Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut

PloS One
Yonatan SherJillian F Banfield

Abstract

Microbes alter their transcriptomic profiles in response to the environment. The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. However, this analysis requires accurate reference genomes to identify the specific genes from which RNA reads originate. In addition, such an analysis should avoid biases in transcript counts related to differences in organism abundance. In this study we describe an approach to address these difficulties. Sample-specific meta-genomic assembled genomes (MAGs) were used as reference genomes to accurately identify the origin of RNA reads, and transcript ratios of genes with opposite transcription responses were compared to eliminate biases related to differences in organismal abundance, an approach hereafter named the "diametric ratio" method. We used this approach to probe the environmental conditions experienced by Escherichia spp. in the gut of 4 premature infants, 2 of whom developed necrotizing enterocolitis (NEC), a severe inflammatory intestinal disease. We analyzed twenty fecal samples taken from four premature infants (4-6 time points from each infant), and fou...Continue Reading

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Citations

Dec 18, 2020·Journal of Pharmaceutical and Biomedical Analysis·Carolin A Kolmeder, Willem M de Vos
Jan 14, 2021·American Journal of Physiology. Gastrointestinal and Liver Physiology·Alain CunaVenkatesh Sampath

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Datasets Mentioned

BETA
PRJNA505710

Methods Mentioned

BETA
RNAseq

Software Mentioned

Cutadapt
Prodigal
UD
R
IDBA
ctbbio
Bowtie2
ggplot2
dRep
DAS tool

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