Search results for "metagenomic"

Are multi-omics enough?

2016

Multi-omic techniques are often seen as the future of microbiome studies. We argue that recent strategies for simplifying complex omic-derived data will need to be combined with improved cultivation techniques to pave the way towards a more targeted approach for understanding microbial communities.

Art‐omics: multi‐omics meet archaeology and art conservation

2020

Summary Multi‐omics can informally be described as the combined use of high‐throughput techniques allowing the characterization of complete microbial communities by the sequencing/identification of total pools of biomolecules including DNA, proteins or metabolites. These techniques have allowed an unprecedented level of knowledge on complex microbial ecosystems, which is having key implications in land and marine ecology, industrial biotechnology or biomedicine. Multi‐omics have recently been applied to artistic or archaeological objects, with the goal of either contributing to shedding light on the original context of the pieces and/or to inform conservation approaches. In this minireview,…

Analisi della comunità microbica intestinale di Reticulitermes lucifugus (Rossi) (Isoptera: Rhinotermitidae).

2009

L’intestino delle termiti ospita una comunità microbica di batteri e flagellati anaerobi, responsabile della degradazione del materiale lignocellulosico. La digestione della lignocellulosa da parte delle termiti dipende dalla simbiosi con microrganismi procarioti ed eucarioti che vivono nel loro intestino. I microrganismi trasformano la cellulosa in zuccheri e acetato, producendo idrogeno, metano e anidride carbonica. Abbiamo analizzato la comunità microbica intestinale di Reticulitermes lucifugus lucifugus, una delle due specie di termiti italiane, che vive in ambienti sotterranei, è distruttiva per le strutture legnose degli ambienti urbani causando seri danni ai monumenti storici e può c…

Large-Scale Clustering of Short Reads for Metagenomics On GPUs

2013

DNA traces the origin of honey by identifying plants, bacteria and fungi

2021

The regional origin of a food product commonly affects its value. To this, DNA-based identification of tissue remains could offer fine resolution. For honey, this would allow the usage of not only pollen but all plant tissue, and also that of microbes in the product, for discerning the origin. Here we examined how plant, bacterial and fungal taxa identified by DNA metabarcoding and metagenomics differentiate between honey samples from three neighbouring countries. To establish how the taxonomic contents of honey reflect the country of origin, we used joint species distribution modelling. At the lowest taxonomic level by metabarcoding, with operational taxonomic units, the country of origin …

Mining virulence genes using metagenomics.

2011

When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enter…

Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies

2013

High-throughput sequencing technologies produce large collections of data, mainly DNA sequences with additional information, requiring the design of efficient and effective methodologies for both their compression and storage. In this context, we first provide a classification of the main techniques that have been proposed, according to three specific research directions that have emerged from the literature and, for each, we provide an overview of the current techniques. Finally, to make this review useful to researchers and technicians applying the existing software and tools, we include a synopsis of the main characteristics of the described approaches, including details on their impleme…

Classification of Sequences with Deep Artificial Neural Networks: Representation and Architectural Issues

2021

DNA sequences are the basic data type that is processed to perform a generic study of biological data analysis. One key component of the biological analysis is represented by sequence classification, a methodology that is widely used to analyze sequential data of different nature. However, its application to DNA sequences requires a proper representation of such sequences, which is still an open research problem. Machine Learning (ML) methodologies have given a fundamental contribution to the solution of the problem. Among them, recently, also Deep Neural Network (DNN) models have shown strongly encouraging results. In this chapter, we deal with specific classification problems related to t…

MOLECULAR ANALYSIS OF COLLETOTRICHUM SPECIES ASSOCIATED TO OLIVE IN CALABRIA.

2013

A new molecular approach based on the use of genus-specific primers targeting the internal transcribed spacer (ITS) regions of rDNA, was developed and used to study the diversity of Colletotrichum species associated with the olive canopy in the Gioia Tauro plain (Calabria, southern Italy). Representative symptomatic and symptomless samples of leaves, flowers and fruits were collected during 2012 and analyzed by extracting total DNA and amplifying the target region with the genus-specific primers. Amplicons were cloned and sequenced in order to use the ITS as a barcode gene. No Colletotrichum species were detected in the first sampling period (May 28, 2012), whereas around 15% of the analyze…

ANALISI DELLA COMUNITÀ MICROBICA INTESTINALE DI Reculitermes lucifugus (ROSSI) (ISOPTERA: RHINOTERMITIDAE)

2012

Reticulitermes lucifugus è una specie di termite diffusa in Italia e che causa gravi danni alle strutture legnose di monumenti storici e artistici. L’intestino delle termiti ospita una comunità microbica di batteri e flagellati, responsabile della degradazione del materiale lignocellulosico. Studi preliminari sulla comunità microbica dei simbionti di R. lucifugus, hanno descritto alcune specie di protozoi, ma non ci sono ancora informazioni sui simbionti batterici. Al fine di caratterizzare la comunità microbica intestinale di R. lucifugus è stato utilizzato un approccio molecolare coltura indipendente e colture di arricchimento per l’isolamento dei batteri cellulosolitici. Per l’analisi co…