Computational Modeling of the Human Microbiome.

Shomeek Chowdhury,Stephen S Fong

doi:10.3390/microorganisms8020197

Shomeek Chowdhury, Stephen S Fong

Open Access

https://doi.org/10.3390/microorganisms8020197

Copy DOI

Journal: Microorganisms	Publication Date: Jan 31, 2020
Citations: 21	License type: CC BY 4.0

Affiliation: Virginia Commonwealth University

Abstract

The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.

Highlights

Interest in microorganisms associated with the human body has a long history dating back to the handcrafted microscopes built by Antonie van Leewenhoek in the 1670s, where bacteria in van Leeuwenhoek’s oral and fecal samples were referred to as “animalcules” [1]
Another interesting property people have witnessed in gut microbiomes associated with obesity is energy metabolism [67] where microbiota associated with obesity have the ability to harvest more energy from the diet than in non-obese individuals
People have predicted the function of the nonribosomal peptide synthetase (NRPS) gene that is serine protease inhibition using this method which they found in the cells of a number of gut microbes including E. coli and B. subtilis

Summary

Introduction

Interest in microorganisms associated with the human body has a long history dating back to the handcrafted microscopes built by Antonie van Leewenhoek in the 1670s, where bacteria in van Leeuwenhoek’s oral and fecal samples were referred to as “animalcules” [1]. Shotgun metagenomic sequencing was the first step in this direction where bacteria’s whole genomic DNA from human/environmental samples is analyzed for both species identification and understanding gene function potential of the microbe [12,16] Another example is the HMP Unified Metabolic Analysis Network (HUMAnN) that performs metabolic and functional reconstructions of metagenomic data [17]. Microorganisms 2020, 8, 197 and computational work is properly used collaboratively, there will be identification of the representative species of the human microbiome but of the other unknown species with whom these leader microbes coordinate through vast number of metabolite exchanges [21] Computational analyses such as network analysis, agent-based modeling, and genome scale metabolic modeling (GEM) have used to study various aspects of the human microbiome including structure, dynamics, and coordinated function [22,23,24]. Bringing all of them under one banner will help us to get a holistic view of the global human microbial interactions which can be used in future for the development of effective and novel treatment strategies

Background

High-Throughput Studies

Modeling Methodologies

Perspectives and Future Work

Findings

Conclusions