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Uncovering oral Neisseria tropism and persistence using metagenomic sequencing

Nature Microbiology volume 1, Article number: 16070 (2016) Cite this article

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Abstract

Microbial epidemiology and population genomics have previously been carried out near-exclusively for organisms grown in vitro. Metagenomics helps to overcome this limitation, but it is still challenging to achieve strain-level characterization of microorganisms from culture-independent data with sufficient resolution for epidemiological modelling. Here, we have developed multiple complementary approaches that can be combined to profile and track individual microbial strains. To specifically profile highly recombinant neisseriae from oral metagenomes, we integrated four metagenomic analysis techniques: single nucleotide polymorphisms in the clade's core genome, DNA uptake sequence signatures, metagenomic multilocus sequence typing and strain-specific marker genes. We applied these tools to 520 oral metagenomes from the Human Microbiome Project, finding evidence of site tropism and temporal intra-subject strain retention. Although the opportunistic pathogen Neisseria meningitidis is enriched for colonization in the throat, N. flavescens and N. subflava populate the tongue dorsum, and N. sicca, N. mucosa and N. elongata the gingival plaque. The buccal mucosa appeared as an intermediate ecological niche between the plaque and the tongue. The resulting approaches to metagenomic strain profiling are generalizable and can be extended to other organisms and microbiomes across environments.

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Figure 1: The phylogenetic structure of the family Neisseriaceae identifies well-defined subtrees of closely related species.
Figure 2: Biogeographical patterns of oral Neisseria strain colonization identified using metagenomic SNP calling.
Figure 3: Metagenomically inferred multilocus sequence types of oral neisseriae from the HMP data set segregate into three main body site clusters.
Figure 4: Characterization of N. sicca strain clusters using genetic polymorphisms and genomic variants from multiple subjects and body site metagenomes.
Figure 5: Persistent subject-specific, site-specific and strain-specific colonization by neisseriae identified using longitudinal metagenomic core genome SNP and genomic marker analyses.

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Acknowledgements

The authors acknowledge the Human Microbiome Project Consortium and the generous participation of individuals from the Saint Louis (MO) and Houston (TX) areas who made the Human Microbiome Project possible. This work was supported in part by NIH grants R01HG005969 and U54DE023798, NSF grant DBI-1053486 and Army Research Office grant W911NF-11-1-0473 to C.H., and a European Union FP7 Marie-Curie grant (PCIG13-618833), MIUR grant FIR RBFR13EWWI, Fondazione Caritro grant Rif.Int.2013.0239, CIBIO Start-up funds and Terme di Comano grants to N.S.

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Authors and Affiliations

  1. Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010 San Michele All'adige, Italy

    Claudio Donati & Davide Albanese

  2. Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy

    Moreno Zolfo, Duy Tin Truong, Francesco Asnicar, Olivier Jousson & Nicola Segata

  3. Department of Public Health and Infectious Diseases, Institute Pasteur Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Roma, Italy

    Valerio Iebba

  4. Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy

    Duccio Cavalieri

  5. Institute of Biometeorology, National Research Council (IBIMET-CNR), Via Caproni 8, 50145 Firenze, Italy

    Duccio Cavalieri & Carlotta De Filippo

  6. Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115, USA

    Curtis Huttenhower

  7. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    Curtis Huttenhower

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  1. Claudio Donati
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Contributions

C.D. and N.S. conceived the study, implemented the software and performed the analyses. M.Z., D.A., D.T.T., F.A., V.I. and C.H. contributed to the analyses. D.C., O.J., C.D.F. and C.H. provided feedback and contributed to the writing. C.D., C.H. and N.S. wrote the manuscript.

Corresponding authors

Correspondence to Claudio Donati or Nicola Segata.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1–20, legends for Supplementary Tables 1–4, Supplementary Tables 5 and 6 and Supplementary References. (PDF 2969 kb)

Supplementary Table 1

List of the genomes from the Neisseriaceae families. considered in this work. (XLSX 18 kb)

Supplementary Table 2

DNA uptake sequences (DUS) from 241 genomes of Neisseriaceae family members. (XLSX 185 kb)

Supplementary Table 3

Clustering of the metagenomic samples and the genomic sequences of the reference strains obtained by performing a discriminant analysis of principal components. (XLSX 17 kb)

Supplementary Table 4

DNA uptake sequences (DUS) from the oral metagenomes. (XLSX 449 kb)

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Donati, C., Zolfo, M., Albanese, D. et al. Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nat Microbiol 1, 16070 (2016). https://doi.org/10.1038/nmicrobiol.2016.70

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