Uncovering microbial duality within human microbiomes: A novel algorithm for the analysis of host-pathogen interactions

Microbial species thrive within human hosts by establishing complex associations between themselves and the host. Even though species diversity can be measured (alpha- and beta-diversity), a methodology to estimate the impact of microorganisms in human pathways is still lacking. In this work we propose a computational approach to estimate which human pathways are targeted the most by microorganisms, while also identifying which microorganisms are prominent in this targeting. Our results were consistent with literature evidence, and thus we propose this methodology as a new prospective approach to be used for screening potentially impacted pathways.

[1]  Y. Aso,et al.  Prophylactic effect of a Lactobacillus casei preparation on the recurrence of superficial bladder cancer. BLP Study Group. , 1992, Urologia internationalis.

[2]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[3]  E. Lundberg,et al.  Towards a knowledge-based Human Protein Atlas , 2010, Nature Biotechnology.

[4]  Niklas Söderholm,et al.  Lactobacillus Decelerates Cervical Epithelial Cell Cycle Progression , 2013, PloS one.

[5]  V. Tremaroli,et al.  Functional interactions between the gut microbiota and host metabolism , 2012, Nature.

[6]  José Luís Oliveira,et al.  Computational prediction of the human-microbial oral interactome , 2014, BMC Systems Biology.

[7]  Yoshinori Sugiyama,et al.  Activation of TLR2 Enhances Tight Junction Barrier in Epidermal Keratinocytes , 2011, The Journal of Immunology.

[8]  M. Blaser,et al.  The human microbiome: at the interface of health and disease , 2012, Nature Reviews Genetics.

[9]  Raquel Seruca,et al.  Helicobacter pylori infection generates genetic instability in gastric cells. , 2010, Biochimica et biophysica acta.

[10]  R. Knight,et al.  The human microbiome project: exploring the microbial part of ourselves in a changing world , 2022 .

[11]  Richard J Lamont,et al.  The degree of microbiome complexity influences the epithelial response to infection , 2009, BMC Genomics.

[12]  Chun-Ming Huang,et al.  Commensal bacteria regulate TLR3-dependent inflammation following skin injury , 2009, Nature Medicine.

[13]  C. B. Pickett,et al.  Regulatory mechanisms controlling gene expression mediated by the antioxidant response element. , 2003, Annual review of pharmacology and toxicology.

[14]  Giri Narasimhan,et al.  Distinct transcriptional profiles characterize oral epithelium‐microbiota interactions , 2005, Cellular microbiology.

[15]  D. Žgur-Bertok,et al.  DNA Damage Repair and Bacterial Pathogens , 2013, PLoS pathogens.

[16]  José Luís Oliveira,et al.  From protein-protein interactions to rational drug design: are computational methods up to the challenge? , 2013, Current topics in medicinal chemistry.

[17]  H. Tlaskalova-Hogenova.  Faculty Opinions recommendation of Commensal bacteria regulate Toll-like receptor 3-dependent inflammation after skin injury. , 2010 .

[18]  Henning Hermjakob,et al.  The Reactome pathway Knowledgebase , 2015, Nucleic acids research.

[19]  Gabriel Renaud,et al.  A diversity profile of the human skin microbiota. , 2008, Genome research.

[20]  Mike Tyers,et al.  BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..

[21]  Y. Gu,et al.  Cross-talk between the Aryl Hydrocarbon Receptor and Hypoxia Inducible Factor Signaling Pathways , 1999, The Journal of Biological Chemistry.

[22]  Masahira Hattori,et al.  The Human Intestinal Microbiome: A New Frontier of Human Biology , 2009, DNA research : an international journal for rapid publication of reports on genes and genomes.

[23]  J. Nicholson,et al.  Host-Gut Microbiota Metabolic Interactions , 2012, Science.

[24]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[25]  Allen F Ryan,et al.  Activation of TLR2 by a small molecule produced by Staphylococcus epidermidis increases antimicrobial defense against bacterial skin infections. , 2010, The Journal of investigative dermatology.