Detection of multi-dimensional co-exclusion patterns in microbial communities

Levent Albayrak, Kamil Khanipov, George Golovko, Yuriy Fofanov

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Motivation: Identification of complex relationships among members of microbial communities is key to understand and control the microbiota. Co-exclusion is arguably one of the most important patterns reflecting micro-organisms' intolerance to each other's presence. Knowing these relations opens an opportunity to manipulate microbiotas, personalize anti-microbial and probiotic treatments as well as guide microbiota transplantation. The co-exclusion pattern however, cannot be appropriately described by a linear function nor its strength be estimated using covariance or (negative) Pearson and Spearman correlation coefficients. This manuscript proposes a way to quantify the strength and evaluate the statistical significance of co-exclusion patterns between two, three or more variables describing a microbiota and allows one to extend analysis beyond micro-organism abundance by including other microbiome associated measurements such as, pH, temperature etc., as well as estimate the expected numbers of false positive co-exclusion patterns in a co-exclusion network.

Results: The implemented computational pipeline (CoEx) tested against 2380 microbial profiles (samples) from The Human Microbiome Project resulted in body-site specific pairwise co-exclusion patterns.

Availability and implementation: C++ source code for calculation of the score and P-value for two, three and four dimensional co-exclusion patterns as well as source code and executable files for the CoEx pipeline are available at https://scsb.utmb.edu/labgroups/fofanov/co-exclusion_in_microbial_communities.asp.

Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)3695-3701
Number of pages7
JournalBioinformatics (Oxford, England)
Volume34
Issue number21
DOIs
StatePublished - Nov 1 2018

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Microbiota
Pipelines
Bioinformatics
Microorganisms
Availability
Transplantation
Statistical Significance
Probiotics
Viperidae
Computational Biology
C++
False Positive
Correlation coefficient
Linear Function
Temperature
Community
Pairwise
Quantify
Evaluate
Estimate

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Detection of multi-dimensional co-exclusion patterns in microbial communities. / Albayrak, Levent; Khanipov, Kamil; Golovko, George; Fofanov, Yuriy.

In: Bioinformatics (Oxford, England), Vol. 34, No. 21, 01.11.2018, p. 3695-3701.

Research output: Contribution to journalArticle

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