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Total RNA Sequencing reveals microbial communities in human blood and disease specific effects

Serghei Mangul, Loes M Olde Loohuis, Anil P Ori, Guillaume Jospin, David Koslicki, Harry Taegyun Yang, Timothy Wu, Marco P Boks, Catherine Lomen-Hoerth, Wiedau-Pazos Martina, Rita M Cantor, Willem M de Vos, René S Kahn, Eleazar Eskin, Roel A Ophoff
doi: https://doi.org/10.1101/057570
Serghei Mangul
1Department of Computer Science, University of California Los Angeles, Los Angeles, USA
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Loes M Olde Loohuis
2Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, USA
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Anil P Ori
2Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, USA
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Guillaume Jospin
3Davis Genome Center, University of California, Davis, USA
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David Koslicki
4Mathematics Department, Oregon State University, Corvallis, USA
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Harry Taegyun Yang
1Department of Computer Science, University of California Los Angeles, Los Angeles, USA
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Timothy Wu
2Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, USA
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Marco P Boks
5Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
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Catherine Lomen-Hoerth
6Department of Neurology, University of California San Francisco, San Francisco, USA
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Wiedau-Pazos Martina
7Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
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Rita M Cantor
8Department of Human Genetics, University of California Los Angeles, Los Angeles, USA
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Willem M de Vos
9Laboratory of Microbiology, Wageningen University, Ede, The Netherlands
10Department of Bacteriology and Immunology, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
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René S Kahn
5Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
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Eleazar Eskin
1Department of Computer Science, University of California Los Angeles, Los Angeles, USA
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Roel A Ophoff
2Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, USA
5Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
8Department of Human Genetics, University of California Los Angeles, Los Angeles, USA
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  • For correspondence: ophoff@ucla.edu
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Abstract

An increasing body of evidence suggests an important role of the human microbiome in health and disease. We propose a ‘lost and found’ pipeline, which examines high quality unmapped sequence reads for microbial taxonomic classification. Using this pipeline, we are able to detect bacterial and archaeal phyla in blood using RNA sequencing (RNA-Seq) data. Careful analyses, including the use of positive and negative control datasets, suggest that these detected phyla represent true microbial communities in whole blood and are not due to contaminants. We applied our pipeline to study the composition of microbial communities present in blood across 192 individuals from four subject groups: schizophrenia (n=48), amyotrophic lateral sclerosis (n=47), bipolar disorder (n=48) and healthy controls (n=49). We observe a significantly increased microbial diversity in schizophrenia compared to the three other groups and replicate this finding in an independent schizophrenia case-control study. Our results demonstrate the potential use of total RNA to study microbes that inhabit the human body.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 07, 2016.
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Total RNA Sequencing reveals microbial communities in human blood and disease specific effects
Serghei Mangul, Loes M Olde Loohuis, Anil P Ori, Guillaume Jospin, David Koslicki, Harry Taegyun Yang, Timothy Wu, Marco P Boks, Catherine Lomen-Hoerth, Wiedau-Pazos Martina, Rita M Cantor, Willem M de Vos, René S Kahn, Eleazar Eskin, Roel A Ophoff
bioRxiv 057570; doi: https://doi.org/10.1101/057570
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Total RNA Sequencing reveals microbial communities in human blood and disease specific effects
Serghei Mangul, Loes M Olde Loohuis, Anil P Ori, Guillaume Jospin, David Koslicki, Harry Taegyun Yang, Timothy Wu, Marco P Boks, Catherine Lomen-Hoerth, Wiedau-Pazos Martina, Rita M Cantor, Willem M de Vos, René S Kahn, Eleazar Eskin, Roel A Ophoff
bioRxiv 057570; doi: https://doi.org/10.1101/057570

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