0000000000956225
AUTHOR
Miguel Carda-diéguez
Metagenomics of the Mucosal Microbiota of European Eels
ABSTRACT European eels are an economically important and threatened species that are prone to rapid collapse in farm conditions. Using metagenomics, we show that the eel mucosal microbiota has specific features distinguishing it from the surrounding aquatic community. This is a first step in dissecting the resident microbiota of this critical barrier that may have implications for maintenance of healthy eel populations.
A Method of Transposon Insertion Sequencing in Comprehensively Identifying Vibrio vulnificus Genes Required for Growth in Human Serum
One of the most powerful approaches to detect the loci that enable a pathogen to cause disease is the creation of a high-density transposon mutant library by transposon insertion sequencing (TIS) and the screening of the library using an adequate in vivo and/or ex vivo model of the disease. Here we describe the procedure for detection of the putative loci required for a septicemic pathogen to cause sepsis in humans by using TIS plus an ex vivo model of septicaemia: to grow the pathogen in fresh and inactivated human serum. We selected V. vulnificus because it is a highly invasive pathogen capable of spreading from an infection site to the bloodstream, causing sepsis and death in less than 2…
Pyrosequencing survey of intestinal microbiota diversity in cultured sea bass (Dicentrarchus labrax) fed functional diets.
The routine use of chemotherapy to control bacterial diseases in aquatic populations has resulted in the development and spread of antibiotic resistance. The inclusion of immunostimulants in fish diets (functional diets) is one of the main strategies to solve this threat. This study aimed to analyse the intestinal microbiota of cultured European sea bass (Dicentrarchus labrax) fed two functional diets applying pyrosequencing of PCR-amplified 16S rRNA gene. Quality-filtered reads were assigned to family and genus taxonomic levels using the Ribosomal Database Project classifier. The autochthonous intestinal microbiota of sea bass consisted of two dominant bacterial genera: Dysgonomonas (Bacte…
Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla)
In this work, we used the eel (Anguilla anguilla) as an animal model to test the hypothesis of Barr et al. (2013a,b) about the putative role of the epidermal mucosa as a phage enrichment layer. To this end, we analyzed the microbial content of the skin mucus of wild and farmed eels by using a metagenomic approach. We found a great abundance of replicating phage genomes (concatemers) in all the samples. They were assembled in four complete genomes of three Myovirus and one Podovirus. We also found evidences that ΦKZ and Podovirus phages could be part of the resident microbiota associated to the eel mucosal surface and persist on them over the time. Moreover, the viral abundance estimated by …
Draft genome sequences of Vibrio vulnificus strains recovered from moribund tilapia
Potentially zoonotic Vibrio vulnificus strains were isolated from vibriosis outbreaks occurring on eastern Mediterranean tilapia farms between 2016 and 2019. In this work, the draft genome sequences of three representative isolates are presented.
Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution
Background Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host. Results Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibr…
Additional file 1: Table S1. of Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution
Metagenomes used to detect MGE. Table S2. General data for each metagenome and alpha diversity. Table S3. Contigs with MGE detected using the methodology described in Fig. 1. Figure S1. Sampling points, location and description. Figure S2. From nature to the laboratory: skin mucus sampling from wild eels and DNA extraction. Figure S3. Mobile genetic elements (MGE) detection workflow diagram. Figure S4. %GC content profiles of the eel’s SMS- and W-metagenomes. Figure S5. Wild eel’s versus farmed eel’s SMS metagenomes. Figure S6. V. metoecus M12v BLAST atlas. Figure S7. Schematic representation of VPI-2 in M12v. Figure S8. Main bacterial genera detected in eel’s SMS- and W-metagenomes. Figure…
Comprehensive identification of Vibrio vulnificus genes required for growth in human serum.
ABSTRACT Vibrio vulnificus can be a highly invasive pathogen capable of spreading from an infection site to the bloodstream, causing sepsis and death. To survive and proliferate in blood, the pathogen requires mechanisms to overcome the innate immune defenses and metabolic limitations of this host niche. We created a high-density transposon mutant library in YJ016, a strain representative of the most virulent V. vulnificus lineage (or phylogroup) and used transposon insertion sequencing (TIS) screens to identify loci that enable the pathogen to survive and proliferate in human serum. Initially, genes underrepresented for insertions were used to estimate the V. vulnificus essential gene set;…
Additional file 2: Table S1. of Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution
Abundance and comparison of functions in water and skin-mucus surface microbiomes. (XLSX 646 kb)