Metagenomic microbial community profiling using unique clade-specific marker genes
Open accessAbstract
Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large data sets. We present an approach that uses clade-specific marker genes to unambiguously assign reads to microbial clades more accurately and >50× faster than current approaches. We validated our metagenomic phylogenetic analysis tool, MetaPhlAn, on terabases of short reads and provide the largest metagenomic profiling to date of the human gut. It can be accessed at http://huttenhower.sph.harvard.edu/metaphlan/.
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A metagenomic check of six gut and six oral artificial community samples, profiled with MetaPhlAn2 and compared with 16S amplicon abundances, supported the expected ground truth and confirmed protocol variability even for low-complexity communities.
“this experiment supported the expected ground truth and further confirmed the variability of laboratory and bioinformatics protocols when reading out even these low-complexity communities.”
From Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium (2017) · cites this paper as [22]
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Self-citation
- Authors
- Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C.
- Affiliations
- Harvard University (US)
- University of Trento (IT)
- Corresponding author
- Huttenhower, Curtis
- Venue
- Nature Methods
- Published
- 2012-06-10
- Volume
- 9
- Issue
- 8
- Pages
- 811-814
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC3443552
- OpenAlex
- W2131026689
- Semantic Scholar
- 9375edf4fffa6738280e6d684917f4b7ee95e8da
- Cited by
- 1,776
- References
- 37
- Citations by year
- 2026: 47 · 2025: 79 · 2024: 95 · 2023: 107 · 2022: 209 · 2021: 224 · 2020: 206 · 2019: 145 · 2018: 133 · 2017: 123 · 2016: 144 · 2015: 114 · 2014: 88 · 2013: 47 · 2012: 10
- FWCI
- 33.32
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Iris (University of Trento) (submittedVersion)
- Funders
- National Human Genome Research Institute (R01HG005969)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- MetaPhlAn, microbial community analysis, taxonomic profiling, shotgun sequencing, human gut microbiome, microbial identification
- MeSH terms
- Bacteria, Genetic Markers, Humans, Phylogeny, Reproducibility of Results, Metagenomics
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