Metagenomic systems biology and metabolic modeling of the human microbiome

  title={Metagenomic systems biology and metabolic modeling of the human microbiome},
  author={Roie Levy and Elhanan Borenstein},
  journal={Gut Microbes},
  pages={265 - 270 - 9}
The human microbiome is a key contributor to health and development. Yet little is known about the ecological forces that are at play in defining the composition of such host-associated communities. Metagenomics-based studies have uncovered clear patterns of community structure but are often incapable of distinguishing alternative structuring paradigms. In a recent study, we integrated metagenomic analysis with a systems biology approach, using a reverse ecology framework to model numerous… 
Computational Modeling of the Human Microbiome
By providing an overview of different human microbiome sites, this work hopes 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.
Fitness effects of host-bacterial interactions – the microbial perspective
It is found that rare microbiome members are essential for achieving the observed community composition, which ultimately sets the maximum carrying capacity.
Microbial Species Coexistence Depends on the Host Environment
Both microbial species can only stably coexist in the host environment, whereas Duganella outcompetes Curvibacter in both in vitro environments irrespective of initial starting frequencies, which indicates that rare microbial community members might be relevant for achieving the native community composition and carrying capacity.
RevEcoR: an R package for the reverse ecology analysis of microbiomes
RevEcoR, an R package and a Shiny Web application that implements the reverse ecology algorithm for determining microbe–microbe interactions in microbial communities allows users to obtain large-scale ecological insights into species’ ecology directly from high-throughput metagenomic data.
Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome
Significance Deep molecular phenotyping of individuals provides the opportunity for biological insight into host physiology. As the human microbiome is increasingly being recognized as an important
Mapping the InnerWorkings of theMicrobiome : Genomic-andMetagenomic-BasedStudyofMetabolism andMetabolic Interactions in the HumanMicrobiome
Two interrelated lines of work are highlighted, the first aiming to deconvolve the microbiome and to characterize the metabolic capacity of various microbiome species and the second aiming to utilize computational modeling to infer and study metabolic interactions between these species.
NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome
This article presents nasal community modeling workflow (NCMW)—a python package based on GEMs of species as a starting point for understanding the composition of the nasal microbiome community, constructed as a step-by-step mathematical framework for metabolic modeling and analysis of the nose microbial community.


Computational systems biology and in silico modeling of the human microbiome
The pressing need for the development of predictive system- level models and for a system-level understanding of the microbiome is highlighted, and potential computational frameworks for metagenomic-based modeling of the microbiota at the cellular, ecological and supra-organismal level are discussed.
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
A system-level approach lays the foundation for a unique framework for studying the human microbiome, its organization, and its impact on human health, by integrating metagenomic data with an in silico systems-level analysis of metabolic networks.
A framework for human microbiome research
Resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times are presented, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far.
The Application of Ecological Theory Toward an Understanding of the Human Microbiome
This work explores three core scenarios of human microbiome assembly: development in infants, representing assembly in previously unoccupied habitats; recovery from antibiotics, representingassembly after disturbance; and invasion by pathogens, representingAssembly in the context of invasive species.
Structure, Function and Diversity of the Healthy Human Microbiome
The Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far, finding the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals.
Understanding the interactions between bacteria in the human gut through metabolic modeling
This work reconstructed GEMs for three key species, (Bacteroides thetaiotamicron, Eubacterium rectale and Methanobrevibacter smithii) as relevant representatives of three main phyla in the human gut and demonstrated that these models can be used as a scaffold for understanding bacterial interactions in the gut.
Microbial Co-occurrence Relationships in the Human Microbiome
An ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomic marker (16S rRNA gene) profiles of this cohort resulted in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome.
Bacterial colonization factors control specificity and stability of the gut microbiota
These findings reveal that intestinal Bacteroides have evolved species-specific physical interactions with the host that mediate stable and resilient gut colonization, and the CCF system represents a novel molecular mechanism for symbiosis.