Dataset Information

Uncertainty quantification of the effects of biotic interactions on community dynamics from nonlinear time-series data.

ABSTRACT: Biotic interactions are expected to play a major role in shaping the dynamics of ecological systems. Yet, quantifying the effects of biotic interactions has been challenging due to a lack of appropriate methods to extract accurate measurements of interaction parameters from experimental data. One of the main limitations of existing methods is that the parameters inferred from noisy, sparsely sampled, nonlinear data are seldom uniquely identifiable. That is, many different parameters can be compatible with the same dataset and can generalize to independent data equally well. Hence, it is difficult to justify conclusive assertions about the effect of biotic interactions without information about their associated uncertainty. Here, we develop an ensemble method based on model averaging to quantify the uncertainty associated with the effect of biotic interactions on community dynamics from non-equilibrium ecological time-series data. Our method is able to detect the most informative time intervals for each biotic interaction within a multivariate time series and can be easily adapted to different regression schemes. Overall, this novel approach can be used to associate a time-dependent uncertainty with the effect of biotic interactions. Moreover, because we quantify uncertainty with minimal assumptions about the data-generating process, our approach can be applied to any data for which interactions among variables strongly affect the overall dynamics of the system.

SUBMITTER: Cenci S

PROVIDER: S-EPMC6228481 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Publications

Uncertainty quantification of the effects of biotic interactions on community dynamics from nonlinear time-series data.

Cenci Simone S Saavedra Serguei S

Journal of the Royal Society, Interface 20181031 147

Biotic interactions are expected to play a major role in shaping the dynamics of ecological systems. Yet, quantifying the effects of biotic interactions has been challenging due to a lack of appropriate methods to extract accurate measurements of interaction parameters from experimental data. One of the main limitations of existing methods is that the parameters inferred from noisy, sparsely sampled, nonlinear data are seldom uniquely identifiable. That is, many different parameters can be compa ...[more]

PMID: 30381342

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Project description:The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention.

Project description:BACKGROUND:New technologies have given rise to an abundance of -omics data, particularly metabolomic data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring the development of innovative computational visualization methodologies. Here, we present GEM-Vis, an original method for the visualization of time-course metabolomic data within the context of metabolic network maps. We demonstrate the utility of the GEM-Vis method by examining previously published data for two cellular systems-the human platelet and erythrocyte under cold storage for use in transfusion medicine. RESULTS:The results comprise two animated videos that allow for new insights into the metabolic state of both cell types. In the case study of the platelet metabolome during storage, the new visualization technique elucidates a nicotinamide accumulation that mirrors that of hypoxanthine and might, therefore, reflect similar pathway usage. This visual analysis provides a possible explanation for why the salvage reactions in purine metabolism exhibit lower activity during the first few days of the storage period. The second case study displays drastic changes in specific erythrocyte metabolite pools at different times during storage at different temperatures. CONCLUSIONS:The new visualization technique GEM-Vis introduced in this article constitutes a well-suitable approach for large-scale network exploration and advances hypothesis generation. This method can be applied to any system with data and a metabolic map to promote visualization and understand physiology at the network level. More broadly, we hope that our approach will provide the blueprints for new visualizations of other longitudinal -omics data types. The supplement includes a comprehensive user's guide and links to a series of tutorial videos that explain how to prepare model and data files, and how to use the software SBMLsimulator in combination with further tools to create similar animations as highlighted in the case studies.

Dataset Information

Uncertainty quantification of the effects of biotic interactions on community dynamics from nonlinear time-series data.

Publications

Uncertainty quantification of the effects of biotic interactions on community dynamics from nonlinear time-series data.

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