Frédéric Boyer

Université Grenoble Alpes, Grenoble, Rhône-Alpes, France

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Publications (35)108.8 Total impact

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    ABSTRACT: Background: The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results: We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ∼460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ∼12-10 ka ago. Conclusions: Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (∼130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds.
    Full-text · Article · Dec 2015 · BMC Genomics
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    ABSTRACT: Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present into the environment. In this study, we tested if an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro, and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) versus 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems. This article is protected by copyright. All rights reserved.
    Full-text · Article · Oct 2015 · Molecular Ecology
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    ABSTRACT: The capacity of mosquitoes to resist insecticides threatens the control of diseases such as dengue and malaria. Until alternative control tools are implemented, characterizing resistance mechanisms is crucial for managing resistance in natural populations. Insecticide biodegradation by detoxification enzymes is a common resistance mechanism; however, the genomic changes underlying this mechanism have rarely been identified, precluding individual resistance genotyping. In particular, the role of copy number variations (CNVs) and polymorphisms of detoxification enzymes have never been investigated at the genome level, although they can represent robust markers of metabolic resistance. In this context, we combined target enrichment with high-throughput sequencing for conducting the first comprehensive screening of gene amplifications and polymorphisms associated with insecticide resistance in mosquitoes. More than 760 candidate genes were captured and deep sequenced in several populations of the dengue mosquito Ae. aegypti displaying distinct genetic backgrounds and contrasted resistance levels to the insecticide deltamethrin. CNV analysis identified 41 gene amplifications associated with resistance, most affecting cytochrome P450s overtranscribed in resistant populations. Polymorphism analysis detected more than 30,000 variants and strong selection footprints in specific genomic regions. Combining Bayesian and allele frequency filtering approaches identified 55 nonsynonymous variants strongly associated with resistance. Both CNVs and polymorphisms were conserved within regions but differed across continents, confirming that genomic changes underlying metabolic resistance to insecticides are not universal. By identifying novel DNA markers of insecticide resistance, this study opens the way for tracking down metabolic changes developed by mosquitoes to resist insecticides within and among populations.
    Full-text · Article · Jul 2015 · Genome Research
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    ABSTRACT: The "niche variation hypothesis" (NVH) predicts that populations with wider niches should display higher among-individual variability. This prediction originally stated at the intra-specific level may be extended to the inter-specific level: individuals of generalist species may differ to a greater extent than individuals of a specialist species. We tested the NVH at intra- and inter-specific levels based on a large diet database of three large herbivore feces collected in the field and analyzed using DNA metabarcoding. The three herbivores (roe deer Capreolus capreolus, chamois Rupicapra rupicapra and mouflon Ovis musimon) are highly contrasted in terms of sociality (solitary to highly gregarious) and diet. The NVH at the intraspecific level was tested by relating, for the same population, diet breadth and inter-individual variation across the four seasons. Compared to null models, our data supported the NVH both at the intra- and inter-specific levels. Inter-individual variation of the diet of solitary species was not larger than in social species, although social individuals feed together and could therefore have more similar diets. Hence, the NVH better explained diet breadth than other factors such as sociality. The expansion of the population niche of the three species was driven by resource availability, and achieved by an increase in inter-individual variation, and the level of inter-individual variability was larger in the generalist species (mouflon) than in the specialist one (roe deer). This mechanism at the base of the NVH appears at play at different levels of biological organization, from populations to communities.
    Full-text · Article · Jul 2015 · Oecologia
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    ABSTRACT: DNA metabarcoding offers new perspectives in biodiversity research. This recently-developed approach to ecosystem study relies heavily on the use of next-generation sequencing (NGS), and thus calls upon the ability to deal with huge sequence datasets. The OBITools package satisfies this requirement thanks to a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to setup tailored-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The OBITools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools. A Galaxy wrapper is available on the GeneOuest Core facility Toolshed: http://toolshed.genouest.org. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    No preview · Article · May 2015 · Molecular Ecology Resources
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    ABSTRACT: Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12× coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g., panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.
    Full-text · Article · Apr 2015 · Frontiers in Genetics
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    ABSTRACT: Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA-based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high-elevation lake in the Alps over the last 6,400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6,400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agro-pastoral landscape was detected during the Late Holocene, approximately 4,500 years ago, with the replacement of mountain forests and tall-herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long-term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appears to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long-term ecosystem dynamics under the influence of human-induced and environmental drivers.This article is protected by copyright. All rights reserved.
    Full-text · Article · Mar 2015 · Molecular Ecology
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    ABSTRACT: Closely related sympatric species commonly develop different ecological strategies to avoid competition. Ctenomys minutus and C. flamarioni are subterranean rodents parapatrically distributed in the southern Brazilian coastal plain, showing a narrow sympatric zone. To gain understanding on food preferences and possible competition for food resources, we evaluated their diet composition performing DNA metabarcoding analyzes of 67 C. minutus and 100 C. flamarioni scat samples, collected along the species geographical ranges. Thirteen plant families, mainly represented by Poaceae, Araliaceae, Asteraceae and Fabaceae, were identified in the diet of C. minutus. For C. flamarioni, 10 families were recovered, with a predominance of Poaceae, Araliaceae and Asteraceae. A significant correlation between diet composition and geographical distance was detected in C. minutus, whereas the diet of C. flamarioni was quite homogeneous throughout its geographical distribution. No significant differences were observed between males and females of each species. However, differences in diet composition between species were evident according to multivariate analysis. Our results suggest some level of diet partitioning between C. flamarioni and C. minutus in the sympatric region. While the first species is more specialized on few plant items, the second showed a more varied and heterogeneous diet pattern among individuals. These differences might have been developed to avoid competition in the region of co-occurrence. Resource availability in the environment also seems to influence food choices. Our data indicate that C. minutus and C. flamarioni are generalist species, but that some preference for Poaceae, Asteraceae and Araliaceae families can be suggested for both rodents.Heredity advance online publication, 4 February 2015; doi:10.1038/hdy.2014.109.
    Full-text · Article · Feb 2015 · Heredity

  • No preview · Conference Paper · Jan 2015
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    ABSTRACT: Environmental DNA (eDNA) metabarcoding is increasingly used to study present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of presence / absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts, and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in presence of observational errors can successfully estimate true prevalence, detection probability, and false positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability, and false positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies, and could be explicitly estimated to improve the reliability of results.This article is protected by copyright. All rights reserved.
    Full-text · Article · Oct 2014 · Molecular Ecology Resources
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    ABSTRACT: Among apicomplexan parasites, ticks are known vector of several species belongs to three protozoan genera (Babesia, Theileria and Hepatozoon). During their life cycle, tick-transmitted apicomplexan parasites alternate between asexual (in vertebrate host) and sexual (in ticks) developmental stages. The major constraint for the proper diagnostics of those pathogens is the high possibility of mix infection, both in ticks and vertebrate hosts, with several species or genotypes. The aim of this study was to apply the Next Generation Sequencing (NGS) as a method of choice for simultaneous determination of the full spectrum of api-complexan pathogens in ticks and the mammalian hosts. Therefore, A pair of universal primers were designed to flank a 167 bp barcode region of the 18s rRNA gene of all Babesia, Theileria and Hepatozoon species. The new protocol was evaluated on DNA samples isolated from 195 dogs and 144 ticks (Rhipicephalus armatus and R. pulchellus) collected from Northern Kenya. In total 301 sample (89%) were positive for apicomplexan infections; ranging from single to multiple infection with one species or several species and/or genotypes in a single sample. The most abundant apicomplexan pathogens were Hepatozoon followed by Babesia and Theileria, respectively. Further, the result shows that the barcode region entails enough variability that allows identifying the pathogens up to the subspecies and genotypes level. The exact methodological and results detailed will be presented later.
    Full-text · Conference Paper · May 2014
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    ABSTRACT: Among apicomplexan parasites, ticks are known vector of several species belongs to three protozoan genera (Babesia, Theileria and Hepatozoon). During their life cycle, tick-transmitted apicomplexan parasites alternate between asexual (in vertebrate host) and sexual (in ticks) developmental stages. The major constraint for the proper diagnostics of those pathogens is the high possibility of mix infection, both in ticks and vertebrate hosts, with several species or genotypes. The aim of this study was to apply the Next Generation Sequencing (NGS) as a method of choice for simultaneous determination of the full spectrum of api-complexan pathogens in ticks and the mammalian hosts. Therefore, A pair of universal primers were designed to flank a 167 bp barcode region of the 18s rRNA gene of all Babesia, Theileria and Hepatozoon species. The new protocol was evaluated on DNA samples isolated from 195 dogs and 144 ticks (Rhipicephalus armatus and R. pulchellus) collected from Northern Kenya. In total 301 sample (89%) were positive for apicomplexan infections; ranging from single to multiple infection with one species or several species and/or genotypes in a single sample. The most abundant apicomplexan pathogens were Hepatozoon followed by Babesia and Theileria, respectively. Further, the result shows that the barcode region entails enough variability that allows identifying the pathogens up to the subspecies and genotypes level. The exact methodological and results detailed will be presented later.
    Full-text · Conference Paper · Apr 2014
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    Full-text · Article · Apr 2014 · Parasites & Vectors
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    ABSTRACT: Ecological understanding of the role of consumer-resource interactions in natural food webs is limited by the difficulty of accurately and efficiently determining the complex variety of food types animals have eaten in the field. We developed a method based on DNA metabarcoding multiplexing and next-generation sequencing to uncover different taxonomic groups of organisms from complex diet samples. We validated this approach on 91 faeces of a large omnivorous mammal, the brown bear, using DNA metabarcoding markers targeting the plant, vertebrate, and invertebrate components of the diet. We included internal controls in the experiments and performed PCR replication for accuracy validation in post-sequencing data analysis. Using our multiplexing strategy, we significantly simplified the experimental procedure and accurately and concurrently identified different prey DNA corresponding to the targeted taxonomic groups, with ≥60% of taxa of all diet components identified to genus/species level. The systematic application of internal controls and replication was a useful and simple way to evaluate the performance of our experimental procedure, standardize the selection of sequence filtering parameters for each marker data, and validate the accuracy of the results. Our general approach can be adapted to the analysis of dietary samples of various predator species in different ecosystems, for a number of conservation and ecological applications entailing large-scale population level diet assessment through cost effective screening of multiple DNA metabarcodes, and the detection of fine dietary variation among samples or individuals and of rare food items. This article is protected by copyright. All rights reserved.
    Full-text · Article · Oct 2013 · Molecular Ecology Resources
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    ABSTRACT: The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, -80oC) and cryoprotectants (PBS-glycerol, ethanol) on quality and quantity parameters of extracted DNA was evaluated by bacterial DGGE analysis, real-time PCR quantification and metabarcoding approach using high-throughput sequencing. Samples clustered according to the type of extracted DNA due to considerable differences between iDNA and eDNA bacterial profiles, while storage temperature and cryoprotectants additives had little effect on sample clustering. The numbers of Firmicutes and Bacteroidetes were lower (P<0.01) in eDNA samples. The qPCR indicated significantly higher amount of Firmicutes in iDNA sample frozen with glycerol (P<0.01). Deep sequencing analysis of iDNA samples revealed the prevalence of Bacteroidetes and similarity of samples frozen with and without cryoprotectants, which differed from sample stored with ethanol at room temperature. Centrifugation and consequent filtration of rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at - 80°C was found as the optimal method to study ruminal bacterial profile.
    Full-text · Article · Oct 2013 · Anaerobe
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    ABSTRACT: This paper considers a statistical modelling approach to investigate spatial cross-correlations between species in an ecosystem. A special feature is the origin of the data from high-troughput environmental DNA sequencing of soil samples. Here we use data collected at the Nourague CNRS Field Station in French Guiana. We describe bivariate spatial relationships in these data by a separable linear model of coregionalisation and estimate a cross-correlation parameter. Based on this estimate, we visualise plant taxa co-occurrence pattern in form of 'interaction graphs' which can be interpreted in terms of ecological interactions. Limitations of this approach are discussed along with possible alternatives.
    No preview · Conference Paper · May 2013
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    ABSTRACT: Wildlife is considered to be mainly exposed to environmental contaminants via oral route. Food web analysis is therefore crucial in environmental risk assessment and management. In this context, diet information is commonly obtained from literature and little attention has been given to site-specific considerations (habitat, season…), which might considerably affect diet composition and thus wildlife exposure assessment. By associating next-generation sequencing and DNA barcoding techniques, the metabarcoding molecular approach of diet analysis could achieve a better taxonomic identification of food items with lower time investment than traditional micro- and macro-histological observations of food remains. In this context, the aim of this study is to evaluate the use of this new molecular method to investigate the diet of wild small mammals exposed to arsenic (As) and eventually to better understand and model its transfers. On a partially remediated former gold mine in southern France, small mammals were captured in spring and autumn in zones differing by their remediation treatment and in a control site. Botanical surveys were also performed on the polluted site. DNA was extracted from stomach content (n=96) and faeces (n=19) and then amplified with 3 primers sets, allowing to get plants and invertebrates (molluscs, arthropods and earthworms) DNA. Finally, amplified DNA was sequenced on next-generation sequencer. Preliminary results on plant DNA showed that 95% of the sequences were at least identified to family level and among them 13% were identified up to species level. This attests the possibility to reach a precise taxonomic level with this molecular method. Stomach contents and faeces from a given small mammal specimen gave complementary information, probably because they correspond to different meals. The results also suggested different food patterns among small mammal species, probably related to their foraging ecology. Comparisons between plant taxa identified in the diet and local botanical survey showed some mismatches, which may be related to small mammal mobility during their foraging activity. As a conclusion, the recent DNA metabarcoding is a promising approach to relate local food web structure to resource availability and thus to better understand pollutant trophic transfer in ecosystems.
    No preview · Conference Paper · May 2013
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    ABSTRACT: Pseudomonas aeruginosa is capable of injecting protein toxins into other bacterial cells through one of its three type VI secretion systems (T6SSs). The activity of this T6SS is tightly regulated on the posttranslational level by phosphorylation-dependent and -independent pathways. The phosphorylation-dependent pathway consists of a Threonine kinase/phosphatase pair (PpkA/PppA) that acts on a forkhead domain-containing protein, Fha1, and a periplasmic protein, TagR, that positively regulates PpkA. In the present work, we biochemically and functionally characterize three additional proteins of the phosphorylation-dependent regulatory cascade that controls T6S activation: TagT, TagS and TagQ. We show that similar to TagR, these proteins act upstream of the PpkA/PppA checkpoint and influence phosphorylation of Fha1 and, apparatus assembly and effector export. Localization studies demonstrate that TagQ is an outer membrane lipoprotein and TagR is associated with the outer membrane. Consistent with their homology to lipoprotein outer membrane localization (Lol) components, TagT and TagS form a stable inner membrane complex with ATPase activity. However, we find that outer membrane association of T6SS lipoproteins TagQ and TssJ1, and TagR, is unaltered in a ΔtagTS background. Notably, we found that TagQ is indispensible for anchoring of TagR to the outer membrane fraction. As T6S-dependent fitness of P. aeruginosa requires TagT, S, R and Q, we conclude that these proteins likely participate in a trans-membrane signalling pathway that promotes H1-T6SS activity under optimal environmental conditions.
    Full-text · Article · Jun 2012 · Environmental Microbiology
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    ABSTRACT: The automatic identification of syntenies across multiple species is a key step in comparative genomics that helps biologists shed light both on evolutionary and functional problems. In this paper, we present a versatile tool to extract all syntenies from multiple bacterial species based on a clear-cut and very flexible definition of the synteny blocks that allows for gene quorum, partial gene correspondence, gaps, and a partial or total conservation of the gene order. We apply this tool to two different kinds of studies. The first one is a search for functional gene associations. In this context, we compare our tool to a widely used heuristic--I-ADHORE--and show that at least up to ten genomes, the problem remains tractable with our exact definition and algorithm. The second application is linked to evolutionary studies: we verify in a multiple alignment setting that pairs of orthologs in synteny are more conserved than pairs outside, thus extending a previous pairwise study. We then show that this observation is in fact a function of the size of the synteny: the larger the block of synteny is, the more conserved the genes are.
    Full-text · Article · May 2011 · BMC Bioinformatics
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    ABSTRACT: Bacteria that live in the environment have evolved pathways specialized to defend against eukaryotic organisms or other bacteria. In this manuscript, we systematically examined the role of the five type VI secretion systems (T6SSs) of Burkholderia thailandensis (B. thai) in eukaryotic and bacterial cell interactions. Consistent with phylogenetic analyses comparing the distribution of the B. thai T6SSs with well-characterized bacterial and eukaryotic cell-targeting T6SSs, we found that T6SS-5 plays a critical role in the virulence of the organism in a murine melioidosis model, while a strain lacking the other four T6SSs remained as virulent as the wild-type. The function of T6SS-5 appeared to be specialized to the host and not related to an in vivo growth defect, as ΔT6SS-5 was fully virulent in mice lacking MyD88. Next we probed the role of the five systems in interbacterial interactions. From a group of 31 diverse bacteria, we identified several organisms that competed less effectively against wild-type B. thai than a strain lacking T6SS-1 function. Inactivation of T6SS-1 renders B. thai greatly more susceptible to cell contact-induced stasis by Pseudomonas putida, Pseudomonas fluorescens and Serratia proteamaculans-leaving it 100- to 1000-fold less fit than the wild-type in competition experiments with these organisms. Flow cell biofilm assays showed that T6S-dependent interbacterial interactions are likely relevant in the environment. B. thai cells lacking T6SS-1 were rapidly displaced in mixed biofilms with P. putida, whereas wild-type cells persisted and overran the competitor. Our data show that T6SSs within a single organism can have distinct functions in eukaryotic versus bacterial cell interactions. These systems are likely to be a decisive factor in the survival of bacterial cells of one species in intimate association with those of another, such as in polymicrobial communities present both in the environment and in many infections.
    Full-text · Article · Aug 2010 · PLoS Pathogens

Publication Stats

595 Citations
108.80 Total Impact Points

Institutions

  • 2015
    • Université Grenoble Alpes
      Grenoble, Rhône-Alpes, France
  • 2014-2015
    • University of Grenoble
      Grenoble, Rhône-Alpes, France
  • 2013-2015
    • French National Centre for Scientific Research
      Lutetia Parisorum, Île-de-France, France
  • 2012-2014
    • University Joseph Fourier - Grenoble 1
      • Laboratoire d'Ecologie Alpine
      Grenoble, Rhône-Alpes, France
  • 2011
    • University of Lyon
      Lyons, Rhône-Alpes, France
  • 2005-2010
    • Claude Bernard University Lyon 1
      • Laboratoire de biométrie et biologie evolutive (LBBE)
      Villeurbanne, Rhône-Alpes, France
  • 2009
    • Cea Leti
      Grenoble, Rhône-Alpes, France