Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients

The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatic approaches, based on mapping of the reads onto databases and on the reconstruction of putative draft genomes, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with Shiga Toxin-producing E. coli (STEC) infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Both the bioinformatic procedures used, produced similar result with a good resolution of the taxonomic profiles of the specimens. The stool samples collected from the STEC infected patients showed a lower abundance of the members of Bifidobacteriales and Clostridiales orders in comparison to controls where those microorganisms predominated. These differences seemed to correlate with the STEC infection although a flexion in the relative abundance of the Bifidobacterium genus, part of the Bifidobacteriales order, was observed also in samples from Crohn's disease patients, displaying a STEC-unrelated dysbiosis. The metagenomics also allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak as assessed through isolation of the epidemic strain and whole genome sequencing. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection

Extensive Set of 16S rRNA-Based Probes for Detection of Bacteria in Human Feces

For the detection of six groups of anaerobic bacteria in human feces, we designed seven new 16S rRNA-based oligonucleotide probes. This set of probes extends the current set of probes and gives more data on the composition of the human gut flora. Probes were designed for Phascolarctobacterium and relatives (Phasco741), Veillonella (Veil223), Eubacterium hallii and relatives (Ehal1469), Lachnospira and relatives (Lach571), and Eubacterium cylindroides and relatives (Ecyl387), and two probes were designed for Ruminococcus and relatives (Rbro730 and Rfla729). The hybridization conditions for the new probes were optimized for fluorescent in situ hybridization, and the probes were validated against a set of reference organisms. The probes were applied to fecal samples of 11 volunteers to enumerate their target bacterial groups. The Phasco741 and Veil223 probes both detected average numbers below 1% of the total number of bacteria as determined with the bacterial kingdom-specific Bact338 probe. The Ecyl387 probe detected about 1.4%, the Lach571 and Ehal1469 probes detected 3.8 and 3.6%, respectively, and a combination of the Rbro730 and Rfla729 probes detected 10.3%. A set of 15 probes consisting of probes previously described and those presented here were evaluated in hybridization with the fecal samples of the same volunteers. Together, the group-specific probes detected 90% of the total bacterial cells

Microbial detection and monitoring in advanced life support systems like the international space station

Potentially pathogenic microbes and so-called technophiles may form a serious threat in advanced life support systems, such as the International Space Station (ISS). They not only pose a threat to the health of the crew, but also to the technical equipment and materials of the space station. The development of fast and easy to use molecular detection and quantification methods for application in manned spacecraft is therefore desirable and may also be valuable for applications on Earth. In this paper we present the preliminary results of the SAMPLE experiment in which we performed molecular microbial analysis on environmental samples of the ISS as part of an ESA-MAP project

Antibiotic susceptibility profiles of oral pathogens

Periodontitis is a bacterial disease that can be treated with systemic antibiotics. The aim of this study was to establish the antibiotic susceptibility profiles of five periodontal pathogens to six commonly used antibiotics in periodontics. A total of 247 periodontal bacterial isolates were tested for susceptibility to the six antibiotics using the Etest method. MIC50 and MIC90 values (minimum inhibitory concentrations for 50% and 90% of the organisms, respectively) were calculated. Both European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) breakpoints were used in the study to interpret results. beta-Lactamase production was tested when amoxicillin resistance was found. MIC90 values of the anaerobic bacteria were all well below breakpoint values, except for three isolates of Prevotella intermedia and one isolate of Fusobacterium nucleatum that were resistant to amoxicillin (CLSI breakpoints); these isolates were beta-lactamase-positive. Two isolates of the capnophilic Aggregatibacter actinomycetemcomitans appeared to be amoxicillin-resistant but failed to show beta-lactamase activity. Comparison with a previous study from The Netherlands showed minor differences in susceptibility profiles, but the MIC90 values of A. actinomycetemcomitans for amoxicillin, clindamycin, azithromycin and tetracycline were higher. Geographical differences in the susceptibility profiles of Porphyromonas gingivalis and A. actinomycetemcomitans between European countries were noted. Comparison of European susceptibility profiles with that of a South American country (Colombia) revealed a much higher resistance in the latter. Owing to these differences in susceptibility profiles, it is of concern to regularly perform surveillance studies on antibiotic resistance. (C) 2012 Elsevier B. V. and the International Society of Chemotherapy. All rights reserved

Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNAtargeted probes and its application in fecal samples

Three 16S rRNA hybridization probes were developed and tested for genus-specific detection of Bifidobacterium species in the human fecal flora. Variable regions V2, V4, and V8 of the 16S rRNA contained sequences unique to this genus and proved applicable as target sites for oligodeoxynucleotide probes. Determination of the genus specificity of the oligonucleotides was performed by whole-cell hybridization with fluorescein isothiocyanate-labelled probes. To this end, cells were fixed on glass slides, hybridized with the probes, and monitored by videomicroscopy. In combination with image analysis, this allowed quantification of the fluorescence per cell and objective evaluation of hybridization experiments. One of the probes developed was used to determine the population of Bifidobacterium spp. in human fecal samples. A comparison was made with results obtained by cultural methods for enumeration. Since both methods gave similar population estimates, it was concluded that all bifidobacteria in feces were culturable. However, since the total culturable counts were only a fraction of the total microscopic counts, the contribution of bifidobacteria to the total intestinal microflora was overestimated by almost 10-fold when cultural methods were used as the sole method for enumeration. The human intestinal tract harbors an active and complex bacterial ecosystem. The composition and activity of this indigenou

Changes in oral microflora after full-mouth tooth extraction:A prospective cohort study

AIM: The aim of the study was to evaluate the effect of full-mouth tooth extraction on the oral microflora, with emphasis on the presence and load of Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis. MATERIAL AND METHODS: Adult patients (n = 30), with moderate to advanced periodontitis and scheduled for full-mouth tooth extraction, were consecutively selected. Prior to and 1 and 3 months after full-mouth tooth extraction saliva, tongue, buccal and gingival mucosa and subgingival plaque/prosthesis samples were obtained. Aerobic and anaerobic culture techniques and quantitative real-time polymerase chain reaction (qPCR) were employed for the detection of oral pathogens. RESULTS: Full-mouth tooth extraction resulted in reduction below detection level of A. actinomycetemcomitans and P. gingivalis in 15 of 16 and 8 of 16 previously positive patients using culture techniques and qPCR, respectively. Those patients remaining qPCR positive showed a significant reduction in load of these bacteria. CONCLUSION: Full-mouth tooth extraction significantly changes the oral microflora. These changes include reduction of A. actinomycetemcomitans and P. gingivalis, frequently to levels below detection threshold. In some patients, A. actinomycetemcomitans and P. gingivalis can persist in the edentulous oral cavity up to 3 months after full-mouth tooth extraction

Design and application of group-specific oligonucleotide probes for detecting and monitoring mouse clostridia

Clostridia dominate the rodent intestinal bacterial community and play an important role in physiological functions of the host. However, their ecology and diversity are still unclear. In our previous report, we showed that phylogenetically novel groups of clostridia inhabit the mouse intestine and contribute to the normalization of germfree mice. In this study, five new oligonucleotide probes were designed and applied to detect these clostridial groups that are essential for the normalization of germfree mice. Faecal microbiota of conventional mouse strains and specific pathogen-free mice from different breeding colonies were analysed by fluorescence in situ hybridization using these five probes. Our results showed that the composition of clostridia differed among mouse strains and also among mouse groups of the same inbred strain from different breeding colonies. These five new probes for mouse clostridia were able to detect the difference in clostridial diversity in each mouse group. In addition to Clostridium, we also analysed Bacteroides and Lactobacillus using previously described probes and the number or the frequency of occurrence of Bacteroides was shown to be different among mouse groups analysed. The oligonucleotide probe set including our newly developed and previously described probes used in this study can be applied to monitoring of significant groups of mouse intestinal microbiota.</p