Omnigene-Guttm ensures fecal microbiome stability in the pediatric population

Raoull Hoogendijk*, Thijs J.M. van den Broek, Hyunju Lee, Sabine Mueller, Cassie Kline, John Bianco, Janetta Top, Marcel R. de Zoete, Lennart Kester, Friso Calkoen, Jasper van der Lugt*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

Increasing evidence exists that the gut microbiome influences toxicity as well as outcomes in a variety of cancers. To investigate the role of the gut microbiome in pediatric neuro-oncology, microbiome analysis has been included in multiple prospective pediatric neuro-oncology clinical trials (NCT05009992, NCT04732065, NCT04775485). In these trials, the OMNIgene-GUTtm preservation tubes are used for the collection of the feces. OMNIgene-GUTtm has demonstrated reliability in preserving the composition of the gut microbiome in adults; however, its validation for use in the pediatric population remains limited. Therefore, we compared the quality of the DNA by 16S rRNA gene sequencing after various methods of stabilizing fecal samples in pediatric populations, from the direct freeze method at − 80 °C to preserving samples with OMNIgene-GUTtm at room temperature for various durations. Our results showed that there were no statistically significant differences between the alpha-diversity, and beta-diversity. However, pairwise differential abundance analyses demonstrated that OMNIgene-GUT™ is superior in maintaining microbial community structure compared to storing samples without any preservation method. With the OMNIgene-GUTtm’s stabilization of the fecal samples being superior and its ease-of-use benefits, it proves to be a valid and ideal method of stabilizing fecal samples for current and future pediatric clinical trials.

Original languageEnglish
Article number132
JournalAMB Express
Volume14
Issue number1
DOIs
Publication statusPublished - 6 Dec 2024

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