mixOmics: An R package for ‘omics feature selection and multiple data integration

PLoS Computational Biology, Journal Year: 2017, Volume and Issue: 13(11), P. e1005752 - e1005752

Published: Nov. 3, 2017

The advent of high throughput technologies has led to a wealth publicly available 'omics data coming from different sources, such as transcriptomics, proteomics, metabolomics. Combining large-scale biological sets can lead the discovery important insights, provided that relevant information be extracted in holistic manner. Current statistical approaches have been focusing on identifying small subsets molecules (a 'molecular signature') explain or predict conditions, but mainly for single type 'omics. In addition, commonly used methods are univariate and consider each feature independently. We introduce mixOmics, an R package dedicated multivariate analysis with specific focus exploration, dimension reduction visualisation. By adopting systems biology approach, toolkit provides wide range statistically integrate several at once probe relationships between heterogeneous sets. Our recent extend Projection Latent Structure (PLS) models discriminant analysis, integration across multiple independent studies, identification molecular signatures. illustrate our latest mixOmics integrative frameworks analyses package.

Language: Английский

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Scientists’ warning to humanity: microorganisms and climate change

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(9), P. 569 - 586

Published: June 18, 2019

In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support existence of all higher trophic forms. To understand how humans and other forms Earth (including those are yet to discover) can withstand anthropogenic change, it vital incorporate knowledge microbial 'unseen majority'. We must learn not just microorganisms affect production consumption greenhouse gases) but also they will be affected by human activities. This Consensus Statement documents central role global importance biology. It puts humanity notice that impact depend heavily responses microorganisms, essential for achieving an environmentally sustainable future. The majority with share often goes unnoticed despite underlying major biogeochemical cycles food webs, thereby taking a key change. highlights microbiology issues call action microbiologists.

Language: Английский

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Environmental stress destabilizes microbial networks

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(6), P. 1722 - 1734

Published: Jan. 15, 2021

Language: Английский

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How to make more out of community data? A conceptual framework and its implementation as models and software

Ecology Letters, Journal Year: 2017, Volume and Issue: 20(5), P. 561 - 576

Published: March 20, 2017

Abstract Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate integration between conceptual statistical approaches in community ecology, we propose Hierarchical Modelling Species Communities ( HMSC ) as a general, flexible framework for modern analysis data. While non‐manipulative data allow only correlative not causal inference, this facilitates formulation data‐driven hypotheses regarding processes that structure communities. We model environmental filtering by variation covariation responses individual characteristics their environment, with potential contingencies on traits phylogenetic relationships. capture biotic rules species‐to‐species association matrices, which may be estimated multiple spatial or temporal operationalise hierarchical Bayesian joint distribution model, implement it R‐ Matlab‐packages enable computationally efficient analyses large sets. Armed tool, ecologists can make sense many types data, including spatially explicit time‐series illustrate use through series diverse ecological examples.

Language: Английский

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Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Cell, Journal Year: 2019, Volume and Issue: 177(5), P. 1109 - 1123.e14

Published: April 25, 2019

Language: Английский

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Influence of diatom diversity on the ocean biological carbon pump

Nature Geoscience, Journal Year: 2017, Volume and Issue: 11(1), P. 27 - 37

Published: Dec. 17, 2017

Language: Английский

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Phage puppet masters of the marine microbial realm

Nature Microbiology, Journal Year: 2018, Volume and Issue: 3(7), P. 754 - 766

Published: June 1, 2018

Language: Английский

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Host-linked soil viral ecology along a permafrost thaw gradient

Nature Microbiology, Journal Year: 2018, Volume and Issue: 3(8), P. 870 - 880

Published: July 13, 2018

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms mediate of methane and dioxide are poorly understood1-7. The role viruses, which known affect dynamics, metabolism biogeochemistry in oceans8-10, remains largely unexplored soil. Here, we aimed investigate how viruses influence ecology peatland soils along a permafrost thaw gradient Sweden. We recovered 1,907 viral populations (genomes large genome fragments) from 197 bulk soil size-fractionated metagenomes, 58% were detected metatranscriptomes presumed be active. In silico predictions linked 35% host populations, highlighting likely predators key carbon-cycling microorganisms, including methanogens methanotrophs. Lineage-specific virus/host ratios varied, suggesting infection dynamics may differentially impact responses changing climate. Virus-encoded glycoside hydrolases, an endomannanase with confirmed functional activity, indicated complex degradation abundances significant predictors dynamics. These findings suggest ecosystem function climate-critical, terrestrial habitats identify multiple potential contributions cycling.

Language: Английский

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Mixotrophy in the Marine Plankton

Annual Review of Marine Science, Journal Year: 2016, Volume and Issue: 9(1), P. 311 - 335

Published: Aug. 2, 2016

Mixotrophs are important components of the bacterioplankton, phytoplankton, microzooplankton, and (sometimes) zooplankton in coastal oceanic waters. Bacterivory among phytoplankton may be for alleviating inorganic nutrient stress increase primary production oligotrophic Mixotrophic phytoflagellates dinoflagellates often dominant plankton during seasonal stratification. Many microzooplankton grazers, including ciliates Rhizaria, mixotrophic owing to their retention functional algal organelles or maintenance endosymbionts. Phototrophy gross growth efficiency carbon transfer through higher trophic levels. Characteristic assemblages mixotrophs associated with warm, temperate, cold seas stratification, fronts, upwelling zones. Modeling has indicated that mixotrophy a profound impact on marine planktonic ecosystems enhance production, biomass levels, functioning biological pump.

Language: Английский

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From hairballs to hypotheses–biological insights from microbial networks

FEMS Microbiology Reviews, Journal Year: 2018, Volume and Issue: 42(6), P. 761 - 780

Published: July 25, 2018

Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these is not straightforward, the biological implications network properties unclear. Analysis allows researchers predict hub species interactions. Additionally, such analyses can help identify alternative states niches. Here, we review factors that result in spurious predictions address emergent be meaningful context microbiome. We also give overview studies analyse new hypotheses. Moreover, show a simulation how affected by choice environmental factors. For example, consistent across tools, heterogeneity induces modularity. highlight need for robust inference suggest strategies infer more reliably.

Language: Английский

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