Nicolas Rascovan

Nicolas Rascovan
Institut Pasteur · Department of Genomes and Genetics

Ph.D.

About

41
Publications
15,014
Reads
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1,207
Citations
Additional affiliations
September 2020 - present
Institut Pasteur
Position
  • Group Leader
Description
  • The research interest of my lab is centered in the study of infectious diseases and human microbiomes from an evolutionary, ecological and historical perspective. Using ancient DNA techniques, we reconstruct whole genomes from ancient strains of human microbes (including pathogens and commensals) and use phylogenetic driven approaches to understand how, where and when these microbes emerged in human populations and how they spread and evolved over time and geographies.
July 2014 - present
Aix-Marseille Université, Marseille · Faculté de Médecine
Position
  • PostDoc Position
Description
  • Metagenomics and Bioinformatics in human related and environmental samples
September 2008 - March 2014
Instituto de Agrobiotecnologia Rosario
Position
  • PhD Student
Description
  • Agricultural soils and extreme environmental metagenomics.
Education
July 2008 - December 2013
Universidad de Buenos Aires
Field of study
  • Metagenomics
March 2002 - December 2007
Universidad de Buenos Aires
Field of study
  • Biology
March 1996 - December 2001
Colegio Nacional Buenos Aires
Field of study
  • College

Publications

Publications (41)
Article
In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than...
Article
Full-text available
Background The Zika virus (ZIKV) epidemic of 2015/2016 spread throughout numerous countries. It emerged in mainland Latin America and spread to neighboring islands, including the Caribbean island of Barbados. Recent studies have indicated that the virus must have already been circulating in local mosquito populations in Brazil for almost 2 years be...
Article
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic...
Article
Full-text available
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic...
Article
Full-text available
Mosquitoes are the most important vectors for arthropod-borne viral diseases. Mixed viral infections of mosquitoes allow genetic recombination or reassortment of diverse viruses, turning mosquitoes into potential virologic mixing bowls. In this study, we field-collected mosquitoes of different species (Aedes aegypti and Culex pipiens complex), from...
Preprint
Full-text available
Although studies have shown that urban environments and mass-transit systems have geospatially distinct metagenomes, no study has ever systematically studied these dense, human/microbial ecosystems around the world. To address this gap in knowledge, we created a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit syste...
Article
Full-text available
Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient kn...
Article
Full-text available
Plant-microbial interactions in the litter layer represent one of the most relevant interactions for biogeochemical cycling as litter decomposition is a key first step in carbon and nitrogen turnover. However, our understanding of these interactions in the litter layer remains elusive. In an old-growth mixed Nothofagus forest in Patagonia, we studi...
Data
Fig. S1. Tree triangle in a native Patagonian forest. Tree species of the genus Nothofagus in a temperate forest in Patagonia, South America. The intersection of the tree canopies (N. obliqua on the upper left, N. nervosa on the bottom left and N. dombeyi on the right) directly control belowground conditions. This "tree triangle" design allows stud...
Article
Full-text available
Background Several archaeal species from the order Sulfolobales are interesting from the biotechnological point of view due to their biomining capacities. Within this group, the genus Acidianus contains four biomining species (from ten known Acidianus species), but none of these have their genome sequenced. To get insights into the genetic potentia...
Article
Full-text available
Ancient dental pulps are highly precious samples because they conserve DNA from humans and blood-borne pathogens for ages. However, little is known about the microbial communities present in dental pulps. Here, we analyzed ancient and modern dental pulp samples from different time periods and geographic regions and found that they are colonized by...
Article
Full-text available
High-throughput sequencing technologies have revolutionized how we think about viruses. Investigators can now go beyond pathogenic viruses and have access to the thousands of viruses that inhabit our bodies without causing clinical symptoms. By studying their interactions with each other, with other microbes, and with host genetics and immune syste...
Article
Full-text available
Mycobacterium acapulcensis is a rapidly growing scotochromogenic acid-fast bacillus. The draft genome of M. acapulcensis CSURP1424 comprises 5,290,974 bp, exhibiting a 66.67% G+C content, 4,870 protein-coding genes, and 71 predicted RNA genes.
Article
Full-text available
Antibiotic resistance in pathogenic bacteria is a major problem for human health. We analyzed metagenomic datasets from ancient and remote samples from diverse environmental sources and observed the presence of all the eleven antibiotic resistance genes (ARG) groups evaluated. Since ancient samples are not subjected to modern effects of antibiotic...
Article
Full-text available
Root associated bacteria are critical for plant growth and health. Understanding the composition and role of root microbiota is crucial toward agricultural practices that are less dependent on chemical fertilization, which has known negative effects on the environment and human health. Here we analyzed the root-associated microbiomes of soybean and...
Article
Full-text available
Human polyomavirus 6 (HPyV6) is mostly detected at the skin surface of healthy individuals. Here, we demonstrate for the first time that HPyV6 also infect internal tissues, by showing direct evidence of HPyV6 infecting a lymph node of a patient with an angiolymphoid hyperplasia with eosinophilia (ALHE) or Kimura disease.
Article
Full-text available
Mycobacterium mucogenicum is a rapid-growing, nontuberculosis Mycobacterium species. The draft genome of M. mucogenicum CSUR P2099 comprises 6,210,127 bp exhibiting a 67.2% G+C content, 6,003 protein-coding genes, and 91 predicted RNA genes.
Article
Full-text available
Mycobacterium peregrinum is a nonpigmented rapid growing nontuberculosis species belonging to the Mycobacterium fortuitum group. The draft genome of M. peregrinum type I CSUR P2098 comprises 7,109,836 bp exhibiting a 66.23% G+C content, 6,894 protein-coding genes, and 100 predicted RNA genes. Its genome analysis suggests this species differs from M...
Article
Full-text available
Arsenic metabolism is proposed to be an ancient mechanism in microbial life. Different bacteria and archaea use detoxification processes to grow under high arsenic concentration. Some of them are also able to use arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. However, among the...
Article
Full-text available
The aim of this study was to assess the effects of agronomic practices on the arbuscular mycorrhizal (AM) fungal community in soils from the Pampa Ondulada region (Argentina), and to compare conclusions reached when using pyrosequencing or a morphological approach. The AM fungal diversity of 3 agricultural exploitations located in the Pampa Ondulad...
Article
Full-text available
Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to diff...
Article
Full-text available
Acidianus copahuensis is a recently characterized thermoacidophilic archaeon isolated from the Copahue volcanic area in Argentina. Here, we present its draft genome sequence, in which we found genes involved in key metabolic pathways for developing under Copahue’s extreme environmental conditions, such as sulfur and iron oxidation, carbon fixation,...
Article
Full-text available
Halorubrum sp. strain AJ67, an extreme halophilic UV-resistant archaeon, was isolated from Laguna Antofalla in the Argentinian Puna. The draft genome sequence suggests the presence of potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high UV radiation, elevated salinity, and the presen...
Article
Full-text available
Halorubrum sp. strain AJ67, an extreme halophilic UV-resistant archaeon, was isolated from Laguna Antofalla in the Argentinian Puna. The draft genome sequence suggests the presence of potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high UV radiation, elevated salinity, and the presen...
Article
Full-text available
Soil is among the most diverse and complex environments in the world. Soil microorganisms play an essential role in biogeochemical cycles and affect plant growth and crop production. However, our knowledge of the relationship between species-assemblies and soil ecosystem processes is still very limited. The aim of this study was to generate a compr...
Article
Full-text available
We describe stromatolites forming at an altitude of 3570 m at the shore of a volcanic lake Socompa, Argentinean Andes. The water at the site of stromatolites formation is alkaline, hypersaline, rich in inorganic nutrients, very rich in arsenic, and warm (20-24°C) due to a hydrothermal input. The stromatolites do not lithify, but form broad, rounded...
Data
Full-text available
Arsenic (As) is one of the most important global environmental pollutants and a persistent bioaccumulative carcinogen. As an ubiquitous toxic metalloid it was released in the environment mainly by volcanic activity. The ars gene system can be chromosomal or plasmid-borne and provides arsenic resistance to a variety of microorganisms. The arsC gene,...
Conference Paper
Full-text available
Background / Purpose: If both metagenomics and metatranscriptomics are done for the same community, the most interesting question to address is which of the identified metabolic pathways are active. When the analysis involves different environmental or experimental conditions, the analyses focus on the identification of those metabolic functions...
Article
Full-text available
In search for physiological pathways affecting alternative splicing through its kinetic coupling with transcription, we found that membrane depolarization of neuronal cells triggers the skipping of exon 18 from the neural cell adhesion molecule (NCAM) mRNA, independently of the calcium/calmodulin protein kinase IV pathway. We show that this exon re...

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Projects

Projects (3)
Project
The goal of my project will be to understand the impact that the transition from nomadic foraging to agricultural and sedentary lifestyles had on the organisation and health of human populations of the past, and the consequences, of such change, on modern societies.
Project
The goal of this project is to screen and recover whole genomes from ancient and modern human pathogens and use evolutionary and genomic approaches to understand how pathogens emerged, spread and evolved over the human history.
Project
High Andean Mountain lakes are a unique extreme environment all over the world since their locations are in high altitude saline deserts, largely influenced by volcanic activity. UV radiation, arsenic content, high salinity, and low dissolved oxygen content, together with extreme daily temperature fluctuations and oligotrophic conditions, shape up an environment that recreates the early earth and, even more, the extraterrestrial conditions. The discovery of living microbialites and microbial mats in 2009 has increased the interest in this area as an early earth counterpart. Since then, and up to now, we have started a prospection for this kind of environments in Argentina, Chile and Bolivia. We have prospected around 60 lakes and salt flats, out of which, about 30% harbor any kind of these ecosystems (microbialites, mats and endoevaporitic domes).