Biology subjects

Rogers, M. R. C.

Publications and source records attributed to Rogers, M. R. C..

4 recordsLinked to original sources

bioRxiv2018

Bariatric surgery changes gut microbiota composition independent of operation type

BackgroundBariatric surgery in patients with morbid obesity, either through gastric sleeve gastrectomy or Roux-Y gastric bypass surgery, leads to sustainable weight loss, improvement of metabolic disorders and changes in the intestinal microbiota. Yet, the relationship between changes in gut microbiota, weight loss and the surgical procedure remains incompletely understood.\n\nSubjects/MethodsWe determined temporal changes in microbiota composition in 45 obese patients undergoing a crash diet followed by gastric sleeve gastrectomy (n= 22) or Roux-Y gastric bypass (n= 23). Intestinal microbiota composition was determined before intervention (baseline, S1), 2 weeks after a crash diet (S2), and 1 week (S3), 3 months (S4) and 6 months (S5) after surgery.\n\nResultsRelative to S1, the microbial diversity index declined at S2 and S3 (p< 0.05), and gradually returned to baseline levels at S5. The crash diet was associated with an increased abundance of Rikenellaceae and decreased abundances of Ruminococcaceae and Streptococcaceae (p< 0.05). After surgery, at S3, the relative abundance of Bifidobacteriaceae had decreased (compared to the moment directly after the crash diet), whereas those of Streptococcaceae and Enterobacteriaceae had increased (p< 0.05). Increased weight loss during the next 6 months was not associated without major changes in microbiota composition. Significant differences between both surgical procedures were not observed at any of the time points.\n\nConclusionsIn conclusion, undergoing a crash diet and bariatric surgery were associated with an immediate but temporary decline in the microbial diversity, with immediate and permanent changes in microbiota composition, with no differences between patients undergoing gastric sleeve gastrectomy or Roux-Y gastric bypass surgery.

microbiology↗

bioRxiv2018

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

Assembly of bacterial short-read whole genome sequencing (WGS) data frequently results in hundreds of contigs for which the origin, plasmid or chromosome, is unclear. Long-read sequencing has emerged as a solution to resolve plasmid structures and to obtain complete genomes for most bacterial species. This information can be used to generate and label datasets from short-read based contigs as plasmid- or chromosome-derived. We investigated the use of several popular machine learning methods to classify short-read contigs with known plasmid- or chromosome-origin from Enterococcus faecium, Klebsiella pneumoniae and Escherichia coli using pentamer frequencies. Based on resulting F1-scores we selected support-vector machine (SVM) models as best classifier for all three bacterial species (F1-score E. faecium = 0.94, F1-score K. pneumoniae = 0.90, F1-score E. coli = 0.76), which outperformed other existing plasmid tools using an independent set of isolates (precision E. faecium = 0.92, precision K. pneumoniae = 0.86, precision E. coli = 0.82). We demonstrated the scalability of our model by accurately predicting the plasmidome of a large collection of 1,644 E. faecium isolates with only short-read WGS available using a standard laptop with a single core. A low number of false positive predicted sequences suggests that the assignment of a particular gene of interest as plasmid- or chromosome-encoded by the models is plausible. The SVM classifiers are publicly available as a new R package called mlplasmids at https://gitlab.com/sirarredondo/mlplasmids under the GNU General Public License v3.0. We additionally developed a graphical-user interface using the Shiny package which can be accessed at https://sarredondo.shinyapps.io/mlplasmids/. Single genomes can easily be predicted by uploading genome assemblies. We anticipate that this tool may significantly facilitate research on the dissemination of plasmids encoding antibiotic resistance and/or contributing to host adaptation.

microbiology↗

bioRxiv2018

Staphylococcal superantigen-like protein 13 activates neutrophils via Formyl Peptide Receptor 2

Staphylococcal Superantigen-Like (SSL) proteins, one of major virulence factor families produced by Staphylococcus aureus, were previously demonstrated to be immune evasion molecules that interfere with a variety of innate immune defenses. However, in contrast to these characterized SSLs, that inhibit immune functions, we show that SSL13 is a strong activator of neutrophils via the formyl-peptide receptor 2 (FPR2). Moreover, our data show that SSL13 acts as a chemoattractant, induces degranulation and oxidative burst in neutrophils. As with many other staphylococcal immune evasion proteins, SSL13 shows a high degree of human specificity. SSL13 is not able to efficiently activate mouse neutrophils, hampering in vivo experiments.\n\nIn conclusion, SSL13 is a neutrophil chemoattractant and activator that acts via the FPR2. Therefore, SSL13 is a unique SSL member that does not belong to the immune evasion class, but is a pathogen alarming molecule.

microbiology↗

bioRxiv2017

Fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum

Enterococcus faecium is a commensal of the human gastrointestinal tract and a frequent cause of bloodstream infections in hospitalized patients. Here, we identify genes that contribute to growth of E. faecium in human serum. We first sequenced the genome of E. faecium E745, a vancomycin-resistant clinical isolate, to completion and then compared its transcriptome during exponential growth in rich medium and in human serum by RNA-seq. This analysis revealed that 27.8% of genes on the E. faecium E745 genome were differentially expressed in these two conditions. A gene cluster with a role in purine biosynthesis was among the most upregulated genes in E. faecium E745 upon growth in serum. A high-throughput transposon sequencing (Tn-seq) approach was used to identify conditionally essential genes in E. faecium E745 during growth in serum. Genes involved in de novo nucleotide biosysnthesis (including pyrK_2, pyrF, purD, purH) and a gene encoding a phosphotransferase system subunit (manY_2) were thus identified to be contributing to E. faecium growth in human serum. Transposon mutants in pyrK_2, pyrF, purD, purH and manY_2 were isolated from the library and their impaired growth in human serum was confirmed. In addition, the pyrK_2 and manY_2 mutants also exhibited significantly attenuated virulence in an intravenous zebrafish infection model. We conclude that genes involved in carbohydrate and nucleotide metabolism of E. faecium are essential for growth in human serum and contribute to the pathogenesis of this organism.

microbiology↗