A5101695390- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Antimicrobial Resistance in Staphylococcus
- Mycobacterium research and diagnosis
- Bacterial Identification and Susceptibility Testing
- Bacteriophages and microbial interactions
- Probiotics and Fermented Foods
- Streptococcal Infections and Treatments
- Tryptophan and brain disorders
- Diet and metabolism studies
- RNA and protein synthesis mechanisms
- Bacterial biofilms and quorum sensing
Universitat Autònoma de Barcelona
2021-2023
INCLIVA Health Research Institute
2015
Abstract The human intestine is home to a diverse range of bacterial and fungal species, forming an ecological community that contributes normal physiology disease susceptibility. Here, the microbiota (mycobiome) in obese non-obese subjects was characterized using Internal Transcribed Spacer (ITS)-based sequencing. results demonstrate patients could be discriminated by their specific composition, which also distinguished metabolically “healthy” from “unhealthy” obesity. Clusters according...
Abstract Background Long-read sequencing in metagenomics facilitates the assembly of complete genomes out complex microbial communities. These include essential biologic information such as ribosomal genes or mobile genetic elements, which are usually missed with short-reads. We applied long-read Nanopore to retrieve high-quality metagenome-assembled (HQ MAGs) from a dog fecal sample. Results used nanopore and frameshift aware correction on canine sample retrieved eight single-contig HQ...
Staphylococcus pseudintermedius is a commensal bacterium of the canine skin but also key opportunistic pathogen that responsible for most cases pyoderma in dogs. The current paradigm indicates infection arises when predisposing factors alter healthy barrier. Despite their importance, characteristics S. populations colonizing dogs are yet largely unknown. Here, we retrieved 67 complete circular genomes and 19 associated plasmids from isolated 9 via long-reads Nanopore sequencing. Within skin,...
Staphylococcus pseudintermedius is the main aetiological agent of canine pyoderma. Whole genome sequencing most comprehensive way obtaining relevant genomic information about micro-organisms.Oxford Nanopore technology enables quality and de novo assembly whole S. pseudintermedius. analysis may help to better understand pathogenesis pyodermas.Twenty-two strains isolated from skin five healthy dogs 33 with pyoderma were analysed. DNA was extracted sequenced using Oxford MinION, a new that...
The human gut microbiome has been extensively studied, yet the canine is still largely unknown. availability of high-quality genomes essential in fields veterinary medicine and nutrition to unravel biological role key microbial members environment. Our aim was evaluate nanopore long-read metagenomics Hi-C (high-throughput chromosome conformation capture) proximity ligation provide metagenome-assembled (HQ MAGs) By combining ligation, we retrieved 27 HQ MAGs 7 medium-quality a faecal sample...
Staphylococcus pseudintermedius, a common commensal canine bacterium, is the main cause of skin infections in dogs and potential zoonotic pathogen. The emergence methicillin-resistant S. pseudintermedius (MRSP) has compromised treatment caused by these bacteria. In this study, we compared phenotypic results obtained minimum inhibitory concentration (MICs) for 67 isolates from nine healthy versus genotypic data with Nanopore sequencing. A total 17 antibiotic resistance genes (ARGs) were...
We have de novo assembled 67 Staphylococcus pseudintermedius genomes, with median values of 2.6 Mbp size and 99.43% completeness, 2,386 coding sequences, 19 complete rRNAs, 59 tRNAs, 4 noncoding RNAs. released 51 single-contig genomes 16 a circular main contig using Nanopore sequencing.
Abstract Background. Metagenomics is a powerful and rapidly developing approach that provides new biological insights into the microbes inhabiting underexplored environments, such as canine fecal microbiome. We investigate long-read metagenomics with Nanopore sequencing to profile microbiome retrieve high-quality metagenome-assembled genomes (HQ MAGs) from healthy dog. Results. More than 99% of total classified reads corresponded Bacteria. The most abundant phylum was Bacteroidetes (~80%...
We have de novo assembled and polished 61 Staphylococcus pseudintermedius genome sequences with Nanopore-only long reads. Completeness was 99.25%. The average size 2.70 Mbp, comprising 2,506 coding sequences, 19 complete rRNAs, 56 to 59 tRNAs, 4 noncoding RNAs (ncRNAs), as well CRISPR arrays.
Abstract Long-read metagenomics facilitates the assembly of high-quality metagenome-assembled genomes (HQ MAGs) out complex microbiomes. It provides highly contiguous assemblies by spanning repetitive regions, complete ribosomal genes, and mobile genetic elements. Hi-C proximity ligation data bins long contigs their associated extra-chromosomal elements to bacterial host. Here, we characterized a canine fecal sample combining long-read with data, further correcting frameshift errors. We...
Abstract BackgroundLong-read sequencing in metagenomics facilitates the assembly of complete genomes out complex microbial communities. These include essential biologic information such as ribosomal genes or mobile genetic elements, which are usually missed with short-reads. We applied long-read Nanopore to retrieve high-quality metagenome-assembled (HQ MAGs) from a dog fecal sample.ResultsWe used nanopore and frameshift aware correction on canine sample retrieved eight single-contig HQ...