Natàlia Timoneda

Natàlia Timoneda
Institut de Ciències del Mar · Department of Marine Biology

PhD in Environmental Microbiology and Biotechnology

About

29
Publications
3,680
Reads
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398
Citations

Publications

Publications (29)
Article
Full-text available
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food saf...
Article
Parasites in aquatic systems are highly diverse and ubiquitous. In marine environments, parasite‐host interactions contribute substantially to shaping microbial communities, but their nature and complexity remain poorly understood. In this study, we examined the relationship between Perkinsea parasitoids and bloom‐forming dinoflagellate species. Ou...
Article
Full-text available
Background Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portability, affordability and speed in data production make of it an attractive device for whole genome sequencing. The objective of this study is t...
Article
Abstract Fecal pollution of water bodies poses a serious threat for public health and ecosystems. Microbial source tracking (MST) is used to track the source of this pollution facilitating better management of pollution at the source. In this study we tested 12 MST markers to track human, ruminant, sheep, horse, pig and gull pollution to assess the...
Article
NGS techniques are excellent tools to monitor and identify viral pathogens circulating among the population with some limitations that need to be overcome, especially in complex matrices. Sewage contains a high amount of other microorganisms that could interfere when trying to sequence viruses for which random PCR amplifications are needed before N...
Article
Viruses (e.g., noroviruses and hepatitis A and E virus), bacteria (e.g., Salmonella spp. and pathogenic Escherichia coli) and protozoa (e.g., Cryptosporidium parvum and Giardia intestinalis) are well-known contributors to food-borne illnesses linked to contaminated fresh produce. As agricultural irrigation increases the total amount of water used a...
Preprint
Full-text available
Fecal pollution of water bodies poses a serious threat for public health and ecosystems. Microbial source tracking (MST) using host specific bacteria are used to track the source of this potential pollution and be able to perform a better management of the pollution at the source. In this study we tested 12 molecular MST markers to track human, rum...
Article
In Quito, the microbiological contamination of surface water represents a public health problem, mainly due to the lack of sewage treatment from urban wastewater. Contaminated water contributes to the transmission of many enteric pathogens through direct consumption, agricultural and recreational use. Among the different pathogens present in urban...
Article
Full-text available
Hepatitis is a general term meaning inflammation of the liver, which can be caused by a variety of viruses. However, a substantial number of cases remain with unknown aetiology. We analysed the serum of patients with clinical signs of hepatitis using a metagenomics approach to characterize their viral species composition. Four pools of patients wit...
Data
Individual phylogenetic trees computed from contigs over reference genome locations in HEV. (DOCX)
Data
Individual phylogenetic trees computed from contigs over reference genome locations in Anelloviridae family. (DOCX)
Article
The application of next-generation sequencing (NGS) techniques for the identification of viruses present in urban sewage has not been fully explored. This is partially due to a lack of reliable and sensitive protocols for studying viral diversity and to the highly complex analysis required for NGS data processing. One important step towards this go...
Article
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contam...
Article
Full-text available
Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentrati...
Data
Distribution of reads on kingdom level of the 16 method combinations and their associated negative controls. Samples were processed in triplicate, and the data shown is the average. _S = sample, _C = Negative extraction control. Databases used are listed in S1 Table. (PDF)
Data
HAdV concentration measured by qPCR. (A) HAdV concentration in extracts obtained by using four different concentration methods and (B) extraction methods. The bar, box, whiskers and circles represents median, inter-quartile range, inter-quartile range times 1.5, and outliers, respectively. Asterisks represent significance level of a pairwise t-test...
Data
Overview of reference sequence databases and associated download information. Reference sequence information can be obtained from the URL’s shown in ‘Download information’. (PDF)
Data
Sequence information. Number of raw reads, reads after quality assessment, and reads not mapping to PhiX, and thus usable for subsequent analysis. _S = sample, _C = Negative control. (PDF)
Data
qPCR inhibition of MNV and HAdV. Inhibition of the 16 combinations of concentration and extraction methods. Inhibition was measured using qPCR of undiluted (1:1) and tenfold diluted (1:10) DNA/RNA extracts. The values in the tables represents Δct between the undiluted and 10 fold diluted samples. A Δct = -3.3 represent a perfect 10 fold dilution. S...
Data
MNV concentrations measured by qPCR. (A) MNV concentration in extracts obtained by using four different concentration methods and (B) extraction methods. The bar, box and whiskers represents the median, the inter-quartile range, and the inter-quartile range times 1.5, respectively. Asterisks represent significance level of a pairwise t-test with “H...
Data
Abundance of all detected viral families. Heatmap showing the abundance of all detected viral families, measured in reads per million, in each biological replica for the different method combinations as well as the controls. _S = sample, _C = Negative control. (PDF)
Data
Specifications of the four concentration methods applied in this study. (PDF)
Data
Properties of the four nucleic acid extraction kits applied in this study. (PDF)
Article
Full-text available
Conventional wastewater treatment does not completely remove and/or inactive viruses; consequently, viruses excreted by the population can be detected in the environment. This study was undertaken to investigate the distribution and seasonality of human viruses and faecal indicator bacteria (FIB) in a river catchment located in a typical Mediterran...
Article
Wastewater is a valuable resource for water-scarce regions, and is becoming increasingly important due to the rising frequency of droughts as a result of climate change. The health risks derived from ingestion of lettuce that has been irrigated with effluent from a wastewater treatment plant (WWTP) in Catalonia (Spain) were estimated following a qu...

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Project (1)
Project
Metawater aims to develop European scale tools for the rapid evaluation of the role that irrigation water has in the transmission of existing, new and emerging pathogens to the human population. The diverse sources of irrigation water used in the European countries (reclaimed water, superficial water, ground water and distribution water) will be characterized and critical points for the quality of irrigation water and the treatment processes will be analyzed for standard fecal bacteria, new viral indicators and existing, new and emerging water-borne microbiological risks, characterizing the population of human viruses, emerging pathogenic bacteria (including antibiotic-resistant bacteria), protozoa and cyanobacterial toxins