A Graph-Based Molecular Communications Model Analysis of the Human Gut Bacteriome

Alterations in the human gut bacteriome can be associated with human health issues, such as type-2 diabetes and cardiovascular disease. Both external and internal factors can drive changes in the composition and in the interactions of the human gut bacteriome, impacting negatively on the host cells. In this paper, we focus on the human gut bacteriome metabolism and we propose a two-layer network system to investigate its dynamics. Furthermore, we develop an in-silico simulation model (virtual GB), allowing us to study the impact of the metabolite exchange through molecular communications in the human gut bacteriome network system. Our results show that the regulation of molecular inputs can strongly affect bacterial population growth and create an unbalanced network, as shown by the shift in the node weights based on the molecular signals that are produced. Additionally, we show that the metabolite molecular communication production is greatly affected when directly manipulating the composition of the human gut bacteriome network in the virtual GB. These results indicate that our human GB interaction model can help to identify hidden behaviors of the human gut bacteriome depending on the molecular signal interactions. Moreover, the virtual GB can support the research and development of novel medical treatments based on the accurate control of bacterial growth and exchange of metabolites.

[1]  Elena Deza,et al.  Encyclopedia of Distances , 2014 .

[2]  Ian F. Akyildiz,et al.  Molecular Communication Noise and Capacity Analysis for Particulate Drug Delivery Systems , 2014, IEEE Transactions on Communications.

[3]  M. Díaz,et al.  Microbial amensalism in Lactobacillus casei and Pseudomonas taetrolens mixed culture , 2017, Bioprocess and Biosystems Engineering.

[4]  Murat Kuscu,et al.  Transmitter and Receiver Architectures for Molecular Communications: A Survey on Physical Design With Modulation, Coding, and Detection Techniques , 2019, Proceedings of the IEEE.

[5]  H. Ali,et al.  A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships , 2019, BMC Genomics.

[6]  D. van Sinderen,et al.  Bifidobacteria and Their Role as Members of the Human Gut Microbiota , 2016, Front. Microbiol..

[7]  A. Duffy,et al.  Factors Influencing the Gut Microbiota, Inflammation, and Type 2 Diabetes. , 2017, The Journal of nutrition.

[8]  M. A. Henson,et al.  Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis , 2017, BMC Systems Biology.

[9]  F. Shanahan,et al.  Feeding the microbiota: transducer of nutrient signals for the host , 2017, Gut.

[10]  K. Shimizu.  Metabolic Regulation of a Bacterial Cell System with Emphasis on Escherichia coli Metabolism , 2013, ISRN biochemistry.

[11]  Andrew W. Eckford,et al.  A Comprehensive Survey of Recent Advancements in Molecular Communication , 2014, IEEE Communications Surveys & Tutorials.

[12]  H. Tilg,et al.  Translating the gut microbiome: ready for the clinic? , 2019, Nature Reviews Gastroenterology & Hepatology.

[13]  C. Mayer,et al.  Whole-Genome Transcription Profiling Reveals Genes Up-Regulated by Growth on Fucose in the Human Gut Bacterium “Roseburia inulinivorans” , 2006, Journal of bacteriology.

[14]  E. Allen-Vercoe,et al.  Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health , 2019, Microbiome.

[15]  Sasitharan Balasubramaniam,et al.  Using Competing Bacterial Communication to Disassemble Biofilms , 2016, NANOCOM.

[16]  Rob Knight,et al.  Regional variation limits applications of healthy gut microbiome reference ranges and disease models , 2018, Nature Medicine.

[17]  Minoru Kanehisa,et al.  Toward understanding the origin and evolution of cellular organisms , 2019, Protein science : a publication of the Protein Society.

[18]  Minoru Kanehisa,et al.  KEGG: integrating viruses and cellular organisms , 2020, Nucleic Acids Res..

[19]  Massimiliano Pierobon,et al.  Detection Techniques for Diffusion-based Molecular Communication , 2013, IEEE Journal on Selected Areas in Communications.

[20]  T. Spector,et al.  Interplay between the human gut microbiome and host metabolism , 2019, Nature Communications.

[21]  Pan-Jun Kim,et al.  Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis , 2017, Nature Communications.

[22]  Massimiliano Pierobon,et al.  Moving Forward With Molecular Communication: From Theory to Human Health Applications , 2019, Proc. IEEE.

[23]  Rob Knight,et al.  Defining the human microbiome. , 2012, Nutrition reviews.

[24]  Barbara M. Bakker,et al.  The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism , 2013, Journal of Lipid Research.

[25]  Thomas E. Gorochowski,et al.  BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology , 2012, PloS one.

[26]  Frédéric Leroy,et al.  Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut , 2016, Front. Microbiol..

[27]  T. Lesker,et al.  Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation , 2020, Mucosal Immunology.

[28]  T. Preston,et al.  Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism , 2016, Gut microbes.

[29]  Jingyuan Fu,et al.  Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases , 2019, Nature Genetics.

[30]  R. Talukdar,et al.  Role of the normal gut microbiota. , 2015, World journal of gastroenterology.

[31]  M. Wong,et al.  Landscapes of bacterial and metabolic signatures and their interaction in major depressive disorders , 2020, Science Advances.

[32]  U. Günther,et al.  Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn’s disease and healthy individuals , 2014, Metabolomics.

[33]  A. Bernalier-Donadille,et al.  H2 and acetate transfers during xylan fermentation between a butyrate-producing xylanolytic species and hydrogenotrophic microorganisms from the human gut. , 2006, FEMS microbiology letters.

[34]  Junling Shi,et al.  Interaction between diet composition and gut microbiota and its impact on gastrointestinal tract health , 2017 .

[35]  Jason A. Papin,et al.  Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome , 2015, PLoS Comput. Biol..

[36]  W. Liao,et al.  Influence of diet on the gut microbiome and implications for human health , 2017, Journal of Translational Medicine.

[37]  Ian F. Akyildiz,et al.  The Impact of Social Behavior on the Attenuation and Delay of Bacterial Nanonetworks , 2016, IEEE Transactions on NanoBioscience.

[38]  J. Gordon,et al.  Commensal Host-Bacterial Relationships in the Gut , 2001, Science.

[39]  I. Thiele,et al.  Gut microbiota functions: metabolism of nutrients and other food components , 2017, European Journal of Nutrition.

[40]  J. Sung,et al.  A predictive index for health status using species-level gut microbiome profiling , 2020, Nature Communications.