The study of diversity in biological communities is an intriguing field. Huge amount of data are ... more The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity
Additional file 2: Table S1. Service groups and capabilities for processing and analysis in biodi... more Additional file 2: Table S1. Service groups and capabilities for processing and analysis in biodiversity science.
Raw and Denoised sequences of the two environmental samples (MPE4, MPE5) and the reference datase... more Raw and Denoised sequences of the two environmental samples (MPE4, MPE5) and the reference datasets used in taxonomic assignment methods.
Background: Recent years have seen a surge in projects that produce large volumes of structured, ... more Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source "data enrichment" workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries:
Overview Altered species distributions, the changing nature of ecosystems and increased risks of ... more Overview Altered species distributions, the changing nature of ecosystems and increased risks of extinction all have an impact in important areas of societal concern. Biologists and environmental scientists are asked to provide decision support for managing the biodiversity component of our environment at multiple scales (genomic, organism, habitat, ecosystem, landscape) to prevent and mitigate such losses. BioVeL want to address this needs offering a series of robust and reliable web services that could be managed with the suite of tools of the myGRID project. The project will propose workflow for these services that will ensure best practice and efficiency of usage. Within the first round of services produced by the project there are phylogenetic inference workflows. These workflows will provide to end user the capabilities to execute application that could easily exploit several kind of resources, like: EGI grid infrastructure, local batch farm or dedicated servers.
Nucleotide sequences reference collections or databases are fundamental components in DNA barcodi... more Nucleotide sequences reference collections or databases are fundamental components in DNA barcoding and metabarcoding data analyses pipelines. In such analyses, the accurate taxonomic assignment is a crucial aspect, relying directly on the availability of comprehensive and curated reference sequence collection and its taxonomy information. The currently wide use of the mitochondrial cytochrome oxidase subunit-I (COXI) as a standard DNA barcode marker in metazoan biodiversity studies highlights the need to shed light on the availability of the related relevant information from different data sources and their eventual integration. To adequately address data integration process, many aspects should be markedly considered starting from DNA sequence curation followed by taxonomy alignment with solid reference backbone and metadata harmonization according to universal standards. Here, we present MetaCOXI, an integrated collection of curated metazoan COXI DNA sequences with their associat...
The study of diversity in biological communities is an intriguing field. Huge amount of data are ... more The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity
Additional file 2: Table S1. Service groups and capabilities for processing and analysis in biodi... more Additional file 2: Table S1. Service groups and capabilities for processing and analysis in biodiversity science.
Raw and Denoised sequences of the two environmental samples (MPE4, MPE5) and the reference datase... more Raw and Denoised sequences of the two environmental samples (MPE4, MPE5) and the reference datasets used in taxonomic assignment methods.
Background: Recent years have seen a surge in projects that produce large volumes of structured, ... more Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source "data enrichment" workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries:
Overview Altered species distributions, the changing nature of ecosystems and increased risks of ... more Overview Altered species distributions, the changing nature of ecosystems and increased risks of extinction all have an impact in important areas of societal concern. Biologists and environmental scientists are asked to provide decision support for managing the biodiversity component of our environment at multiple scales (genomic, organism, habitat, ecosystem, landscape) to prevent and mitigate such losses. BioVeL want to address this needs offering a series of robust and reliable web services that could be managed with the suite of tools of the myGRID project. The project will propose workflow for these services that will ensure best practice and efficiency of usage. Within the first round of services produced by the project there are phylogenetic inference workflows. These workflows will provide to end user the capabilities to execute application that could easily exploit several kind of resources, like: EGI grid infrastructure, local batch farm or dedicated servers.
Nucleotide sequences reference collections or databases are fundamental components in DNA barcodi... more Nucleotide sequences reference collections or databases are fundamental components in DNA barcoding and metabarcoding data analyses pipelines. In such analyses, the accurate taxonomic assignment is a crucial aspect, relying directly on the availability of comprehensive and curated reference sequence collection and its taxonomy information. The currently wide use of the mitochondrial cytochrome oxidase subunit-I (COXI) as a standard DNA barcode marker in metazoan biodiversity studies highlights the need to shed light on the availability of the related relevant information from different data sources and their eventual integration. To adequately address data integration process, many aspects should be markedly considered starting from DNA sequence curation followed by taxonomy alignment with solid reference backbone and metadata harmonization according to universal standards. Here, we present MetaCOXI, an integrated collection of curated metazoan COXI DNA sequences with their associat...
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