Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome

Luca Masucci, Giovanni Cammarota, Gianluca Ianiro, Brunella Posteraro, Maurizio Sanguinetti, Giovanni Battista Gasbarrini, Antonio Gasbarrini, Claudio Durán, Sara Ciucci, Alessandra Palladini, Umer Z. Ijaz, Antonio G. Zippo, Pirjo Spuul, Michael Schroeder, Stephan W. Grill, Bryony N. Parsons, D. Mark Pritchard, Carlo Vittorio Cannistraci

Risultato della ricerca: Contributo in rivistaArticolo in rivista

1 Citazioni (Scopus)

Abstract

The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in early phase and rely principally on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques with nonlinear ones to unveil hidden patterns that remain unseen by linear embedding. Then, we prove the advantages to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of bacterial network re-organizations which emerge from perturbations induced by a medical treatment (PPIs) or an infectious state (H. pylori). Finally, we show how to build bacteria-metabolite multilayer networks that can deepen our understanding of the metabolite pathways significantly associated to the perturbed microbial communities.
Lingua originaleEnglish
pagine (da-a)1926-1926
Numero di pagine1
RivistaNature Communications
Volume12
DOI
Stato di pubblicazionePubblicato - 2021

Keywords

  • Bacteria
  • Gastrointestinal Microbiome
  • Helicobacter Infections
  • Helicobacter pylori
  • Humans
  • Machine Learning
  • Microbiota
  • Population Dynamics
  • Proton Pump Inhibitors
  • RNA, Ribosomal, 16S
  • Stomach

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