Taxonomie et inférence fonctionnelle des procaryotes : développement de MACADAM, une base de données devoies métaboliques associées à une taxonomie

Les procaryotes sont des organismes ubiquitaires vivant en communauté et possédant une extrême diversité métabolique en lien avec leur omniprésence. Pour contribuer à la compréhension du rôle fonctionnel des procaryotes, nous avons développé MACADAM : une base de données de voies métaboliques associées à une taxonomie centrée sur les procaryotes.L'objectif était de mettre à disposition de la communauté scientifique des données d'informations fonctionnelles sélectionnées sur leur qualité (qualité des génomes, qualité des annotations), enaccès libre et interopérables. MACADAM regroupe les PGDBs (Pathway/Genome DataBase)construites à partir de génome RefSeq répondant aux critères de qualité complete genome enutilisant le logiciel Pathway Tools. Afin d’enrichir MACADAM, MicroCyc, une collection de PGDBsmanuellement curées par des experts, a été ajoutée. Enfin, les informations fonctionnellessourcées à partir de la littérature contenues dans FAPROTAX et IJSEM phenotypic databasessont ajoutées. MACADAM contient 13195 PGDBs bactériennes, 314 PGDBs d’archées et 1260voies métaboliques uniques. Construit à l'aide de technologies interopérables (Python 3, SQLite),sous un format téléchargeable et avec un code ouvert, MACADAM peut être intégré dans desoutils qui nécessitent de lier une information taxonomique à une information fonctionnelle. Pouraméliorer sa visibilité auprès de la communauté de microbiologistes, MACADAM est consultableen ligne (http://macadam.toulouse.inra.fr). Utilisant la taxonomie de la base de données NCBITaxonomy, MACADAM permet de relier un taxon allant du phylum à l'espèce à une informationfonctionnelle. Chaque voie métabolique est associée à deux scores de complétude (PathwayScore et Pathway Frequency Score). A chaque mise à jour, MACADAM intègre les nouvellesversions de RefSeq, du NCBI Taxonomy et de MicroCyc, permettant de suivre au plus près lescorrections apportées à la taxonomie et d'inclure les informations disponibles pour les nouveauxgénomes déposés. Deux exemples d'utilisation de MACADAM et une comparaison avec uneapproche d'inférence à partir de lectures métagénomiques ont permis de discuter les points fortset les faiblesses (i) de MACADAM et (ii) de l'inférence par une approche d'identificationtaxonomique préalable. L'identification des individus au sein de la communauté procaryotebénéficie largement des avancées en technologie de séquençage et du raffinement des pipelinesd’analyses bioinformatiques. L’analyse des lectures issues de séquençages métagénomiquesaboutit à la reconstruction de génomes putatifs ou espèces métagénomiques. Dans ce cadre,nous nous sommes penchés sur la problématique de correction d’assignation taxonomiqued’espèces métagénomiques en utilisant une approche par reconstruction d’un arbrephylogénétique d’une part et en utilisant un indice global de parenté génomique (ANI) d’autre part.Ce travail nous a permis de préciser le positionnement de neuf groupes d'espècesmétagénomiques et mis en évidence des erreurs d'affiliation de génome de référence chezMegasphaera et Blautia Obeum et de confirmer le reclassement de Ruminococcus gauvreauiidans le genre Blautia. Pour limiter les erreurs et leur réplication il convient de veiller à la qualité del'information contenue dans les bases de données. Dans ce cadre, la communauté scientifiquedevrait avoir une meilleure connaissance des règles de la nomenclature et des méthodes de systématique. Un intérêt accru devrait être porté pour valoriser les efforts de correction des données présentes dans les bases de données. Enfin, bien que la métagénomique permette de mieux comprendre les communautés microbiennes qui nous entourent, un effort de culture desorganismes réputés incultivables permettrait d'accroître les connaissances et la diversité desorganismes procaryotes dans les banques de données. Ces efforts se répercuteront directementsur la qualité des informations de MACADAM

Diversity and Co-occurrence Pattern Analysis of Cecal Microbiota Establishment at the Onset of Solid Feeding in Young Rabbits

This study aimed to evaluate how the feeding strategy of rabbit kits at the onset of solid feed intake could affect ecological diversity and co-occurrence patterns of the cecal bacterial community. From birth to 18 days of age kits were exclusively milk-fed, and between 18 and 35 days the young rabbits also had access to solid feed. After weaning at (35 days), young rabbits were exclusively fed solid feed. Three experimental feeds were used: a high concentrate diet [H: 10.16 MJ digestible energy (DE)/kg and 15.3% crude protein (CP)], a low concentrate diet (L: 9.33 MJ DE/kg and 14.7% CP) and a reproductive female diet (R: 10.57 MJ DE/kg and 17.3% CP). The rabbit kits (n = 357) were divided into three groups, differing by the diet received during two periods: from 18 to 28 and from 28 to 49 days of age. In the groups LL and HH, rabbit kits were fed L or H diets, respectively, during both periods. Kits in the group RL received feeds R and L from 18 to 28 and 28 to 49 days of age, respectively. Cecal bacterial communities of 10 rabbits per group were carried out at 18, 28, 35, 43 and 49 days of age by MiSeq Illumina sequencing 16S rRNA encoding genes. Between 18 and 28 days of age, solid feed intake was higher in the group RL compared to the other two groups (+24%; P < 0.01). Overall, 13.4% of the OTUs detected were present in the cecal ecosystem from 18 to 49 days old, whereas 17.4% were acquired with the onset of solid feeding and kept from 28 days on. Exclusive milk consumption constrains the bacterial community toward a similar structure but high phylogenetic beta-diversity. Introduction of solid feed induced a sharp change of microbial community structure and decreased phylogenetic diversity. A strong relationship in bacterial community network occurred only from 43 days on. Our feeding strategy at the onset of solid feed ingestion exhibited only a moderate effect on the microbial community structure (P = 0.072), although the LL group seemed to reach faster maturity compared to the two other groups

Taxonomy and functional inference of prokaryotes : development of MACADAM, a database of metabolic pathways associated with a taxonomy

Les procaryotes sont des organismes ubiquitaires vivant en communauté et possédant une extrême diversité métabolique en lien avec leur omniprésence. Pour contribuer à la compréhension du rôle fonctionnel des procaryotes, nous avons développé MACADAM : une base de données de voies métaboliques associées à une taxonomie centrée sur les procaryotes.L'objectif était de mettre à disposition de la communauté scientifique des données d'informations fonctionnelles sélectionnées sur leur qualité (qualité des génomes, qualité des annotations), enaccès libre et interopérables. MACADAM regroupe les PGDBs (Pathway/Genome DataBase)construites à partir de génome RefSeq répondant aux critères de qualité complete genome enutilisant le logiciel Pathway Tools. Afin d’enrichir MACADAM, MicroCyc, une collection de PGDBsmanuellement curées par des experts, a été ajoutée. Enfin, les informations fonctionnellessourcées à partir de la littérature contenues dans FAPROTAX et IJSEM phenotypic databasessont ajoutées. MACADAM contient 13195 PGDBs bactériennes, 314 PGDBs d’archées et 1260voies métaboliques uniques. Construit à l'aide de technologies interopérables (Python 3, SQLite),sous un format téléchargeable et avec un code ouvert, MACADAM peut être intégré dans desoutils qui nécessitent de lier une information taxonomique à une information fonctionnelle. Pouraméliorer sa visibilité auprès de la communauté de microbiologistes, MACADAM est consultableen ligne (http://macadam.toulouse.inra.fr). Utilisant la taxonomie de la base de données NCBITaxonomy, MACADAM permet de relier un taxon allant du phylum à l'espèce à une informationfonctionnelle. Chaque voie métabolique est associée à deux scores de complétude (PathwayScore et Pathway Frequency Score). A chaque mise à jour, MACADAM intègre les nouvellesversions de RefSeq, du NCBI Taxonomy et de MicroCyc, permettant de suivre au plus près lescorrections apportées à la taxonomie et d'inclure les informations disponibles pour les nouveauxgénomes déposés. Deux exemples d'utilisation de MACADAM et une comparaison avec uneapproche d'inférence à partir de lectures métagénomiques ont permis de discuter les points fortset les faiblesses (i) de MACADAM et (ii) de l'inférence par une approche d'identificationtaxonomique préalable. L'identification des individus au sein de la communauté procaryotebénéficie largement des avancées en technologie de séquençage et du raffinement des pipelinesd’analyses bioinformatiques. L’analyse des lectures issues de séquençages métagénomiquesaboutit à la reconstruction de génomes putatifs ou espèces métagénomiques. Dans ce cadre,nous nous sommes penchés sur la problématique de correction d’assignation taxonomiqued’espèces métagénomiques en utilisant une approche par reconstruction d’un arbrephylogénétique d’une part et en utilisant un indice global de parenté génomique (ANI) d’autre part.Ce travail nous a permis de préciser le positionnement de neuf groupes d'espècesmétagénomiques et mis en évidence des erreurs d'affiliation de génome de référence chezMegasphaera et Blautia Obeum et de confirmer le reclassement de Ruminococcus gauvreauiidans le genre Blautia. Pour limiter les erreurs et leur réplication il convient de veiller à la qualité del'information contenue dans les bases de données. Dans ce cadre, la communauté scientifiquedevrait avoir une meilleure connaissance des règles de la nomenclature et des méthodes de systématique. Un intérêt accru devrait être porté pour valoriser les efforts de correction des données présentes dans les bases de données. Enfin, bien que la métagénomique permette de mieux comprendre les communautés microbiennes qui nous entourent, un effort de culture desorganismes réputés incultivables permettrait d'accroître les connaissances et la diversité desorganismes procaryotes dans les banques de données. Ces efforts se répercuteront directementsur la qualité des informations de MACADAM.Prokaryotes are ubiquitous organisms living in communities, whose extreme metabolic diversity iscorrelated with their ubiquity. To contribute to a better understanding of the functional role ofprokaryotes, we developed MACADAM: a database of metabolic pathways associated with aprokaryote-centric taxonomy. The aim is to provide the scientific community with open access tofunctional information data which has been selected for its genomic and annotation quality, whichis interoperable and simply structured, thereby enabling updates to be made to the data gatheredfrom data sources such as MetaCyc, MicroCyc and RefSeq by MACADAM. MACADAM meetsthese criteria. MACADAM includes PGDBs (Pathway/Genome DataBases) assembled fromRefSeq genomes meeting the complete genome quality criteria, by using the Pathway Toolssoftware made available by MetaCyc, a metabolic pathway database. In order to enrich thedatabase and increase the quality of functional information in MACADAM, a collection of expertcurated PGDBs named MicroCyc was added. Its PGDBs are favoured over those of RefSeq.Functional information sourced from the literature contained in FAPROTAX and IJSEM phenotypicdatabases was also added. MACADAM contains 13 509 PGDBs (13 195 bacterial PGDBs and314 archaeal PGDBs) and 1 260 unique metabolic pathways. Built using interoperabletechnologies (Python 3, SQLite), in a downloadable format and with open-source code,MACADAM can be integrated into tools requiring the pairing of functional and taxonomicinformation. To improve its visibility among the microbiology community, MACADAM is availableonline (http://macadam.toulouse.inra.fr). By using the taxonomy of the NCBI Taxonomy database,MACADAM makes it possible to link any taxon—ranging from phylum to species—to its functionalinformation. Each metabolic pathway is associated with two completeness scores (a PS: PathwayScore and a PFS: Pathway Frequency Score). With each update, MACADAM integrates the newversions of RefSeq, NCBI Taxonomy and MicroCyc, allowing any corrections made to thetaxonomy to be promptly amended and to add information on recently-submitted genomes. Twoexamples of ways in which to use MACADAM, and a comparison with an inference approachbased on metagenomic readings allowed for a discussion of the strengths and weaknesses (i)MACADAM and (ii) of inference by a prior taxonomic identification approach. The identification ofindividuals within the prokaryotic community benefits greatly from advances in sequencingtechnology and the refinement of bioinformatics analysis pipelines. The analysis of readings frommetagenomic sequencing leads to the reconstruction of putative genomes and metagenomicspecies. In this context, we examined the problem of correcting taxonomic assignments ofmetagenomic species, by using a phylogenetic tree reconstruction approach on the one hand, andby using an overall genome relatedness index (ANI) on the other hand. This work allowed us toclarify the positioning of nine groups of metagenomic species, and highlighted errors in referencegenome affiliation in Megasphaera and Blautia Obeum. It also allowed us to confirm thereclassification of Ruminococcus gauvreauii into the genus Blautia. To limit errors and preventtheir replication, it is important to ensure the quality of the information contained in the databases.In this context, the scientific community should have better knowledge of the rules of nomenclatureand systematic methods. Further efforts should be made to advocate the merits of correctingdatabase data. Finally, although metagenomics provides a better understanding of the microbialcommunities around us, an effort to cultivate organisms that are said to be uncultivable wouldincrease the knowledge and diversity of prokaryotic organisms in databases. These efforts willhave a direct impact on the quality of functional information and the coverage of MACADAM'sprokaryotic diversit

Image_3_Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient.PDF

<p>Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.</p

Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient

Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon-function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, andmore importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels

The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups

Progress in genome sequencing and bioinformatics opens up new possibilities, including that of correlating genome annotations with functional information such as metabolic pathways. Thanks to the development of functional annotation databases, scientists are able to link genome annotations with functional annotations. We present MetAboliC pAthways DAtabase for Microbial taxonomic groups (MACADAM) here, a user-friendly database that makes it possible to find presence/absence/completeness statistics for metabolic pathways at a given microbial taxonomic position. For each prokaryotic ‘Ref- Seq complete genome’, MACADAM builds a pathway genome database (PGDB) using Pathway Tools software based on MetaCyc data that includes metabolic pathways as well as associated metabolites, reactions and enzymes. To ensure the highest quality of the genome functional annotation data, MACADAM also contains MicroCyc, a manually curated collection of PGDBs; Functional Annotation of Prokaryotic Taxa (FAPROTAX), a manually curated functional annotation database; and the IJSEM phenotypic database. TheMACADAMdatabase contains 13 509 PGDBs (13 195 bacterial and 314 archaeal), 1260 unique metabolic pathways, completed with 82 functional annotations from FAPROTAX and 16 from the IJSEM phenotypic database. MACADAM contains a total of 7921 metabolites, 592 enzymatic reactions, 2134 EC numbers and 7440 enzymes. MACADAM can be queried at any rank of the NCBI taxonomy (from phyla to species). It provides the possibility to explore functional information completed with metabolites, enzymes, enzymatic reactions and EC numbers. MACADAM returns a tabulated file containing a list of pathways with two scores (pathway score and pathway frequency score) that are present in the queried taxa. The file also contains the names of the organisms in which the pathways are found and the metabolic hierarchy associated with the pathways. Finally,MACADAM can be downloaded as a single file and queried with SQLite or python command lines or explored through a web interface

Data_Sheet_2_Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient.XLSX

<p>Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.</p

Data_Sheet_5_Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient.xlsx

<p>Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.</p