Next-generation sequencing as a clinical laboratory tool for describing different microbiotas: an urgent need for future paediatric practice

• Published in: Archives of disease in childhood 2021-10, Vol.106 (10), p.1035-1035
• Main Authors: Hansen, Richard, Bajaj-Elliott, Mona, Hold, Georgina L, Gerasimidis, Konstantinos, Iqbal, Tariq H, Amos, Gregory, Thomas, Linda V, Marchesi, Julian R
• Format: Article
• Language: English
• Subjects: Bacteria; Celiac disease; Children; Colorectal cancer; Community Relations; Crohn's disease; Enteral nutrition; Gastroenterology; Genetic testing; Genetics; Hematopoietic stem cells; Laboratories; Medical laboratories; Metagenomics; Microbial activity; microbiology; Microbiomes; Microbiota; Molecular Biology; Next-generation sequencing; Nutrition; Nutrition research; Pediatrics; PostScript; rRNA 16S; Stem cell transplantation; Stem cells; Viremia
• ISSN: 0003-9888; 1468-2044
• DOI: 10.1136/archdischild-2021-321683

Correspondence to Dr Richard Hansen, Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow G514TF, UK; [e-mail] We read with interest the editorial by Baralle and Ismail exploring the utility of next-generation sequencing in paediatric clinical genetics.1 The other major use of this technology, which has emerged over the last decade, is in cataloguing complex microbial communities, for instance the different human microbiomes. Briefly, two main approaches are used to identify and describe bacterial communities using next-generation sequencing: amplicon sequencing (metataxonomics) and metagenomics.2 Amplicon sequencing relies on PCR amplification of a single bacterial ‘housekeeping’ gene (the 16S rRNA gene) which is considered ubiquitous but helpfully contains both highly conserved and variable regions across species. [...]a reduction in 11 different bacteria in faeces from children with coeliac disease are specific to that disease state;3 a distinct faecal bacterial cluster described in children postallogenic haematopoietic stem cell transplantation confers distinct prognostic outcomes in terms of subsequent viraemia episodes (unpublished data from author MBE); and exploration of microbiota changes during exclusive enteral nutrition treatment for Crohn’s disease4 has led directly to the development of new solid food approaches to treating the condition.5 If we are to embrace the diagnostic, prognostic and therapeutic revolution offered to us by a greater understanding of the microbiome, there is an urgent need to integrate microbiome analysis into clinical practice.