Metagenomic Sequencing of an In Vitro-Simulated Microbial Community
Open accessAbstract
BACKGROUND: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. METHODOLOGY/PRINCIPAL FINDINGS: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. CONCLUSIONS/SIGNIFICANCE: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with different protocols are not suitable for comparative metagenomics.
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Previous detailed investigations of variables such as DNA extraction method, like the present results, enriched for broad classes of Gram-negative rather than Gram-positive bacteria because of technical rather than biological variables.
“Previous detailed investigations of specific variables in microbiome experiments such as DNA extraction method have, in common with the results we report, enriched for broad classes of Gram-negative rather than Gram-positive bacteria due to technical rather than biological variables9, 24, 27, 28.”
From Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium (2017) · cites this paper as [28]
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- Authors
- Morgan, J. L., Darling, A. E., & Eisen, J. A.
- Affiliations
- Joint Genome Institute (US)
- University of California, Davis (US)
- Corresponding author
- Eisen, Jonathan A.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-04-16
- Volume
- 5
- Issue
- 4
- Pages
- e10209
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC2855710
- OpenAlex
- W2073909558
- Cited by
- 248
- References
- 54
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 4 · 2023: 6 · 2022: 11 · 2021: 18 · 2020: 8 · 2019: 7 · 2018: 9 · 2017: 19 · 2016: 10 · 2015: 23 · 2014: 30 · 2013: 37 · 2012: 24
- FWCI
- 11.59
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- University of North Texas Digital Library (University of North Texas) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- UTS ePRESS (University of Technology Sydney) (submittedVersion)
- OPUS - Open Publications of UTS Scholars (University of Technology Sydney) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Lawrence Berkeley National Laboratory
- Funders
- National Science Foundation (DEAC02-05CH11231, 0630765)
- U.S. Department of Energy (-AC02-05CH11231, Contract No. DE-AC02-05-CH11231, 05CH11231, No. DE-AC02-05-CH11231, DE AC02 05CH11231, DE-AC02-)
- Joint Genome Institute (AC02-05CH11231, DE–AC02–05CH11231)
- Office of Science (No. DE-AC02- 05-CH11231, DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231, Contract No. DE-AC02-05CH11231)
- Lawrence Berkeley National Laboratory (AC02‐05CH11231, DE-AC02-05CH11231, No. DE-AC02-05CH11231, Contract No. DE-AC02-05CH11231, 05CH11231)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- metagenomics, synthetic microbial communities, in vitro simulation, metagenome binning, relative abundance estimation, observation bias, DNA extraction methods, sequencing protocols
- MeSH terms
- Biometry, Computer Simulation, DNA, Bacterial, Genome, Bacterial, Sequence Analysis, DNA, Metagenomics
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