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| Status |
Public on May 25, 2016 |
| Title |
Total RNA Sequencing reveals microbial communities in human blood and disease specific effects |
| Organism |
human blood metagenome |
| Experiment type |
Other
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| Summary |
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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| Overall design |
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)
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| Contributor(s) |
Mangul S, Olde Loohuis LM, Ori AP, Jospin G, Koslicki D, Yang H, Wu T, Boks MP, Lomen-Hoerth C, Wiedau-Pazos M, Cantor RM, de Vos WM, Kahn RS, Eisen JA, Eskin E, Ophoff RA |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
May 02, 2016 |
| Last update date |
May 27, 2016 |
| Contact name |
Harry Taegyun Yang |
| E-mail(s) |
harry2416@gmail.com
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| Organization name |
University of California, Los Angeles
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| Department |
Computer Science
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| Lab |
Eleazar Eskin Lab
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| Street address |
Engineering VI 286
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (1) |
| GPL21801 |
Illumina Hiseq 2000 (human blood metagenome) |
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| Samples (192)
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| Relations |
| BioProject |
PRJNA320217 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE80974_RAW.tar |
1.7 Gb |
(http)(custom) |
TAR (of FASTQ) |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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