PubMed | Lebanese University, Pasteur Institute of Lille, GENES DIFFUSION, Lille University of Science and Technology and Lille University Hospital Center
Type: Journal Article | Journal: The Journal of eukaryotic microbiology | Year: 2016
To quantitatively assess the risk of contamination by Pneumocystis depending on the degree of immunosuppression (ID) of the exposed rat hosts, we developed an animal model, where rats went through different doses of dexamethasone. Then, natural and aerial transmission of Pneumocystis carinii occurred during cohousing of the rats undergoing gradual ID levels (receivers) with nude rats developing pneumocystosis (seeders). Following contact between receiver and seeder rats, the P. carinii burden of receiver rats was determined by toluidine blue ortho staining and by qPCR targeting the dhfr monocopy gene of this fungus. In this rat model, the level of circulating CD4(+) and CD8(+) T lymphocytes remained significantly stable and different for each dose of dexamethasone tested, thus reaching the goal of a new stable and gradual ID rat model. In addition, an inverse relationship between the P. carinii burden and the level of circulating CD4(+) or CD8(+) T lymphocytes was evidenced. This rat model may be used to study other opportunistic pathogens or even co-infections in a context of gradual ID.
PubMed | Lille University Hospital Center, Genes Diffusion and French Institute for Research in Computer Science and Automation
Type: Journal Article | Journal: PloS one | Year: 2017
Targeted metagenomics, also known as metagenetics, is a high-throughput sequencing application focusing on a nucleotide target in a microbiome to describe its taxonomic content. A wide range of bioinformatics pipelines are available to analyze sequencing outputs, and the choice of an appropriate tool is crucial and not trivial. No standard evaluation method exists for estimating the accuracy of a pipeline for targeted metagenomics analyses. This article proposes an evaluation protocol containing real and simulated targeted metagenomics datasets, and adequate metrics allowing us to study the impact of different variables on the biological interpretation of results. This protocol was used to compare six different bioinformatics pipelines in the basic user context: Three common ones (mothur, QIIME and BMP) based on a clustering-first approach and three emerging ones (Kraken, CLARK and One Codex) using an assignment-first approach. This study surprisingly reveals that the effect of sequencing errors has a bigger impact on the results that choosing different amplified regions. Moreover, increasing sequencing throughput increases richness overestimation, even more so for microbiota of high complexity. Finally, the choice of the reference database has a bigger impact on richness estimation for clustering-first pipelines, and on correct taxa identification for assignment-first pipelines. Using emerging assignment-first pipelines is a valid approach for targeted metagenomics analyses, with a quality of results comparable to popular clustering-first pipelines, even with an error-prone sequencing technology like Ion Torrent. However, those pipelines are highly sensitive to the quality of databases and their annotations, which makes clustering-first pipelines still the only reliable approach for studying microbiomes that are not well described.
PubMed | GENES DIFFUSION and Lille University Hospital Center
Type: | Journal: Scientific reports | Year: 2016
Alterations in the composition of commensal bacterial populations, a phenomenon known as dysbiosis, are linked to multiple gastrointestinal disorders, such as inflammatory bowel disease and irritable bowel syndrome, or to infections by diverse enteric pathogens. Blastocystis is one of the most common single-celled eukaryotes detected in human faecal samples. However, the clinical significance of this widespread colonization remains unclear, and its pathogenic potential is controversial. To address the issue of Blastocystis pathogenicity, we investigated the impact of colonization by this protist on the composition of the human gut microbiota. For that purpose, we conducted a cross-sectional study including 48 Blastocystis-colonized patients and 48 Blastocystis-free subjects and performed an Ion Torrent 16S rDNA gene sequencing to decipher the Blastocystis-associated gut microbiota. Here, we report a higher bacterial diversity in faecal microbiota of Blastocystis colonized patients, a higher abundance of Clostridia as well as a lower abundance of Enterobacteriaceae. Our results contribute to suggesting that Blastocystis colonization is usually associated with a healthy gut microbiota, rather than with gut dysbiosis generally observed in metabolic or infectious inflammatory diseases of the lower gastrointestinal tract.
Auvigne V.,Polytechnic University of Valencia |
Leneveu P.,British Petroleum |
Jehannin C.,Genes Diffusion |
Peltoniemi O.,University of Helsinki |
Salle E.,British Petroleum
Theriogenology | Year: 2010
The objective of this study was to analyze the relative roles of high temperature and photoperiod as environmental factors of seasonal infertility in swine. The results of five years (2003-2007) of ultrasound pregnancy diagnosis carried out in 266 indoor farms were analyzed. For all farms, the data covered the entire study period. The farms were situated in four French regions. The data of 22,773 batches and 610,117 sows were included. Seasonal infertility was defined as the relative difference between the fertility rate in 'summer' (inseminations in weeks 25-42) and 'winter' (inseminations in weeks 1-18 of the same year). In each region, two meteorological variableswere defined, based on the data of a referenceweather station: the number of hot days (maximumtemperature ≥ 25 °C) and tropical days (maximum temperature ≥ 32 °C and minimum temperature ≥ 18 ° C). The mean fertility was 85%. The median seasonal infertility was 2.8% and more than 7.1%for a quarter of farms. Seasonal infertility did not vary with areas or baseline fertility (defined for each studied farm as the average winter fertility over five years). Seasonal infertility differed with the year (p < 0.001). Seasonal infertility was significantly higher during 2003 than in the other four years, which did not differ among each other. In the four regions, 2003 was the year with the highest number of hot days and 2007 with the least. Our study strengthens the hypothesis of a prominent role of photoperiod in seasonal infertility and of an additional role of heat stress the hottest years. © 2010 Elsevier Inc. All rights reserved.
Caboche S.,University of Lille Nord de France |
Caboche S.,Institute Pasteur Of Lille |
Audebert C.,Genes Diffusion |
Audebert C.,Institute Pasteur Of Lille |
And 4 more authors.
BMC Genomics | Year: 2014
Background: The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms.Results: In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic variation positions. To measure robustness, we introduced a new definition for a correctly mapped read taking into account not only the expected start position of the read but also the end position and the number of indels and substitutions. We developed CuReSim, a new read simulator, that is able to generate customized benchmark data for any kind of HTS technology by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool to evaluate the mapping quality of the CuReSim simulated reads, are freely available. We applied our benchmark procedure to evaluate 14 mappers in the context of whole genome sequencing of small genomes with Ion Torrent data for which such a comparison has not yet been established.Conclusions: A benchmark procedure to compare HTS data mappers is introduced with a new definition for the mapping correctness as well as tools to generate simulated reads and evaluate mapping quality. The application of this procedure to Ion Torrent data from the whole genome sequencing of small genomes has allowed us to validate our benchmark procedure and demonstrate that it is helpful for selecting a mapper based on the intended application, questions to be addressed, and the technology used. This benchmark procedure can be used to evaluate existing or in-development mappers as well as to optimize parameters of a chosen mapper for any application and any sequencing platform. © 2014 Caboche et al.; licensee BioMed Central Ltd.
Van der Spek D.,Wageningen University |
Van Arendonk J.A.M.,Wageningen University |
Vallee A.A.A.,Genes Diffusion |
Bovenhuis H.,Wageningen University
Journal of Dairy Science | Year: 2013
Claw disorders are important traits relevant to dairy cattle breeding from an economical and welfare point of view. Selection for reduced claw disorders can be based on hoof trimmer records. Typically, not all cows in a herd are trimmed. Our objectives were to estimate heritabilities and genetic correlations for claw disorders and investigate the effect of selecting cows for trimming. The data set contained 50,238 cows, of which 20,474 cows had at least one claw trimming record, with a total of 29,994 records. Six claw trimmers scored 14 different claw disorders: abscess (AB), corkscrew claw (CC), (inter-)digital dermatitis or heel erosion (DER), double sole (DS), hardship groove (HG), interdigital hyperplasia (IH), interdigital phlegmon (IP), sand crack (SC), super-foul (SF), sole hemorrhage (SH), sole injury (SI), sole ulcer (SU), white line separation (WLS), yellow discoloration of the sole (YD), and a combined claw disorder trait. Frequencies of the claw disorders for trimmed cows ranged from 0.1% (CC, YD, HG) to 23.8% (DER). More than half of the cows scored had at least one claw disorder. Heritability on the observed scale ranged from 0.02 (DS, SH) to 0.14 (IH) and on the underlying scale from 0.05 to 0.43 in trimmed cows. Genetic correlations between laminitis-related claw disorders were moderate to high, and the same was found for hygiene-related claw disorders. The effect of selecting cows for trimming was first investigated by including untrimmed cows in the analyses and assuming they were not affected by claw disorders. Heritabilities on the underlying scale showed only minor changes. Second, different subsets of the data were created based on the percentage of trimmed cows in the herd. Heritabilities for IH, DER, and SU tended to decrease when a higher percentage of cows in the herd were trimmed. Finally, a bivariate model with a claw disorder and the trait "trimming status" was used, but heritabilities were similar. Heritability for trimming status was relatively high (0.09). Genetic correlations of trimming status with claw disorders were generally moderate to high. To conclude, the effect of selecting cows for trimming on the heritability for claw disorders is negligible. Selecting herds with a high fraction of cows being trimmed tended to decrease heritability. Trimming status, as such, is a heritable trait and correlated with claw disorders and is therefore an interesting trait to include in the genetic evaluation. © 2013 American Dairy Science Association.
Vallee A.,Wageningen University |
Van Arendonk J.A.M.,Genes Diffusion |
Bovenhuis H.,Genes Diffusion
Journal of Animal Science | Year: 2013
Charolais sires can be mated to Montbéliard or Holstein dairy cows to produce crossbred calves sold for meat production. Heritabilities and correlations between traits can differ when they are calculated within Charolais × Montbéliard or within Charolais × Holstein population. Moreover, the genetic correlation between the same trait measured on Charolais × Montbéliard and on Charolais × Holstein crossbred calves is not necessarily unity. The first objective of this study was to estimate heritability and genetic correlation between traits within Charolais × Montbéliard and within Charolais × Holstein population. The second objective was to investigate if those traits are genetically identical between crossbred populations. Traits studied were calving difficulty, birth weight, height, bone thinness, and muscular develein population. The second objective was to investigate if those traits are genetically identical between crossbred populations. Traits studied were calving difficulty, birth weight, height, bone thinness, and muscular development. Data included 22,852 Charolais × Montbéliard and 16,012 Charolais × Holstein crossbred calves from 391 Charolais sires. Heritabilities estimated separately within each crossbred population were similar. Stronger genetic correlations were observed in Charolais × Holstein population compared with Charolais × Montbéliard between calving difficulty and height (0.67 vs. 0.54), calving difficulty and bone thinness (0.42 vs. 0.27), birth weight and bone thinness (0.52 vs. 0.20), and birth weight and muscular development (0.41 vs. 0.18). Bivariate analysis considering observations on Charolais × Montbéliard and on Charolais × Holstein as different traits showed that genetic variances and heritabilities were similar for all traits except height. Birth weight and muscular development were genetically identical traits in each crossbred populations, with genetic correlations of 0.96 and 0.99. Genetic correlations were 0.91 for calving difficulty, 0.80 for height, and 0.70 for bone thinness and log-likelihood ratio tests indicated that they were significantly different from 1 (P ≤ 0.01). Results show evidence for reranking of Charolais sires for calving difficulty, height, and bone thinness depending on whether they are mated to Montbéliard or Holstein cows. © 2013 American Society of Animal Science. All rights reserved.
Genes Diffusion | Date: 2010-12-06
A porcine seminal material composition intended for artificial insemination of sows includes capsules containing a suspension made of porcine seminal material coated with a bi-valent or tri-valent ion alginate film, wherein the porcine spermatozoon concentration within the porcine seminal material suspension present in the capsules is between 900 and 1500 million spermatozoa per milliliter.
Genes Diffusion | Date: 2016-05-24
PubMed | University of Lille Nord de France and GENES DIFFUSION
Type: Journal Article | Journal: Medical mycology | Year: 2014
In order to standardize a polymerase chain reaction (PCR)-based method of Pneumocystis detection, we describe the development of an improved PCR method that targets the Pneumocystis mtLSUrRNA gene. Design of a new primer pair and PCR program with suitable parameters and optimization resulted in a simpler and faster single-round amplification assay. The sensitivity of the novel Pneumocystis genus-specific PCR proved comparable to the reference nested PCR. The improvement that this new PCR assay offers in the detection and epidemiological studies of Pneumocystis spp. infection in research laboratories is discussed.