The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline, available as a web interface, for microbial identification and characterization through reads analysis. MICRA uses iterative mapping against reference genomes to identify genes and variations. Additional modules allow prediction of antibiotic susceptibility and resistance and comparing the results of several samples. MICRA is fast, producing few false-positive annotations and variant calls compared to current methods, making it a tool of great interest for fully exploiting sequencing data.

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.

INTRODUCTION AND PURPOSE:Propidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine whether a PMA-pretreatment coupled with high-throughput sequencing analysis provides a different picture of the airway mycobiome and bacteriome.RESULTS AND DISCUSSION:We compared deep-sequencing data of mycobiota and microbiota of 15 sputum samples from 5 cystic fibrosis (CF) patients with and without prior PMA-treatment of the DNA-extracts. PMA-pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic units (OTUs) with a relative abundance greater than or equal to 1%), but caused a significant difference in the intermediate community (less than 1%) when analyzing the alpha biodiversity Simpson index (p = 0.03). Regarding PMA impact on the airway mycobiota evaluated for the first time here; no significant differences in alpha diversity indexes between PMA-treated and untreated samples were observed. Regarding beta diversity analysis, the intermediate communities also differed more dramatically than the total and abundant ones when studying both mycobiome and bacteriome. Our results showed that only the intermediate (or low abundance) population diversity is impacted by PMA-treatment, and therefore that abundant taxa are mostly viable during acute exacerbation in CF. Given such a cumbersome protocol (PMA-pretreatment coupled with high-throughput sequencing), we discuss its potential interest within the follow-up of CF patients. Further studies using PMA-pretreatment are warranted to improve our "omic" knowledge of the CF airways.

Le prétraitement par propidium monoazide (PMA) est utilisé combiné aux méthodes de PCR, pour la détection sélective des pathogènes viables. Quelques études ont montré qu’un prétraitement par PMA influait sur les profils des communautés bactériennes obtenues par séquençage haut-débit (SHT), ce qui présente un intérêt dans les approches bio-cliniques du SHT. Dans ce contexte, notre étude vise à déterminer si un traitement par PMA des échantillons humains couplé à leur analyse par SHT donnerait une image plus tangible du microbiote pulmonaire fongique et bactérien de patients atteints de mucoviscidose, et par conséquent refléterait mieux l’état clinique des patients. Nous avons comparé les données obtenues par SHT des microbiotes fongiques et bactériens de 15 expectorations de patients atteints de mucoviscidose. Pour chaque échantillon, la technique Ion Torrent a été utilisée sur l’ADN ayant eu ou non un traitement préalable par PMA. L’analyse des données a été réalisée via les logiciels R et Past3. Si le prétraitement par PMA ne semble pas avoir d’effet significatif sur l’ensemble des communautés fongiques et bactériennes. Cette étape influence la communauté bactérienne de la biosphère rare (espèce représentée à moins de 1 % en abondance [OTU] relative) notamment lors de l’analyse de la biodiversité alpha. En ce qui concerne les données de mycobiomes, nous n’avons pas observé de différence significative entre les échantillons traités par PMA et non traités. Compte tenu de la lourdeur d’un tel protocole (prétraitement par PMA couplé au SHT) et de l’importance démontrée de la biosphère rare dans la stabilité d’une flore, son intérêt potentiel est discuté dans le contexte du suivi des patients atteints de mucoviscidose. D’autres études utilisant le prétraitement par PMA seront nécessaires pour améliorer nos connaissances « omiques » et mieux déterminer le place et/ou l’intérêt d’un tel protocole.

Objective Propidium monoazide (PMA) pretreatment has increasingly been used in molecular biology for detecting viable pathogens. Our study aims to determine whether a PMA pretreatment in high-throughput sequencing (HTS) could provide a more realistic picture of lung mycobiome and bacteriome from cystic fibrosis (CF) patients, and consequently reflect more closely the clinical status of patients. Methods We compared HTS data of bacteriome and mycobiome of 15 sputum samples from 5 CF patients that were characterized using the Ion Torrent technique with and without prior PMA treatment of the DNA-extracts. Results PMA pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic unit with a relative abundance of ≥1%) but caused a significant difference in the rare biosphere community ( Conclusion To conclude, PMA pretreatment seems to change the relative abundance of bacteria, especially in the rare populations, but not fungi. Given such a cumbersome protocol (PMA pretreatment coupled with HTS), we discuss its potential interest within the follow-up of CF patients. As only few studies suggested the use of this protocol in the characterization of the bacteriome may be clinically relevant, further studies using PMA pretreatment are warranted to improve our omic knowledge.

Background:Inflammatory bowel diseases are incurable illnesses of the gastrointestinal tract, which substantially enhance the risk of developing colorectal carcinogenesis. Conventional photodynamic therapy is a clinically approved therapeutic modality used in the treatment of neoplastic diseases. Recent preclinical and clinical studies have shown that photodynamic therapy with low doses of photosensitizer and/or light improves inflammatory conditions, including colitis. This study aims therefore at investigating the therapeutic potential of low-dose photodynamic therapy (LDPDT) with a liposomal formulation of meta-tetra(hydroxyphenyl)chlorin (namely Foslip) in the prevention of colitis-associated cancer in mice.Methods:LDPDT efficacy was evaluated by endoscopic, macroscopic, and histological analysis. Myeloperoxidase levels were quantified by enzyme linked immunosorbent assay and cytokines expression by quantitative RT-PCR analysis. The integrity of the intestinal barrier was evaluated by immunostaining, and bacterial composition of the fecal microbiota was determined by 454 pyrosequencing of V3-V4 region of bacterial 16S rRNA genes.Results:LDPDT reduced intestinal tumor growth by decreasing the expression of a wide range of inflammatory mediators and by lowering neutrophil influx. LDPDT treatment prevents onset of a dysbiotic microbiota in the colitis-associated cancer model.Conclusions:LDPDT with Foslip could be considered as a novel treatment modality to prevent colorectal carcinogenesis in patients with inflammatory bowel disease.