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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.
Microbial interactions: from networks to models
This Review describes how metagenomics and 16S pyrosequencing techniques are opening the way towards global ecosystem network prediction and the development of ecosystem-wide dynamic models.
Microbial Co-occurrence Relationships in the Human Microbiome
- Karoline Faust, J. Sathirapongsasuti, C. Huttenhower
- Biology, Environmental SciencePLoS Comput. Biol.
- 1 July 2012
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.
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.
Population-level analysis of gut microbiome variation
Stool consistency showed the largest effect size, whereas medication explained largest total variance and interacted with other covariate-microbiota associations, and proposed disease marker genera associated to host covariates were found associated to microbiota compositional variation with a 92% replication rate.
CoNet app: inference of biological association networks using Cytoscape
The Cytoscape app version of the association network inference tool CoNet, designed to be generic and can detect associations in any data set where biological entities have been observed repeatedly, is presented.
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
This work benchmarks the performance of eight correlation techniques on simulated and real data in response to challenges specific to microbiome studies: fractional sampling of ribosomal RNA sequences, uneven sampling depths, rare microbes and a high proportion of zero counts.
Computational approaches to predict bacteriophage–host relationships
- R. Edwards, Katelyn McNair, Karoline Faust, J. Raes, B. Dutilh
- BiologyFEMS microbiology reviews
- 9 December 2015
Analysis of 820 phages with annotated hosts shows how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications.
From hairballs to hypotheses–biological insights from microbial networks
The need for robust microbial network inference is highlighted and strategies to infer networks more reliably are suggested and shown in a simulation how network properties are affected by tool choice and environmental factors.
Determinants of community structure in the global plankton interactome
It is found that environmental factors are incomplete predictors of community structure and associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns.