3 documents found, page 1 of 1
Evaluation of the use of formalin-fixed and paraffin- embedded archive gastric ...
Pinto-Ribeiro, I; Ferreira, RM; Pereira-Marques, J; Pinto, V; Macedo, G; Carneiro, F; Figueiredo, CLarge numbers of well-characterized clinical samples are fundamental to establish relevant associations between the microbiota and disease. Formalin-fixed and paraffin-embedded (FFPE) tissues are routinely used and are widely available clinical materials. Since current approaches to study the microbiota are based on next-generation sequencing (NGS) targeting the bacterial 16S rRNA gene, our aim was to evaluate ...
Impact of host DNA and sequencing depth on the taxonomic resolution of whole me...
Pereira-Marques, J; Hout, A; Ferreira, RM; Weber, M; Pinto-Ribeiro, I; Van, Doorn, L; Knetsch, C; Figueiredo, CThe amount of host DNA poses a major challenge to metagenome analysis. However, there is no guidance on the levels of host DNA, nor on the depth of sequencing needed to acquire meaningful information from whole metagenome sequencing (WMS). Here, we evaluated the impact of a wide range of amounts of host DNA and sequencing depths on microbiome taxonomic profiling using WMS. Synthetic samples with increasing leve...
Gastric microbial community profiling reveals a dysbiotic cancer-associated mic...
Ferreira, RM; Pereira-Marques, J; Pinto-Ribeiro, I; Costa, JL; Carneiro, F; Machado, JC; Figueiredo, CObjective Gastric carcinoma development is triggered by Helicobacter pylori. Chronic H. pylori infection leads to reduced acid secretion, which may allow the growth of a different gastric bacterial community. This change in the microbiome may increase aggression to the gastric mucosa and contribute to malignancy. Our aim was to evaluate the composition of the gastric microbiota in chronic gastritis and in gastr...