Search results for "METAGENOMIC"
showing 10 items of 177 documents
Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria
2013
We describe a deep-branching lineage of marine Actinobacteria with very low GC content (33%) and the smallest free living cells described yet (cell volume ca. 0.013 μm(3)), even smaller than the cosmopolitan marine photoheterotroph, 'Candidatus Pelagibacter ubique'. These microbes are highly related to 16S rRNA sequences retrieved by PCR from the Pacific and Atlantic oceans 20 years ago. Metagenomic fosmids allowed a virtual genome reconstruction that also indicated very small genomes below 1 Mb. A new kind of rhodopsin was detected indicating a photoheterotrophic lifestyle. They are estimated to be ~4% of the total numbers of cells found at the site studied (the Mediterranean deep chloroph…
Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach.
2015
Genome-scale metabolic models usually contain inconsistencies that manifest as blocked reactions and gap metabolites. With the purpose to detect recurrent inconsistencies in metabolic models, a large-scale analysis was performed using a previously published dataset of 130 genome-scale models. The results showed that a large number of reactions (~22%) are blocked in all the models where they are present. To unravel the nature of such inconsistencies a metamodel was construed by joining the 130 models in a single network. This metamodel was manually curated using the unconnected modules approach, and then, it was used as a reference network to perform a gap-filling on each individual genome-s…
Assembly methods for nanopore-based metagenomic sequencing: a comparative study
2019
ABSTRACTBackgroundMetagenomic sequencing has lead to the recovery of previously unexplored microbial genomes. In this sense, short-reads sequencing platforms often result in highly fragmented metagenomes, thus complicating downstream analyses. Third generation sequencing technologies, such as MinION, could lead to more contiguous assemblies due to their ability to generate long reads. Nevertheless, there is a lack of studies evaluating the suitability of the available assembly tools for this new type of data.FindingsWe benchmarked the ability of different short-reads and long-reads tools to assembly two different commercially available mock communities, and observed remarkable differences i…
Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes
2015
Thousands of net-heterotrophic and strongly stratifying lakes dominate the boreal landscape. Besides their central role as emitters of greenhouse gases, we have only recently begun to understand the microbial systems driving the metabolic processes and elemental cycles in these lakes. Using shotgun metagenomics, we show that the functional potential differs among lake types, with humic lakes being particularly enriched in carbon degradation genes. Most of the metabolic pathways exhibit oxygen- and temperature-dependent stratification over depth, coinciding with shifts in bacterial community composition, implying that stratification is a major factor controlling lake metabolism. In the botto…
METAGENOMIC ANALYSIS OF PHYTOPHTHORA DIVERSITY IN NURSERIES OF POTTED ORNAMENTAL SPECIES.
2015
The genetic diversity of Phytophthora was investigated in soil and root samples of potted ornamental and fruit tree plants collected in nurseries located in Apulia and Calabria (Southern Italy) using metagenomic approaches based on Phytophthora genus specific primers. PCR amplicons containing the ITS1 region of the rDNA were sequenced using both a conventional cloning and Sanger sequencing approach and a 454 pyrosequencing protocol. All sequences were accurately analyzed with an appropriate software and used as barcode for species identification utilizing a validated ITS database. The cloning/Sanger sequencing approach enabled the identification of nine different Phytophthora taxa (P. nicot…
Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes
2021
ABSTRACT The vertical structuring of methanotrophic communities and its genetic controllers remain understudied in the water columns of oxygen-stratified lakes. Therefore, we used 16S rRNA gene sequencing to study the vertical stratification patterns of methanotrophs in two boreal lakes, Lake Kuivajärvi and Lake Lovojärvi. Furthermore, metagenomic analyses were performed to assess the genomic characteristics of methanotrophs in Lovojärvi and the previously studied Lake Alinen Mustajärvi. The methanotroph communities were vertically structured along the oxygen gradient. Alphaproteobacterial methanotrophs preferred oxic water layers, while Methylococcales methanotrophs, consisting of putative…
Omics approaches to study the oral microbiome
2015
Introducción La visión clásica de los microorganismos como agentes infecciosos ha propiciado que se consideren como meros agentes causales de enfermedades. Sin embargo, la larga historia de coexistencia entre microorganismos y los seres humanos, ha hecho que ambos se hayan adaptado mutuamente y coevolucionen (Dubos et al. 1965, McFall-Ngai 2002). De hecho, en el cuerpo humano habitan 1014 células bacterianas, un orden de magnitud más que células humanas (Savage 1977). Entre los beneficios que la microbiota aporta, están su contribución a digerir alimentos y a aportar nutrientes, regulación del metabolismo, maduración del sistema inmune, etc. Por ello, hoy en día las enfermedades de origen…
Exploring the diversity of the human blood virome
2021
This article belongs to the Special Issue Virus Bioinformatics 2022.
MOLECULAR ANALYSIS OF PHYTOPHTHORA DIVERSITY IN ORNAMENTAL NURSERIES.
2013
A molecular approach based on the use of genus-specific nested-PCR primers (Scibetta et al., 2012; J. Microbiol. Meth. 88: 356-368) was utilized to detect Phytophthora species in soil and root samples of potted ornamentals, collected across Apulia and Calabria, Southern Italy. Analyzed samples comprised many plant species with different levels of symptoms of decline on the canopy and root rots. Extraction protocols were optimized to obtain DNA samples of appropriate quality from soil and roots. The analysis of sequences after cloning of nested-PCR amplicons enabled the identification of different Phytophthora species including P. nicotianae, P. cinnamomi, P. cryptogea, P. palmivora and P. n…
Identification and quantification of meat product ingredients by whole-genome metagenomics (All-Food-Seq)
2019
AbstractComplex food matrices bear the risk of intentional or accidental admixture of non-declared species. Moreover, declared components can be present in false proportions, since expensive taxa might be exchanged for cheaper ones. We have previously reported that PCR-free metagenomic sequencing of total DNA extracted from sausage samples combined with bioinformatic analysis (termed All-Food-Seq, AFS), can be a valuable screening tool to identify the taxon composition of food ingredients. Here we illustrate this principle by analysing regional Doner kebap samples, which revealed unexpected and unlabelled poultry and plant components in three of five cases. In addition, we systematically ap…