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Bioinformatics. 2015 Jun 15;31(12):i142-50. doi: 10.1093/bioinformatics/btv251.

Deconvolving molecular signatures of interactions between microbial colonies.

Author information

1
Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA.
2
Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA, Department of Biology, University of North Carolina, Chapel Hill, NC 27599-32800, USA, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA and Curriculum of Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA.

Abstract

MOTIVATION:

The interactions between microbial colonies through chemical signaling are not well understood. A microbial colony can use different molecules to inhibit or accelerate the growth of other colonies. A better understanding of the molecules involved in these interactions could lead to advancements in health and medicine. Imaging mass spectrometry (IMS) applied to co-cultured microbial communities aims to capture the spatial characteristics of the colonies' molecular fingerprints. These data are high-dimensional and require computational analysis methods to interpret.

RESULTS:

Here, we present a dictionary learning method that deconvolves spectra of different molecules from IMS data. We call this method MOLecular Dictionary Learning ( MOLDL: ). Unlike standard dictionary learning methods which assume Gaussian-distributed data, our method uses the Poisson distribution to capture the count nature of the mass spectrometry data. Also, our method incorporates universally applicable information on common ion types of molecules in MALDI mass spectrometry. This greatly reduces model parameterization and increases deconvolution accuracy by eliminating spurious solutions. Moreover, our method leverages the spatial nature of IMS data by assuming that nearby locations share similar abundances, thus avoiding overfitting to noise. Tests on simulated datasets show that this method has good performance in recovering molecule dictionaries. We also tested our method on real data measured on a microbial community composed of two species. We confirmed through follow-up validation experiments that our method recovered true and complete signatures of molecules. These results indicate that our method can discover molecules in IMS data reliably, and hence can help advance the study of interaction of microbial colonies.

AVAILABILITY AND IMPLEMENTATION:

The code used in this paper is available at: https://github.com/frizfealer/IMS_project.

PMID:
26072476
PMCID:
PMC4765860
DOI:
10.1093/bioinformatics/btv251
[Indexed for MEDLINE]
Free PMC Article

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