Novel strain-level resolution of Crohn’s disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing
| Autor: | Seungha Kang, Jingwan Zhang, Emily C. Hoedt, Fen Zhang, Jessica Y.L. Ching, Erwin Berendsen, Michael A. Kamm, Jun Yu, Mark Morrison, Amy L. Hamilton, S. C. Ng, Joseph J.Y. Sung, Jing-Jie Teh, Amy Wilson-O'Brien, Qin Liu |
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| Rok vydání: | 2021 |
| Předmět: |
Virulence
Microbiology Genome Article 03 medical and health sciences 0302 clinical medicine Crohn Disease Humans Clinical microbiology Axenic Gene Ecology Evolution Behavior and Systematics 030304 developmental biology Genetics 0303 health sciences Mucous Membrane biology Microbiota Strain (biology) Ribosomal RNA Amplicon biology.organism_classification Metagenomics Next-generation sequencing Metagenome 030211 gastroenterology & hepatology Microbiome Biomarkers |
| Zdroj: | The ISME Journal |
| ISSN: | 1751-7370 1751-7362 |
| DOI: | 10.1038/s41396-021-00991-1 |
| Popis: | The mucosa-associated microbiota is widely recognized as a potential trigger for Crohn’s disease pathophysiology but remains largely uncharacterised beyond its taxonomic composition. Unlike stool microbiota, the functional characterisation of these communities using current DNA/RNA sequencing approaches remains constrained by the relatively small microbial density on tissue, and the overwhelming amount of human DNA recovered during sample preparation. Here, we have used a novel ex vivo approach that combines microbe culture from anaerobically preserved tissue with metagenome sequencing (MC-MGS) to reveal patient-specific and strain-level differences among these communities in post-operative Crohn’s disease patients. The 16 S rRNA gene amplicon profiles showed these cultures provide a representative and holistic representation of the mucosa-associated microbiota, and MC-MGS produced both high quality metagenome-assembled genomes of recovered novel bacterial lineages. The MC-MGS approach also produced a strain-level resolution of key Enterobacteriacea and their associated virulence factors and revealed that urease activity underpins a key and diverse metabolic guild in these communities, which was confirmed by culture-based studies with axenic cultures. Collectively, these findings using MC-MGS show that the Crohn’s disease mucosa-associated microbiota possesses taxonomic and functional attributes that are highly individualistic, borne at least in part by novel bacterial lineages not readily isolated or characterised from stool samples using current sequencing approaches. |
| Databáze: | OpenAIRE |
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