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

Sher, Yonatan; Olm, Matthew R.; Raveh-Sadka, Tali; Brown, Christopher T.; Sher, Ruth; Firek, Brian; Baker, Robyn; Morowitz, Michael J.; Banfield, Jillian F.

doi:10.1371/journal.pone.0229537

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

Journal Article · Wed Mar 04 00:00:00 EST 2020 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0229537· OSTI ID:1631619

^[1]; Olm, Matthew R. ^[1]; Raveh-Sadka, Tali ^[1]; Brown, Christopher T. ^[1]; Sher, Ruth ^[2]; Firek, Brian ^[3]; Baker, Robyn ^[4]; Morowitz, Michael J. ^[5]; Banfield, Jillian F. ^[1]

Univ. of California, Berkeley, CA (United States)
Enview, Inc., San Francisco, CA (United States)
Univ. of Pittsburgh, PA (United States). School of Medicine
Magee-Womens Hospital of UPMC, Pittsburgh, PA (United States)
Univ. of Pittsburgh, PA (United States). School of Medicine; Magee-Womens Hospital of UPMC, Pittsburgh, PA (United States)

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 found significantly higher diametric ratios of genes associated with low oxygen levels in samples of infants later diagnosed with NEC than in samples without NEC. We also show this method can be used for examining other physiological conditions, such as exposure to nitric oxide and osmotic pressure. These study results should be treated with caution, due to the presence of confounding factors that might also distinguish between NEC and control infants. Nevertheless, together with benchmarking analyses, we show here that the diametric ratio approach can be applied for evaluating the physiological conditions experienced by microbes in situ. Results from similar studies can be further applied for designing diagnostic methods to detect NEC in its early developmental stages.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); March of Dimes Foundation; USDA

Grant/Contract Number:: AC02-05CH11231; 5-FY10-103; 2016-67012-24717

OSTI ID:: 1631619

Journal Information:: PLoS ONE, Vol. 15, Issue 3; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 5 works

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