FinalData 10 Torrent
diseases can result from pathogen-induced modifications in the host. the number of microbes, which are able to cause disease is in the order of 106 to 107, and the number of human hosts with a mutation in their genome that affects the function of a gene that is exploited by a particular microbe is at least 100 million [ 5, 6 ]. the phylogenetic diversity within the human gut microbiota is quite striking, providing a glimpse of how complex this ecosystem is. in this context, the knowledge of the human host genome is a basic tool for experimental research [ 2, 3, 4 ]. altered dna sequencing in patients caused by mutations in human genes suggests that this alteration may be associated with pathogenic activities. to identify metagenomic modifications that may be related to crohn’s disease [ 7 ] and intestinal inflammation [ 8 ], we focused on the identification of bacterial isolates that were genetically divergent from the normal human gut microbiota, which may be linked to specific pathologies.
this project led to the identification of two novel species of campylobacter (c. rectus and c. lanienae), a novel species of mycobacterium (m. vacae) and a novel species of porphyromonas (p. stomatis). while most of these isolates are known to be associated with disease, the role of the host in the emergence and persistence of campylobacter or porphyromonas in the oropharynx remains unclear. nevertheless, campylobacter and porphyromonas species have also been found in a host in the absence of disease symptoms [ 1, 2, 3 ]. these bacteria are likely to be transient colonizers, which are capable of causing disease in immunocompromised individuals. this project has also provided novel insights into the phylogenetics of campylobacter and porphyromonas species isolated from reptiles and humans. thus, the use of next generation sequencing (ngs) allowed us to differentiate at the species level a variant of campylobacter species isolated in romania from that isolated in humans. it was estimated that the prevalence of campylobacter species in faeces or asymptomatic oropharyngeal and faecal specimens in healthy individuals ranges from 2% to 15% [ 3, 4, 5, 6, 7, 8, 9 ]. the prevalence of campylobacter in patients with and without diarrhoea is however unknown and there is limited information available on the molecular epidemiology of campylobacters in europe. in a country such as romania, the prevalence of campylobacter infections is likely to be very high and campylobacter is well known to cause diarrhoea in children and could be responsible for diarrhoea in adults. therefore, our project had the objective to provide new insights into the ecology of campylobacter in romania, which could lead to the improved diagnosis of infection as well as to the potential development of new vaccines for the prevention of campylobacter-associated diarrhoea. once phylogenetically validated, campylobacter isolates from faeces of diarrhoeic children and adults and/or asymptomatic healthy individuals could be used as targets for a preliminary screening for the presence of genes, which could be candidate determinants of virulence.
mesothelioma is one of the leading causes of deaths due to cancer with an incidence rate of up to 30%. the most frequent site of mesothelioma is the pleura, but the disease may also develop in the peritoneum and the pericardium.
our study supports the use of the miseq platform for 16s rrna amplicon analyses; however, data generated using that platform may not be useful for detailed studies of biodiversity and abundance of bacteria in cecum. although the manufacturer’s recommended protocol provides higher sequencing depth than the standard protocol, the miseq generated a higher proportion of low quality sequences. in addition, with the miseq, the in-solution workflow fails to generate reads in the 400-700 bp length range. as a consequence, in most cases, the correct length range of sequences generated by the miseq is not easily determined. we also demonstrated the usefulness of the gs flx+ as a sequencing platform for microbial community analysis. for the most commonly used parameters of sequencing depth, gs flx+ was at least as robust as miseq, and often generated a higher proportion of high quality reads. since gs flx+ yields longer reads and better sequence quality than miseq, gs flx+ may be an advantageous sequencing platform for bacterial community analyses when longer reads are required, or if accuracy or resolution of taxonomic assignment must be improved. it is worthwhile to note that, although gs flx+ yielded longer reads, the number of reads were not sufficiently large to enable a comparison of alpha diversity and community structure with full confidence. thus, in this study, we focused on comparing the performance of the three popular amplicon platforms for microbial community analyses. our goal was not to rank the platforms based on a power-analysis; however, our results strongly encourage the use of long-read sequencing on the gs flx+ platform to maximize the generality and resolution of the analyses performed.