TY - JOUR
T1 - Omnigene-Guttm ensures fecal microbiome stability in the pediatric population
AU - Hoogendijk, Raoull
AU - van den Broek, Thijs J.M.
AU - Lee, Hyunju
AU - Mueller, Sabine
AU - Kline, Cassie
AU - Bianco, John
AU - Top, Janetta
AU - de Zoete, Marcel R.
AU - Kester, Lennart
AU - Calkoen, Friso
AU - van der Lugt, Jasper
N1 - Publisher Copyright:
© The Author(s) 2024.
PY - 2024/12/6
Y1 - 2024/12/6
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85211141443&partnerID=8YFLogxK
U2 - 10.1186/s13568-024-01798-x
DO - 10.1186/s13568-024-01798-x
M3 - Article
C2 - 39641864
AN - SCOPUS:85211141443
SN - 2191-0855
VL - 14
JO - AMB Express
JF - AMB Express
IS - 1
M1 - 132
ER -