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Article ; Online: MiBiOmics

Johanna Zoppi / Jean-François Guillaume / Michel Neunlist / Samuel Chaffron

BMC Bioinformatics, Vol 22, Iss 1, Pp 1-

an interactive web application for multi-omics data exploration and integration

2021 Volume 14

Abstract: Abstract Background Multi-omics experimental approaches are becoming common practice in biological and medical sciences underlining the need to design new integrative techniques and applications to enable the multi-scale characterization of biological ... ...

Abstract	Abstract Background Multi-omics experimental approaches are becoming common practice in biological and medical sciences underlining the need to design new integrative techniques and applications to enable the multi-scale characterization of biological systems. The integrative analysis of heterogeneous datasets generally allows to acquire additional insights and generate novel hypotheses about a given biological system. However, it can become challenging given the often-large size of omics datasets and the diversity of existing techniques. Moreover, visualization tools for interpretation are usually non-accessible to biologists without programming skills. Results Here, we present MiBiOmics, a web-based and standalone application that facilitates multi-omics data visualization, exploration, integration, and analysis by providing easy access to dedicated and interactive protocols. It implements classical ordination techniques and the inference of omics-based (multilayer) networks to mine complex biological systems, and identify robust biomarkers linked to specific contextual parameters or biological states. Conclusions MiBiOmics provides easy-access to exploratory ordination techniques and to a network-based approach for integrative multi-omics analyses through an intuitive and interactive interface. MiBiOmics is currently available as a Shiny app at https://shiny-bird.univ-nantes.fr/app/Mibiomics and as a standalone application at https://gitlab.univ-nantes.fr/combi-ls2n/mibiomics .
Keywords	Multi-omics ; Ordination ; Biological networks ; Data integration ; R shiny ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	004
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean

Ina M. Deutschmann / Erwan Delage / Caterina R. Giner / Marta Sebastián / Julie Poulain / Javier Arístegui / Carlos M. Duarte / Silvia G. Acinas / Ramon Massana / Josep M. Gasol / Damien Eveillard / Samuel Chaffron / Ramiro Logares

Nature Communications, Vol 15, Iss 1, Pp 1-

2024 Volume 17

Abstract: Abstract Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine ... ...

Abstract	Abstract Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change.
Keywords	Science ; Q
Subject code	551
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic adaptation of giant viruses in polar oceans

Lingjie Meng / Tom O. Delmont / Morgan Gaïa / Eric Pelletier / Antonio Fernàndez-Guerra / Samuel Chaffron / Russell Y. Neches / Junyi Wu / Hiroto Kaneko / Hisashi Endo / Hiroyuki Ogata

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 12

Abstract: Abstract Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of ...

Abstract	Abstract Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus–host network at the polar–nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.
Keywords	Science ; Q
Subject code	551
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Microbial community functioning during plant litter decomposition

Simon A. Schroeter / Damien Eveillard / Samuel Chaffron / Johanna Zoppi / Bernd Kampe / Patrick Lohmann / Nico Jehmlich / Martin von Bergen / Carlos Sanchez-Arcos / Georg Pohnert / Martin Taubert / Kirsten Küsel / Gerd Gleixner

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 10

Abstract: Abstract Microbial life in soil is fueled by dissolved organic matter (DOM) that leaches from the litter layer. It is well known that decomposer communities adapt to the available litter source, but it remains unclear if they functionally compete or ... ...

Abstract	Abstract Microbial life in soil is fueled by dissolved organic matter (DOM) that leaches from the litter layer. It is well known that decomposer communities adapt to the available litter source, but it remains unclear if they functionally compete or synergistically address different litter types. Therefore, we decomposed beech, oak, pine and grass litter from two geologically distinct sites in a lab-scale decomposition experiment. We performed a correlative network analysis on the results of direct infusion HR-MS DOM analysis and cross-validated functional predictions from 16S rRNA gene amplicon sequencing and with DOM and metaproteomic analyses. Here we show that many functions are redundantly distributed within decomposer communities and that their relative expression is rapidly optimized to address litter-specific properties. However, community changes are likely forced by antagonistic mechanisms as we identified several natural antibiotics in DOM. As a consequence, the decomposer community is specializing towards the litter source and the state of decomposition (community divergence) but showing similar litter metabolomes (metabolome convergence). Our multi-omics-based results highlight that DOM not only fuels microbial life, but it additionally holds meta-metabolomic information on the functioning of ecosystems.
Keywords	Medicine ; R ; Science ; Q
Subject code	401
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula

Yajuan Lin / Carly Moreno / Adrian Marchetti / Hugh Ducklow / Oscar Schofield / Erwan Delage / Michael Meredith / Zuchuan Li / Damien Eveillard / Samuel Chaffron / Nicolas Cassar

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 9

Abstract: Over the past century, the Western Antarctic Peninsula has experienced rapid warming and a substantial loss of sea ice with important implications for plankton biodiversity and carbon cycling. Using a 5-year DNA metabarcoding dataset, this study assesses ...

Abstract	Over the past century, the Western Antarctic Peninsula has experienced rapid warming and a substantial loss of sea ice with important implications for plankton biodiversity and carbon cycling. Using a 5-year DNA metabarcoding dataset, this study assesses how interannual variability in sea-ice conditions impacts biodiversity and biological carbon fluxes in this region.
Keywords	Science ; Q
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

Hiroto Kaneko / Romain Blanc-Mathieu / Hisashi Endo / Samuel Chaffron / Tom O. Delmont / Morgan Gaia / Nicolas Henry / Rodrigo Hernández-Velázquez / Canh Hao Nguyen / Hiroshi Mamitsuka / Patrick Forterre / Olivier Jaillon / Colomban de Vargas / Matthew B. Sullivan / Curtis A. Suttle / Lionel Guidi / Hiroyuki Ogata

iScience, Vol 24, Iss 1, Pp 102002- (2021)

2021

Abstract: Summary: The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export ... ...

Abstract	Summary: The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral “shunt” and “shuttle”). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.
Keywords	Oceanography ; Biogeoscience ; Global Carbon Cycle ; Virology ; Viral Microbiology ; Carbon Cycle ; Science ; Q
Subject code	550
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes

Takeuchi, Yayoi / Bibian Diway / Christian von Mering / Jakob Pernthaler / Kentaro K. Shimizu / Masaki J. Kobayashi / Michaela M. Salcher / Rie Shimizu-Inatsugi / Samuel Chaffron

Systematic and applied microbiology. 2015 July, v. 38

2015

Abstract: Pitchers are modified leaves used by carnivorous plants for trapping prey. Their fluids contain digestive enzymes from the plant and they harbor abundant microbes. In this study, the diversity of bacterial communities was assessed in Nepenthes pitcher ... ...

Abstract	Pitchers are modified leaves used by carnivorous plants for trapping prey. Their fluids contain digestive enzymes from the plant and they harbor abundant microbes. In this study, the diversity of bacterial communities was assessed in Nepenthes pitcher fluids and the composition of the bacterial community was compared to that in other environments, including the phyllosphere of Arabidopsis, animal guts and another pitcher plant, Sarracenia. Diversity was measured by 454 pyrosequencing of 16S rRNA gene amplicons. A total of 232,823 sequences were obtained after chimera and singleton removal that clustered into 3260 distinct operational taxonomic units (OTUs) (3% dissimilarity), which were taxonomically distributed over 17 phyla, 25 classes, 45 orders, 100 families, and 195 genera. Pyrosequencing and fluorescence in situ hybridization yielded similar estimates of community composition. Most pitchers contained high proportions of unique OTUs, and only 22 OTUs (<0.6%) were shared by â¥14/16 samples, suggesting a unique bacterial assemblage in each pitcher at the OTU level. Diversity analysis at the class level revealed that the bacterial communities of both opened and unopened pitchers were most similar to that of Sarracenia and to that in the phyllosphere. Therefore, the bacterial community in pitchers may be formed by environmental filtering and/or by phyllosphere bacteria.
Keywords	animals ; Arabidopsis ; bacteria ; bacterial communities ; carnivorous plants ; community structure ; digestive enzymes ; fluorescence in situ hybridization ; genes ; leaves ; Nepenthes ; phyllosphere ; ribosomal RNA ; Sarracenia ; sequence analysis
Language	English
Dates of publication	2015-07
Size	p. 330-339.
Publishing place	Elsevier GmbH
Document type	Article
ZDB-ID	283612-9
ISSN	1618-0984 ; 0723-2020
ISSN (online)	1618-0984
ISSN	0723-2020
DOI	10.1016/j.syapm.2015.05.006
Database	NAL-Catalogue (AGRICOLA)

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Article: Modelling plankton ecosystems in the meta-omics era. Are we ready?

Stec, Krzysztof Franciszek / Chris Bowler / Daniele Iudicone / Domenico D'Alelio / Federico Matias Ibarbalz / Luigi Caputi / Matthew B. Sullivan / Maurizio Ribera d'Alcalà / Pier Luigi Buttigieg / Samuel Chaffron

Marine genomics. 2017 Apr., v. 32

2017

Abstract: Recent progress in applying meta-omics approaches to the study of marine ecosystems potentially allows scientists to study the genetic and functional diversity of plankton at an unprecedented depth and with enhanced precision. However, while a range of ... ...

Abstract	Recent progress in applying meta-omics approaches to the study of marine ecosystems potentially allows scientists to study the genetic and functional diversity of plankton at an unprecedented depth and with enhanced precision. However, while a range of persistent technical issues still need to be resolved, a much greater obstacle currently preventing a complete and integrated view of the marine ecosystem is the absence of a clear conceptual framework. Herein, we discuss the knowledge that has thus far been derived from conceptual and statistical modelling of marine plankton ecosystems, and illustrate the potential power of integrated meta-omics approaches in the field. We then propose the use of a semantic framework is necessary to support integrative ecological modelling in the meta-omics era, particularly when having to face the increased interdisciplinarity needed to address global issues related to climate change.
Keywords	climate change ; functional diversity ; marine ecosystems ; plankton ; scientists ; statistical models
Language	English
Dates of publication	2017-04
Size	p. 1-17.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2429626-0
ISSN	1876-7478 ; 1874-7787
ISSN (online)	1876-7478
ISSN	1874-7787
DOI	10.1016/j.margen.2017.02.006
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Observational Needs Supporting Marine Ecosystems Modeling and Forecasting

Antonietta Capotondi / Michael Jacox / Chris Bowler / Maria Kavanaugh / Patrick Lehodey / Daniel Barrie / Stephanie Brodie / Samuel Chaffron / Wei Cheng / Daniela F. Dias / Damien Eveillard / Lionel Guidi / Daniele Iudicone / Nicole S. Lovenduski / Janet A. Nye / Ivonne Ortiz / Douglas Pirhalla / Mercedes Pozo Buil / Vincent Saba /

Scott Sheridan / Samantha Siedlecki / Aneesh Subramanian / Colomban de Vargas / Emanuele Di Lorenzo / Scott C. Doney / Albert J. Hermann / Terrence Joyce / Mark Merrifield / Arthur J. Miller / Fabrice Not / Stephane Pesant

Frontiers in Marine Science, Vol

From the Global Ocean to Regional and Coastal Systems

2019 Volume 6

Abstract: Many coastal areas host rich marine ecosystems and are also centers of economic activities, including fishing, shipping and recreation. Due to the socioeconomic and ecological importance of these areas, predicting relevant indicators of the ecosystem ... ...

Abstract	Many coastal areas host rich marine ecosystems and are also centers of economic activities, including fishing, shipping and recreation. Due to the socioeconomic and ecological importance of these areas, predicting relevant indicators of the ecosystem state on sub-seasonal to interannual timescales is gaining increasing attention. Depending on the application, forecasts may be sought for variables and indicators spanning physics (e.g., sea level, temperature, currents), chemistry (e.g., nutrients, oxygen, pH), and biology (from viruses to top predators). Many components of the marine ecosystem are known to be influenced by leading modes of climate variability, which provide a physical basis for predictability. However, prediction capabilities remain limited by the lack of a clear understanding of the physical and biological processes involved, as well as by insufficient observations for forecast initialization and verification. The situation is further complicated by the influence of climate change on ocean conditions along coastal areas, including sea level rise, increased stratification, and shoaling of oxygen minimum zones. Observations are thus vital to all aspects of marine forecasting: statistical and/or dynamical model development, forecast initialization, and forecast validation, each of which has different observational requirements, which may be also specific to the study region. Here, we use examples from United States (U.S.) coastal applications to identify and describe the key requirements for an observational network that is needed to facilitate improved process understanding, as well as for sustaining operational ecosystem forecasting. We also describe new holistic observational approaches, e.g., approaches based on acoustics, inspired by Tara Oceans or by landscape ecology, which have the potential to support and expand ecosystem modeling and forecasting activities by bridging global and local observations.
Keywords	marine ecosystems ; modeling and forecasting ; seascapes ; genetics ; acoustics ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	333 ; 551
Language	English
Publishing date	2019-10-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Like will to like

Bärbel Stecher / Samuel Chaffron / Rina Käppeli / Siegfried Hapfelmeier / Susanne Freedrich / Thomas C Weber / Jorum Kirundi / Mrutyunjay Suar / Kathy D McCoy / Christian von Mering / Andrew J Macpherson / Wolf-Dietrich Hardt

PLoS Pathogens, Vol 6, Iss 1, p e

abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria.

2010 Volume 1000711

Abstract: The intestinal ecosystem is formed by a complex, yet highly characteristic microbial community. The parameters defining whether this community permits invasion of a new bacterial species are unclear. In particular, inhibition of enteropathogen infection ... ...

Abstract	The intestinal ecosystem is formed by a complex, yet highly characteristic microbial community. The parameters defining whether this community permits invasion of a new bacterial species are unclear. In particular, inhibition of enteropathogen infection by the gut microbiota ( = colonization resistance) is poorly understood. To analyze the mechanisms of microbiota-mediated protection from Salmonella enterica induced enterocolitis, we used a mouse infection model and large scale high-throughput pyrosequencing. In contrast to conventional mice (CON), mice with a gut microbiota of low complexity (LCM) were highly susceptible to S. enterica induced colonization and enterocolitis. Colonization resistance was partially restored in LCM-animals by co-housing with conventional mice for 21 days (LCM(con21)). 16S rRNA sequence analysis comparing LCM, LCM(con21) and CON gut microbiota revealed that gut microbiota complexity increased upon conventionalization and correlated with increased resistance to S. enterica infection. Comparative microbiota analysis of mice with varying degrees of colonization resistance allowed us to identify intestinal ecosystem characteristics associated with susceptibility to S. enterica infection. Moreover, this system enabled us to gain further insights into the general principles of gut ecosystem invasion by non-pathogenic, commensal bacteria. Mice harboring high commensal E. coli densities were more susceptible to S. enterica induced gut inflammation. Similarly, mice with high titers of Lactobacilli were more efficiently colonized by a commensal Lactobacillus reuteri(RR) strain after oral inoculation. Upon examination of 16S rRNA sequence data from 9 CON mice we found that closely related phylotypes generally display significantly correlated abundances (co-occurrence), more so than distantly related phylotypes. Thus, in essence, the presence of closely related species can increase the chance of invasion of newly incoming species into the gut ecosystem. We provide evidence that this principle ...
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	630
Language	English
Publishing date	2010-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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