to different phylogroups, whereas one was directed against C. minuta 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 C. minuta and were able to detect, isolate, and cultivate new F. prausnitzii and C. minuta strains from healthy volunteer’s fecal samples. Conclusions 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.

Emodin modulates gut microbial community and triggers intestinal immunity

“…We also observed that Faecalibacterium could not grow as a monoculture in GAM but that it was abundantly detected in co‐culture. Regarding monocultures, previous results indicated that Faecalibacterium growth was strongly stimulated in the presence of acetate 35 or that it could grow in GAM supplemented with bovine rumen, cellobiose, and inulin 36 . These findings indicate that this bacterium benefits from interaction with other bacteria included in the synthetic gut microbial consortium.…”

Immunomagnetic Capture of Faecalibacterium prausnitzii Selectively Modifies the Fecal Microbiota and Its Immunomodulatory Profile

“…Therefore, we postulate that such methodologies could be implemented in standard microbiology laboratories. This is a remarkable advantage compared with methods using fluorescence-activated cell sorting, some of which have already been reported in the literature ( 46 ). Second, our method allows the study of host-microbiota interactions from a completely new perspective: by depleting/enriching specific populations in the microbiota, we can infer their role within the community.…”

Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle

“…In the present study, we established an integrated low-cost method compared with Raman-activated cell sorting [ 34 ] and flow cytometry [ 35 ] that allowed for the enrichment and isolation of rumen ureolytic bacteria. This method allowed for the enrichment of ureolytic bacteria, embedding and then allowing the growth of single bacterial cells in agarose microspheres, selection of those that carry urease genes (the bacteria of our interest), and incubation of the selected urease gene-carrying individual strains in dialysis bags placed in rumen-simulating conditions.…”