Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting

Alessandra Riva, Hamid Rasoulimehrabani, José Manuel Cruz-Rubio, Stephanie L. Schnorr, Cornelia Baeckmann, Deniz Inan, Georgi Nikolov, Craig W. Herbold, Bela Hausmann, Petra Pjevac, Arno Schintlmeister, Andreas Spittler, Márton Palatinszky, Aida Kadunic, Norbert Hieger, Giorgia Del Favero, Martin von Bergen, Nico Jehmlich, Margarete Watzka, Kang Soo Lee, Julia Wiesenbauer, Sanaz Khadem, Helmut Viernstein, Roman Stocker, Michael Wagner, Christina Kaiser, Andreas Richter, Freddy Kleitz and David Berry ()
Additional contact information
Alessandra Riva: University of Vienna
Hamid Rasoulimehrabani: University of Vienna
José Manuel Cruz-Rubio: University of Vienna
Stephanie L. Schnorr: University of Vienna
Cornelia Baeckmann: University of Vienna
Deniz Inan: University of Vienna
Georgi Nikolov: University of Vienna
Craig W. Herbold: University of Vienna
Bela Hausmann: Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna
Petra Pjevac: University of Vienna
Arno Schintlmeister: University of Vienna
Andreas Spittler: Medical University of Vienna
Márton Palatinszky: University of Vienna
Aida Kadunic: University of Vienna
Norbert Hieger: University of Vienna
Giorgia Del Favero: University of Vienna
Martin von Bergen: Helmholtz Centre for Environmental Research, Department of Molecular Systems Biology
Nico Jehmlich: Helmholtz Centre for Environmental Research, Department of Molecular Systems Biology
Margarete Watzka: University of Vienna
Kang Soo Lee: Environmental and Geomatic Engineering, ETH Zurich
Julia Wiesenbauer: University of Vienna
Sanaz Khadem: University of Vienna
Helmut Viernstein: University of Vienna
Roman Stocker: Environmental and Geomatic Engineering, ETH Zurich
Michael Wagner: University of Vienna
Christina Kaiser: University of Vienna
Andreas Richter: University of Vienna
Freddy Kleitz: University of Vienna
David Berry: University of Vienna

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin. 16S rRNA gene amplicon sequencing of sorted cells revealed that the ability to bind inulin was widespread in the microbiota. We further evaluate which taxa are metabolically stimulated by inulin and find that diverse taxa from the phyla Firmicutes and Actinobacteria respond to inulin, and several isolates of these taxa can degrade inulin. Incubation with another prebiotic, xylooligosaccharides (XOS), in contrast, shows a more robust bifidogenic effect. Interestingly, the Coriobacteriia Eggerthella lenta and Gordonibacter urolithinfaciens are indirectly stimulated by the inulin degradation process, expanding our knowledge of inulin-responsive bacteria.

Date: 2023
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DOI: 10.1038/s41467-023-43448-z

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