scholarly journals Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics

2020 ◽  
Vol 6 (1) ◽  
pp. 123-135
Author(s):  
Susana Martínez Arbas ◽  
Shaman Narayanasamy ◽  
Malte Herold ◽  
Laura A. Lebrun ◽  
Michael R. Hoopmann ◽  
...  
Keyword(s):  
Time Series ◽  
Community Dynamics ◽  
Time Series Data ◽  
Microbial Consortium ◽  
Control Strategies ◽  
Treatment Plant ◽  
Series Data ◽  
Dynamic Interactions ◽  
Microbial Community Dynamics ◽  
Host Interaction

AbstractViruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR–Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid–host and phage–host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant ‘Candidatus Microthrix parvicella’ population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.

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

2018 ◽  
Vol 15 (147) ◽  
pp. 20180695 ◽  
Author(s):  
Simone Cenci ◽  
Serguei Saavedra
Keyword(s):  
Time Series ◽  
Community Dynamics ◽  
Time Series Data ◽  
Multivariate Time Series ◽  
Model Averaging ◽  
Biotic Interactions ◽  
Series Data ◽  
Time Intervals ◽  
Novel Approach ◽  
Data Generating Process

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.

scholarly journals Inferring phage-bacteria infection networks from time series data

2016 ◽  
Author(s):  
Luis F. Jover ◽  
Justin Romberg ◽  
Joshua S. Weitz
Keyword(s):  
Time Series ◽  
Time Course ◽  
Community Dynamics ◽  
Time Series Data ◽  
Plaque Assay ◽  
Interaction Network ◽  
Series Data ◽  
Factors Affecting ◽  
Evolutionary Changes

In communities with bacterial viruses (phage) and bacteria, the phage-bacteria infection network establishes which virus types infects which host types. The structure of the infection network is a key element in understanding community dynamics. Yet, this infection network is often difficult to ascertain. Introduced over 60 years ago, the plaque assay remains the gold-standard for establishing who infects whom in a community. This culture-based approach does not scale to environmental samples with increased levels of phage and bacterial diversity, much of which is currently unculturable. Here, we propose an alternative method of inferring phage-bacteria infection networks. This method uses time series data of fluctuating population densities to estimate the complete interaction network without having to test each phage-bacteria pair individually. We use in silico experiments to analyze the factors affecting the quality of network reconstruction and find robust regimes where accurate reconstructions are possible. In addition, we present a multi-experiment approach where time series from different experiments are combined to improve estimates of the infection network and mitigate against the possibility of evolutionary changes to infection during the time-course of measurement.

scholarly journals Inferring phage–bacteria infection networks from time-series data

2016 ◽  
Vol 3 (11) ◽  
pp. 160654 ◽  
Author(s):  
Luis F. Jover ◽  
Justin Romberg ◽  
Joshua S. Weitz
Keyword(s):  
Time Series ◽  
Time Course ◽  
Community Dynamics ◽  
Time Series Data ◽  
Plaque Assay ◽  
Interaction Network ◽  
Series Data ◽  
Factors Affecting ◽  
Evolutionary Changes

In communities with bacterial viruses (phage) and bacteria, the phage–bacteria infection network establishes which virus types infect which host types. The structure of the infection network is a key element in understanding community dynamics. Yet, this infection network is often difficult to ascertain. Introduced over 60 years ago, the plaque assay remains the gold standard for establishing who infects whom in a community. This culture-based approach does not scale to environmental samples with increased levels of phage and bacterial diversity, much of which is currently unculturable. Here, we propose an alternative method of inferring phage–bacteria infection networks. This method uses time-series data of fluctuating population densities to estimate the complete interaction network without having to test each phage–bacteria pair individually. We use in silico experiments to analyse the factors affecting the quality of network reconstruction and find robust regimes where accurate reconstructions are possible. In addition, we present a multi-experiment approach where time series from different experiments are combined to improve estimates of the infection network. This approach also mitigates against the possibility of evolutionary changes to relevant phenotypes during the time course of measurement.

scholarly journals Constructing the Microbial Association Network from Large-Scale Time Series Data Using Granger Causality

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 216 ◽  
Author(s):  
Dongmei Ai ◽  
Xiaoxin Li ◽  
Gang Liu ◽  
Xiaoyi Liang ◽  
Li Xia
Keyword(s):  
Time Series ◽  
Microbial Community ◽  
Granger Causality ◽  
Large Scale ◽  
Community Dynamics ◽  
Time Series Data ◽  
Series Data ◽  
Association Network ◽  
Causal Relationships ◽  
Network Analyses

The increasing availability of large-scale time series data allows the inference of microbial community dynamics by association network analysis. However, correlation-based association network analyses are noninformative of causal, mediating and time-dependent relationships between microbial community functional factors. To address this insufficiency, we introduced the Granger causality model to the analysis of a recent marine microbial time series dataset. We systematically constructed a directed acyclic network, representing both internal and external causal relationships among the microbial and environmental factors. We further optimized the network by removing false causal associations using the conditional Granger causality. The final network was visualized as a Granger graph, which was analyzed to identify causal relationships driven by key functional operators in the environment, such as Gammaproteobacteria, which was Granger caused by total organic nitrogen and primary production (p < 0.05 and Q < 0.05).

Impact of the As Samra wastewater treatment plant upgrade on the water quality (COD, electrical conductivity, TP, TN) of the Zarqa River

2013 ◽  
Vol 67 (7) ◽  
pp. 1455-1464 ◽  
Author(s):  
A. Al-Omari ◽  
Z. Al-houri ◽  
R. Al-Weshah
Keyword(s):  
Water Quality ◽  
Electrical Conductivity ◽  
Time Series ◽  
Wastewater Treatment ◽  
Time Series Data ◽  
Wastewater Reuse ◽  
Treatment Plant ◽  
Series Data ◽  
Before And After ◽  
Zarqa River

The impact of the As Samra wastewater treatment plant upgrade on the quality of the Zarqa River (ZR) water was investigated. Time series data that extend from October 2005 until December 2009 obtained by a state-of-the-art telemetric monitoring system were analyzed at two monitoring stations located 4 to 5 km downstream of the As Samra effluent confluence with the Zarqa River and about 25 km further downstream. Time series data that represent the ZR water quality before and after the As Samra upgrade were analyzed for chemical oxygen demand (COD), electrical conductivity (EC), total phosphorus (TP) and total nitrogen (TN). The means of the monitored parameters, before and after the As Samra upgrade, showed that the reductions in the COD, TP and TN were statistically significant, while no reduction in the EC was observed. Comparing the selected parameters with the Jordanian standards for reclaimed wastewater reuse in irrigation and with the Ayers & Westcot guidelines for interpretation of water quality for irrigation showed that the ZR water has improved towards meeting the required standards and guidelines for treated wastewater reuse in irrigation.

scholarly journals Time-series analysis of monthly age-specific numbers of newly registered cases of active tuberculosis in Japan from 1998 to 2013

2016 ◽  
Vol 144 (11) ◽  
pp. 2401-2414 ◽  
Author(s):  
Y. KOHEI ◽  
A. SUMI ◽  
N. KOBAYASHI
Keyword(s):  
Time Series ◽  
Time Series Analysis ◽  
Time Series Data ◽  
Least Squares Method ◽  
Control Strategies ◽  
Age Groups ◽  
Series Data ◽  
Age Group ◽  
Series Analysis ◽  
Winter Temperatures

SUMMARYWe investigated the seasonality of age-specific tuberculosis (TB) in Japan. To allow the development of TB control strategies for different age groups we used a time-series analysis, including a spectral analysis and least squares method, to analyse the monthly age-specific numbers of newly registered cases of all forms of active TB in Japan from January 1998 to December 2013. The time-series data are reported in 10-year age groups: 0–9, 10–19, …, 70–79, and ⩾80 years. We defined the contribution ratio of the 1-year cycle, Q1, as the contribution of the amplitude of a 1-year cycle to the whole amplitude of the time-series data. The Q1 values in the age groups corresponding to adolescence and middle life (10–39 years) and old age (⩾70 years) were high. The peaks in the active TB epidemics for the ⩾70 years age group occurred in August and September, 1–2 months behind the peaks for the 10–39 years age group (June and July). An active TB epidemic might be attributable to travel by public transport and irregular employment in the 10–39 years age group and immune system suppression by low winter temperatures in the ⩾70 years age group.

Graphical Exploratory Data Analysis for Categorical Longitudinal and Time Series Data

2013 ◽  
Author(s):  
Stephen J. Tueller ◽  
Richard A. Van Dorn ◽  
Georgiy Bobashev ◽  
Barry Eggleston
Keyword(s):  
Time Series ◽  
Data Analysis ◽  
Exploratory Data Analysis ◽  
Time Series Data ◽  
Series Data ◽  
Exploratory Data

Faktor-Faktor Yang Mempengaruhi Nilai Tukar Dollar Amerika Serikat Terhadap Rupiah Tahun 2000–2013

2017 ◽  
Vol 1 (2) ◽  
pp. 177-191
Author(s):  
Rizki Rahma Kusumadewi ◽  
Wahyu Widayat
Keyword(s):  
Time Series ◽  
Exchange Rate ◽  
Money Supply ◽  
Time Series Data ◽  
The United States ◽  
Economic Conditions ◽  
Series Data ◽  
Arch Model ◽  
United States Dollar ◽  
The Exchange Rate

Exchange rate is one tool to measure a country’s economic conditions. The growth of a stable currency value indicates that the country has a relatively good economic conditions or stable. This study has the purpose to analyze the factors that affect the exchange rate of the Indonesian Rupiah against the United States Dollar in the period of 2000-2013. The data used in this study is a secondary data which are time series data, made up of exports, imports, inflation, the BI rate, Gross Domestic Product (GDP), and the money supply (M1) in the quarter base, from first quarter on 2000 to fourth quarter on 2013. Regression model time series data used the ARCH-GARCH with ARCH model selection indicates that the variables that significantly influence the exchange rate are exports, inflation, the central bank rate and the money supply (M1). Whereas import and GDP did not give any influence.

An Anomaly Detection Method with Exemplar Subsequence for Time Series Data

2016 ◽  
Vol 136 (3) ◽  
pp. 363-372
Author(s):  
Takaaki Nakamura ◽  
Makoto Imamura ◽  
Masashi Tatedoko ◽  
Norio Hirai
Keyword(s):  
Time Series ◽  
Anomaly Detection ◽  
Time Series Data ◽  
Detection Method ◽  
Series Data
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