Metagenomic microbial community profiling using unique clade-specific marker genes

By Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh M. Narasimhan, O. Jousson, Curtis Huttenhower. 2012

1,647 citations recorded by the source corpus.

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/.

Subfields: Food Science, Molecular Biology

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Citations in the corpus

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights (2016, background): “The importance of cross-cohort consistency and validation of predictions has also been recognized, with some works assessing the structure of the microbiome in European cohorts [29] and combined European-American cohorts [21, 30].”
Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients (2017, methodology): “Taxonomic composition was performed by using the computational tool MetaPhlAn [15].”
Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract (2015, methodology): “Bacterial species were identified with the MetaPhlAn2 package v.2.0.0.b (Segata et al., 2012).”
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis (2013, methodology): “To determine if the presence or absence of these regions within individuals was consistent between samplings, we applied MetaPhlAn (Segata et al., 2012) to Prevotella-positive HMP samples collected over multiple visits (Figure 3B).”
The Dynamics of the Human Infant Gut Microbiome in Development and in Progression towards Type 1 Diabetes (2015, positive): “Phylogenetic community profiling of metagenomic data was performed using MetaPhlAn (Segata et al., 2012), and functional profiling of microbial pathways was characterized with HUMAnN (Abubucker et al.”
The Placenta Harbors a Unique Microbiome (2014, methodology): “The WGS-based taxonomy profile was generated by MetaPhlAn (53).”