Microbial interactions: from networks to models

  title={Microbial interactions: from networks to models},
  author={Karoline Faust and Jeroen Raes},
  journal={Nature Reviews Microbiology},
Metagenomics and 16S pyrosequencing have enabled the study of ecosystem structure and dynamics to great depth and accuracy. Co-occurrence and correlation patterns found in these data sets are increasingly used for the prediction of species interactions in environments ranging from the oceans to the human microbiome. In addition, parallelized co-culture assays and combinatorial labelling experiments allow high-throughput discovery of cooperative and competitive relationships between species. In… 

Network analysis methods for studying microbial communities: A mini review

Elucidation of complexity and prediction of interactions in microbial communities

Current methods and approaches are reviewed, both experimental and computational, to elucidate interactions in microbial communities and to predict their responses to perturbations.

Network-based approaches for the investigation of microbial community structure and function using metagenomics-based data.

A perspective on the methods of network construction, interpretation, and emerging uses for these techniques in understanding host-microbiota interactions is provided.

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.

Network analyses in microbiome based on high-throughput multi-omics data

Existing network modelling methods of microbial studies at multiple layers from metagenomics to metabolomics and further to multi-omics are reviewed and existing network theories used in biological and biomedical research are systemically illustrated.

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome

In vitro experimental data validate a key result of a novel methodology to construct a Boolean dynamic model from time series metagenomic information that B. intestinihominis can in fact slow C. difficile growth.

Deciphering microbial community robustness through synthetic ecology and molecular systems synecology.




Comparative Metagenomics of Microbial Communities

This work characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments.

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges.

Some of the different approaches to community profiling are discussed, highlighting strengths and weaknesses of various experimental approaches, sequencing methodologies, and analytical methods and addressing one key question emerging from various Human Microbiome Projects.

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism, and a network generated from these statistical correlations provides new insights into the natural history of microbes.

Using network analysis to explore co-occurrence patterns in soil microbial communities

The potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly is demonstrated.

Competitive and cooperative metabolic interactions in bacterial communities.

An intricate association between competition and cooperation is charted indicating that the cooperative potential is maximized at moderate levels of resource overlap, which is important for the future design of consortia optimized towards bioremediation and bio-production applications.

Molecular eco-systems biology: towards an understanding of community function

Here, the necessary data types that are required to unite molecular microbiology and ecology to develop an understanding of community function are discussed and the potential shortcomings of these approaches are discussed.

A global network of coexisting microbes from environmental and whole-genome sequence data.

A global meta-analysis of previously sampled microbial lineages in the environment is presented, hypothesizing that groupings of lineages are often ancient, and that they may have significantly impacted on genome evolution.

Coherent dynamics and association networks among lake bacterioplankton taxa

Bacteria have important roles in freshwater food webs and in the cycling of elements in the ecosystem. Yet specific ecological features of individual phylogenetic groups and interactions among these