دورية أكاديمية
Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing
| العنوان: | Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing |
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| المؤلفون: | Philipp Spohr, Sebastian Scharf, Anna Rommerskirchen, Birgit Henrich, Paul Jäger, Gunnar W. Klau, Rainer Haas, Alexander Dilthey, Klaus Pfeffer |
| المصدر: | Scientific Reports, Vol 14, Iss 1, Pp 1-20 (2024) |
| بيانات النشر: | Nature Portfolio, 2024. |
| سنة النشر: | 2024 |
| المجموعة: | LCC:Medicine LCC:Science |
| مصطلحات موضوعية: | Microbiome stability, Whole-genome sequencing (WGS), Metagenomics, Bacteriome, Mycobiome, Archaeome, Medicine, Science |
| الوصف: | Abstract The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 2045-2322 |
| العلاقة: | https://doaj.org/toc/2045-2322Test |
| DOI: | 10.1038/s41598-024-53506-1 |
| الوصول الحر: | https://doaj.org/article/bc1831a5d0a443df95e8b2486f09c558Test |
| رقم الانضمام: | edsdoj.bc1831a5d0a443df95e8b2486f09c558 |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 20452322 |
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| DOI: | 10.1038/s41598-024-53506-1 |