A protocol for characterization of extremely preterm infant gut microbiota in double-blind clinical trials

Magalí Martí; Johanne E. Spreckels; Maria C. Jenmalm; Thomas Abrahamsson

doi:10.1016/j.xpro.2021.100652

A protocol for characterization of extremely preterm infant gut microbiota in double-blind clinical trials

Magalí Martí^*, Johanne E. Spreckels, Maria C. Jenmalm, Thomas Abrahamsson

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

16S rRNA gene sequencing enables microbial community profiling, but recovering fecal DNA from extremely premature infants is challenging. Here, we describe an optimized protocol for fecal DNA isolation, library preparation for 16S rRNA gene sequencing, taxonomy assignation, and statistical analyses. The protocol is complemented with a quantitative PCR for probiotic L. reuteri identification. This protocol describes how to characterize preterm infant gut microbiota and relate it to probiotic supplementation and clinical outcomes. It is customizable for other clinical trials. For complete details on the use and execution of this protocol, please refer to Martí et al. (2021) and Spreckels et al. (2021).

Original language	English
Article number	100652
Number of pages	17
Journal	STAR protocols
Volume	2
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2021.100652
Publication status	Published - 17-Sept-2021

Keywords

Clinical Protocol
Health Sciences
Microbiology
Molecular Biology
Sequencing

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10.1016/j.xpro.2021.100652Licence: CC BY

A protocol for characterization of extremely preterm infant gut microbiota in double-blind clinical trialsFinal publisher's version, 2.15 MBLicence: CC BY

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title = "A protocol for characterization of extremely preterm infant gut microbiota in double-blind clinical trials",

abstract = "16S rRNA gene sequencing enables microbial community profiling, but recovering fecal DNA from extremely premature infants is challenging. Here, we describe an optimized protocol for fecal DNA isolation, library preparation for 16S rRNA gene sequencing, taxonomy assignation, and statistical analyses. The protocol is complemented with a quantitative PCR for probiotic L. reuteri identification. This protocol describes how to characterize preterm infant gut microbiota and relate it to probiotic supplementation and clinical outcomes. It is customizable for other clinical trials. For complete details on the use and execution of this protocol, please refer to Mart{\'i} et al. (2021) and Spreckels et al. (2021).",

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AU - Abrahamsson, Thomas

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AB - 16S rRNA gene sequencing enables microbial community profiling, but recovering fecal DNA from extremely premature infants is challenging. Here, we describe an optimized protocol for fecal DNA isolation, library preparation for 16S rRNA gene sequencing, taxonomy assignation, and statistical analyses. The protocol is complemented with a quantitative PCR for probiotic L. reuteri identification. This protocol describes how to characterize preterm infant gut microbiota and relate it to probiotic supplementation and clinical outcomes. It is customizable for other clinical trials. For complete details on the use and execution of this protocol, please refer to Martí et al. (2021) and Spreckels et al. (2021).

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KW - Molecular Biology

KW - Sequencing

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A protocol for characterization of extremely preterm infant gut microbiota in double-blind clinical trials

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