| Title |
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota
|
|---|---|
| Published in |
PLoS Computational Biology, December 2013
|
| DOI | 10.1371/journal.pcbi.1003388 |
| Pubmed ID | |
| Authors |
Richard R. Stein, Vanni Bucci, Nora C. Toussaint, Charlie G. Buffie, Gunnar Rätsch, Eric G. Pamer, Chris Sander, João B. Xavier |
| Abstract |
The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. We present a novel method to infer microbial community ecology directly from time-resolved metagenomics. This method extends generalized Lotka-Volterra dynamics to account for external perturbations. Data from recent experiments on antibiotic-mediated Clostridium difficile infection is analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Stability analysis reveals that the microbiota is intrinsically stable, explaining how antibiotic perturbations and C. difficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, the analysis suggests a subnetwork of bacterial groups implicated in protection against C. difficile. Due to its generality, our method can be applied to any high-resolution ecological time-series data to infer community structure and response to external stimuli. |
X Demographics
The data shown below were collected from the profiles of 30 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 10 | 33% |
| United Kingdom | 3 | 10% |
| Australia | 2 | 7% |
| Norway | 1 | 3% |
| India | 1 | 3% |
| Switzerland | 1 | 3% |
| Finland | 1 | 3% |
| Germany | 1 | 3% |
| Canada | 1 | 3% |
| Other | 1 | 3% |
| Unknown | 8 | 27% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 18 | 60% |
| Scientists | 11 | 37% |
| Practitioners (doctors, other healthcare professionals) | 1 | 3% |
Mendeley readers
The data shown below were compiled from readership statistics for 831 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 25 | 3% |
| Spain | 2 | <1% |
| Switzerland | 2 | <1% |
| France | 2 | <1% |
| Brazil | 2 | <1% |
| Australia | 1 | <1% |
| Chile | 1 | <1% |
| Colombia | 1 | <1% |
| Israel | 1 | <1% |
| Other | 7 | <1% |
| Unknown | 787 | 95% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 232 | 28% |
| Researcher | 163 | 20% |
| Student > Master | 86 | 10% |
| Student > Bachelor | 55 | 7% |
| Student > Doctoral Student | 47 | 6% |
| Other | 126 | 15% |
| Unknown | 122 | 15% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 285 | 34% |
| Biochemistry, Genetics and Molecular Biology | 98 | 12% |
| Immunology and Microbiology | 47 | 6% |
| Engineering | 43 | 5% |
| Environmental Science | 37 | 4% |
| Other | 166 | 20% |
| Unknown | 155 | 19% |