Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that – in many cases – adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future

Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data

Modulation of interspecies interactions by the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method termed the Minimal Interspecies Interaction Adjustment (MIIA) that predicts the reorganization of interaction networks in response to the addition of new species such that the modulation in interaction coefficients caused by additional members is minimal. While the theoretical basis of MIIA was established through the previous work by assuming the full availability of species abundance data in axenic, binary, and complex communities, its extension to actual microbial ecology can be highly constrained in cases that species have not been cultured axenically (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients – basic parameters required for implementing the MIIA – are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only data from axenic cultures are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, in the case where both axenic and binary populations are missing, we parameterize binary interaction coefficients to determine their values through a sensitivity analysis. Through the case study of two microbial communities with distinct characteristics and complexity (i.e., a three-member community where all members can grow independently, and a four-member community that contains member species whose growth is dependent on other species), we demonstrated that despite data limitation, the proposed new formulation was able to successfully predict interspecies interactions that are consistent with experimentally derived results. Therefore, this technical advancement enhances our ability to predict context-dependent interspecies interactions in a broad range of microbial systems without being limited to specific growth conditions as a pre-requisite

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries using Sparse Linear Regression

Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the interactions between species from sequence data. Any algorithm for inferring species interactions must overcome three obstacles: 1) a correlation between the abundances of two species does not imply that those species are interacting, 2) the sum constraint on the relative abundances obtained from metagenomic studies makes it difficult to infer the parameters in timeseries models, and 3) errors due to experimental uncertainty, or mis-assignment of sequencing reads into operational taxonomic units, bias inferences of species interactions. Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. We tested LIMITS on synthetic data and showed that it could reliably infer the topology of the inter-species ecological interactions. We then used LIMITS to characterize the species interactions in the gut microbiomes of two individuals and found that the interaction networks varied significantly between individuals. Furthermore, we found that the interaction networks of the two individuals are dominated by distinct "keystone species", Bacteroides fragilis and Bacteroided stercosis, that have a disproportionate influence on the structure of the gut microbiome even though they are only found in moderate abundance. Based on our results, we hypothesize that the abundances of certain keystone species may be responsible for individuality in the human gut microbiome

Dead-end filtration of yeast suspensions: correlating specific resistance and flux data using artificial neural networks

The specific cake resistance in dead-end filtration is a complex function of suspension properties and operating conditions. In this study, the specific resistance of resuspended dried bakers yeast suspensions was measured in a series of 150 experiments covering a range of pressures, cell concentrations, pHs, ionic strengths and membrane resistances. The specific resistance was found to increase linearly with pressure and exhibited a complex dependence on pH and ionic strength. The specific resistance data were correlated using an artificial neural network containing a single hidden layer with nine neurons employing the sigmoidal activation function. The network was trained with 104 training points, 13 validation points and 33 test points. Excellent agreement was obtained between the neural network and the test data with average errors of less than 10%. In addition, a network was trained for prediction of the filtrate flux directly from the system inputs and this approach is easily extended to crossflow filtration by adding inputs such as the crossflow velocity and channel height. An attempt was made to interpret the network weights for both the specific resistance and flux networks. The effective contribution of each input to the system output was computed in each case and showed trends that were as expected. Although network weights, and consequently the computed effect of each parameter, is different each time a network is changed (depending on the initial weights used in the training process), the variation was low enough for information contained in the network to be interpreted in a meaningful way

Arctic in Rapid Transition (ART) : science plan

The Arctic is undergoing rapid transformations that have brought the Arctic Ocean to the top of international political agendas. Predicting future conditions of the Arctic Ocean system requires scientific knowledge of its present status as well as a process-based understanding of the mechanisms of change. The Arctic in Rapid Transition (ART) initiative is an integrative, international, interdisciplinary pan-Arctic program to study changes and feedbacks among the physical and biogeochemical components of the Arctic Ocean and their ultimate impacts on biological productivity. The goal of ART is to develop priorities for Arctic marine science over the next decade. Three overarching questions form the basis of the ART science plan: (1) How were past transitions in sea ice connected to energy flows, elemental cycling, biological diversity and productivity, and how do these compare to present and projected shifts? (2) How will biogeochemical cycling respond to transitions in terrestrial, gateway and shelf-to-basin fluxes? (3) How do Arctic Ocean organisms and ecosystems respond to environmental transitions including temperature, stratification, ice conditions, and pH? The integrated approach developed to answer the ART key scientific questions comprises: (a) process studies and observations to reveal mechanisms, (b) the establishment of links to existing monitoring programs, (c) the evaluation of geological records to extend time-series, and (d) the improvement of our modeling capabilities of climate-induced transitions. In order to develop an implementation plan for the ART initiative, an international and interdisciplinary workshop is currently planned to take place in Winnipeg, Canada in October 2010

Microbial and metabolic succession on common building materials under high humidity conditions.

Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material