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.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The association between Cryptosporidium and human colon cancer has been reported in different populations. However, this association has not been well studied. In order to add new strong arguments ...for a probable link between cryptosporidiosis and colon human cancer, the aim of this study was to determine prevalence and to identify species of Cryptosporidium among Lebanese patients.
Overall, 218 digestive biopsies were collected in Tripoli, Lebanon, from three groups of patients: (i) patients with recently diagnosed colon intraepithelial neoplasia/adenocarcinoma before any treatment (n = 72); (ii) patients with recently diagnosed stomach intraepithelial neoplasia/adenocarcinoma before any treatment (n = 21); and (iii) patients without digestive intraepithelial neoplasia/adenocarcinoma but with persistent digestive symptoms (n = 125). DNA extraction was performed from paraffin-embedded tissue. The presence of the parasite in tissues was confirmed by PCR, microscopic observation and immunofluorescence analysis. We identified a high rate (21%) of Cryptosporidium presence in biopsies from Lebanese patients with recently diagnosed colonic neoplasia/adenocarcinoma before any treatment. This prevalence was significantly higher compared to 7% of Cryptosporidium prevalence among patients without colon neoplasia but with persistent gastrointestinal symptoms (OR: 4, CI: 1.65-9.6, P = 0.001). When the comparison was done against normal biopsies, the risk of infection increased 11-fold in the group of patients with colon adenocarcinoma (OR: 11.315, CI: 1.44-89.02, P = 0.003).
This is the first study performed in Lebanon reporting the prevalence of Cryptosporidium among patients with digestive cancer. These results show that Cryptosporidium is strongly associated with human colon cancer being maybe a potential etiological agent of this disease.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In cattle farming, the artificial insemination technique is a biotechnology that brings to farmers a wide range of benefits namely health security, genetic gain and economic costs. The main condition ...for the success of artificial insemination within cattle is the heat (or estrus) detection. In this context, several cow heat detection systems have been recently proposed in the literature to assist the farmer in this task. Nevertheless, they are mainly based on the analysis of the physical behavior of the cow which may be affected by several factors related to its health and its environment. In this paper, we present a new vision system for cow heat detection which is based on the analysis of the genital tract of the cow. The main core of our system is a CNN model that has been designed and tailored for analyzing endoscopic images collected using an innovative insemination technology named Eye breed. The conducted experiments on two datasets namely our own dataset and a public dataset show the high accuracy of our CNN model (more than 97% for both datasets) outperforming 19 methods from the state of the art. Moreover, we propose an optimized version of our model for an Android deployment by exploiting several techniques namely quantization, GPU acceleration and video downsampling. The conducted tests on a smart-phone shows that our heat detection system has a response time of a few seconds.
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CEKLJ, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
•The profile of the seminal microbiota and the microbial diversity indicate differences related to the production centers.•The profile of the porcine seminal microbiota appears to be mainly related ...to the center in which the animals are bred.•A sudden change in the overall profile of the seminal microbiota can be associated with a process problem.•Bacterial metagenomics by HTS can be used in a pig semen production context to better understand bacteriospermia.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
In this article, we propose a new approach for the cow heat detection from endoscopic images. Our approach permits to identify on the fly the cow heat state through two successive stages, namely ...cervix detection then heat classification. For this purpose, images are analyzed by a Transformer based detection model to localize the cervix, in which case they are analyzed by a CNN-based heat classification model. The proposed approach permits to assist the farmer during the insemination operation by localizing the cervix in an accurate way. Moreover, the confidence level of the final decision of the classification model is increased by focusing its analysis only on cervix images. The effectiveness of our method is demonstrated on our generated dataset and the obtained performance outperform the state of the art.
Genotypic and phenotypic data of 1,562 animals were analyzed to find genomic regions that potentially influence the birth weight (BW), weaning weight at seven months of age (WW) and yearling weight ...(YW) of Colombian Brahman cattle, with genotyping conducted using Illumina Bead chip array with 74,669 SNPs. A Single Step Genomic BLUP (ssGBLP), approach was used to estimate the proportion of variance explained by each marker. Multiple regions scattered across the genome were found to influence weights at different ages, also dependent on the trait component (direct or maternal). The most interesting regions were connected to previously identified QTLs and genes, such as ADAMTSL3, CAPN2, CAPN2, FABP6, ZEB2 influencing growth and weight traits. The identified regions will contribute to the development and refinement of genomic selection programs for Zebu Brahman cattle in Colombia.
Despite the major impact of Blastocystis sp. in terms of prevalence in human and animal populations and the risk of zoonotic transmission, no epidemiological survey has yet been conducted in cattle ...herds in France. The aim of this study was thus to assess the prevalence and molecular diversity of Blastocystis sp. and associated factors in dairy cattle from the north of France. A total of 1581 fecal samples were collected from 1246 animals reared in 20 farms. Molecular detection of the protozoan was performed by real-time PCR and indicated an overall prevalence of Blastocystis sp. reaching 54.8% in the study population. Important inter-herd variation (from 22.2% to 76.5%) of Blastocystis sp. prevalence was also reported. Sequence analysis of 159 positive samples highlighted a very large predominance of ST10 (36/159) and ST14 (64/159), and ST2 was only found in 2 samples. Mixed subtype infections were common, representing 35.8% of sequenced samples (57/159). A putative correlation between Blastocystis sp. colonization and various animal and herd characteristics or feed intake was subsequently investigated. The protozoan was less prevalent in cows that have recently calved but Blastocystis sp. carriage was not significantly related to age. Blastocystis sp. colonization also decreased with high beet pulp and pasture grass consumption and increased with corn silage intake. Finally, the only significant association between Blastocystis sp. STs and animal and herd characteristics was the number of lactations of cows, with a predominance of ST14 in cows that calved once only.
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.
In the past decade, metagenomics studies have become widespread due to the arrival of second-generation sequencing platforms characterized by low costs, high throughput and short read lengths. Today, ...although benchtop sequencers are considered to be accurate platforms to deliver data for targeted metagenomics studies, the limiting factor has become the analysis of these data. In a previous paper, we performed an Ion Torrent PGM 16S rDNA gene sequencing of faecal DNAs from 48 Blastocystis-colonized patients and 48 Blastocystis-negative subjects, in order to decipher the impact of this widespread protist on gut microbiota composition and diversity. We report here on the Ion Torrent targeted metagenomic sequencing and analysis of these 96 human faecal samples, and the complete datasets from raw to analysed data. We also provide the key steps of the bioinformatic analyses, from library preparation to data filtering and OTUs tables generation. This data represents a valuable resource for the scientific community, enabling re-processing of these targeted metagenomic datasets through various pipelines and a comparative evaluation of microbiota analysis methods.
In the fight against SARS-COV-2, the development of serological assays based on different antigenic domains represent a versatile tool to get a comprehensive picture of the immune response or ...differentiate infection from vaccination beyond simple diagnosis. Here we use a combination of the Nucleoprotein (NP), the Spike 1 (S1) and Spike 2 (S2) subunits, and the receptor binding domain (RBD) and N-terminal domain (NTD) of the Spike antigens from the CoViDiag® multiplex IgG assay, to follow the immune response to SARS-CoV-2 infection over a long time period and depending on disease severity. Using a panel of 209 sera collected from 61 patients up to eight months after infection, we observed that most patients develop an immune response against multiple viral epitope, but anti-S2 antibodies seemed to last longer. For all the tested IgGs, we have found higher responses for hospitalized patients than for non-hospitalized ones. Moreover the combination of the five different IgG responses increased the correlation to the neutralizing antibody titers than if considered individually. Multiplex immunoassays have the potential to improve diagnostic performances, especially for ancient infection or mild form of the disease presenting weaker antibody responses. Also the combined detection of anti-NP and anti-Spike-derived domains can be useful to differentiate vaccination from viral infection and accurately assess the antibody potential to neutralize the virus.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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