ArticleBMC biology2015
Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms.
Article in BMC biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.Environmental microbiome · 2025Article
- Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes.Microbiome · 2025Article
- The genomic potential of photosynthesis in piconanoplankton is functionally redundant but taxonomically structured at a global scale.Science advances · 2024Article
- Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites.ISME communications · 2023Article
- Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea.Environmental microbiology · 2022Article
- Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding.Microbial ecology · 2021Article
- Towards omics-based predictions of planktonic functional composition from environmental data.Nature communications · 2021Article
- Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition.Genome biology and evolution · 2020Article
- DeSignate: detecting signature characters in gene sequence alignments for taxon diagnoses.BMC bioinformatics · 2020Article
- De novo clustering of long reads by gene from transcriptomics data.Nucleic acids research · 2019Article
- Tracking the Rules of Transmission and Introgression with Networks.Microbiology spectrum · 2018Review
- Bipartite Network Analysis of Gene Sharings in the Microbial World.Molecular biology and evolution · 2018Article
- High-resolution characterization of the human microbiome.Translational research : the journal of laboratory and clinical medicine · 2017Review
- Article
- "Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis.Genome biology and evolution · 2016Article
- Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.Trends in microbiology · 2016Review
- Comparison of three clustering approaches for detecting novel environmental microbial diversity.PeerJ · 2016Article
- Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf.PloS one · 2016Article
- Article
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9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but analyses of the resulting millions of short sequences remain a major bottleneck for these approaches. Here, we introduce the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 small subunit rDNA (SSU-rDNA) sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.
resultsOur broadly applicable protocol quantified the progress in the description of genetic diversity of ciliates by environmental SSU-rDNA surveys, detected a fundamental historical bias in the tendency to recover already known groups in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but are structured by habitat and geographical location at intermediate geographical scale, as observed for bacteria, plants, and animals.
conclusionsCurrently available 'universal' primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought. Network analyses such as presented in this study offer a promising way to guide the design of novel primers and to further explore this vast and structured microbial diversity.
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