Eduardo Castro-Nallar

Eduardo Castro-Nallar
Universidad de Talca · Departamento de Microbiología

PhD

About

94
Publications
26,964
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Introduction
In the Castro Lab, we are interested in understanding the causes and consequences of microbial genetic diversity, and how we can apply this knowledge to gain insights into pathogen diagnostics and discovery, microbial distribution and epidemiology, and novel adaptations. For this, we use molecular and computational biology tools such as high-throughput sequencing, recombinant DNA technology, Bayesian statistics and phylogenetics, transcriptomics and metagenomics.
Education
January 2013
George Washington University
Field of study
  • Infectious disease, Phylogenetics, Genomics
March 2003 - December 2007

Publications

Publications (94)
Article
Full-text available
To analyze the mechanisms involved in anthracene (ANT) degradation in the marine alga Ulva lactuca, total RNA was obtained from the alga cultivated without ANT and with 5 μM of ANT for 24 h, and transcriptomic analyses were performed. A de novo transcriptome was assembled, transcripts differentially expressed were selected, and those overexpressed...
Article
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Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic p...
Preprint
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Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and quantifying the various taxa present in a microbiome sample. Several computational methods exist for analyzing 16S amplicon-based metagenomics. However, the most-used bioi...
Article
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Salmonella spp. is a relevant foodborne pathogen with worldwide distribution. To mitigate Salmonella infections, bacteriophages represent an alternative to antimicrobials and chemicals in food animals and food in general. Bacteriophages (phages) are viruses that infect bacteria, which interact constantly with their host. Importantly, the study of t...
Article
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The study of microbial communities or microbiotas in animals and environments is important because of their impact in a broad range of industrial applications, diseases and ecological roles. High throughput sequencing (HTS) is the best strategy to characterize microbial composition and function. Microbial profiles can be obtained either by shotgun...
Article
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The extreme environmental conditions and lack of water on the soil surface in hyperarid deserts hamper microbial life, allowing only highly specialized microbial communities to the establish colonies and survive. Until now, the microbial communities that inhabit or have inhabited soils of hyperarid environments at greater depths have been poorly st...
Article
Understanding adaptive genetic variation is key for predicting the evolutionary response of species and populations to climate change, decisively influencing management and conservation decisions. Landscape genomics provides a framework to disentangle the effects of local adaptation from those of geographic distance and demographic history, through...
Article
The question addressed by the study Bronchiolitis is not only the leading cause of hospitalisation in U.S. infants but also a major risk factor for asthma development. Growing evidence supports clinical heterogeneity within bronchiolitis. To identify metatranscriptome profiles of infant bronchiolitis, and examine their relationship with host transc...
Article
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Salmonella comprises over 2500 serotypes and foodborne contamination associated with this pathogen remains an important health concern worldwide. During the last decade, a shift in serotype prevalence has occurred as traditionally less prevalent serotypes are increasing in frequency of infections, especially those related to poultry meat contaminat...
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
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As apex predators, pinnipeds are considered to be useful bioindicators of marine and coastal environments. Endemic to a small archipelago in the South Pacific, the Juan Fernandez fur seal (JFFS) is one of the less‐studied members of the pinniped family Otariidae. This study aimed to characterize the fecal microbiome of the JFFS for the first time,...
Article
Natural products (NPs) are synthesized by biosynthetic gene clusters (BGCs), whose genes are involved in producing one or a family of chemically related metabolites. Advances in comparative genomics have been favourable for exploiting huge amounts of data and discovering previously unknown BGCs. Nonetheless, studying distribution patterns of novel...
Article
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As microbial communities inhabiting extreme environments are fundamental for maintaining ecosystems, many studies concerning composition, functionality, and interactions have been carried out. However, much is still unknown.
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...
Preprint
As apex predators, pinnipeds are considered to be useful bioindicators of marine and coastal environments. Endemic to a small archipelago in the South Pacific, the Juan Fernandez fur seal (JFFS) is one of the less-studied members of the pinniped family Otariidae. This study aimed to characterize the fecal microbiome of the JFFS for the first time,...
Article
Full-text available
Arsenic (As) is a metalloid present in the earth’s crust and widely distributed in the environment. Due to its high concentrations in the Andean valleys and its chemical similarity with phosphorus (P), its biological role in Andean Microbial Ecosystems (AMEs) has begun to be studied. The AMEs are home to extremophilic microbial communities that for...
Preprint
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Microbial communities inhabiting extreme environments like Salar de Huasco (SH) are adapted to thrive while exposed to several abiotic pressures and the presence of toxic elements like arsenic (As). Hence, we aimed to uncover the role of arsenic in shaping bacterial composition, structure, and functional potential in five different sites in this Al...
Article
Recent advances in high-throughput sequencing have enabled the large-scale interrogation of microbiota in the most diverse environments, including host-associated microbiota. This has led to the recognition that the skin microbiota of rorquals is specific and structurally different from that of the ocean. This study reveals the skin microbiome of 8...
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Background Radiation-induced rectal epithelial damage is a very common side effect of pelvic radiotherapy and often compromise the life quality and treatment outcome in patients with pelvic malignancies. Unlike small bowel and colon, effect of radiation in rectal stem cells has not been explored extensively. Here we demonstrate that Lgr5-positive r...
Article
The ISAV has a genome composed of eight segments of (-)ssRNA, segment 6 codes for the hemagglutinin-esterase protein, and has the most variable region of the genome, the highly polymorphic region (HPR), which is unique among orthomyxoviruses. The HPR has been associated with virulence, infectivity and pathogenicity. The full length of the HPR is ca...
Preprint
Full-text available
Background Radiation induced rectal epithelial damage is a very common side effect of pelvic radiotherapy and often compromise the life quality and treatment outcome in patients with pelvic malignancies. Unlike small bowel and colon effect of radiation in rectal stem cells has not been explored extensively. Here we demonstrate that Lgr5 positive re...
Article
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Background Our understanding of the composition, function, and health implications of human microbiota has been advanced by high-throughput sequencing and the development of new genomic analyses. However, trade-offs among alternative strategies for the acquisition and analysis of sequence data remain understudied. Methods We assessed eight popular...
Article
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Here, we report the results from PCR and sequencing of bacterial 16S rRNA and fungal internal transcribed spacer 1 (ITS1) genes from needle, branch, trunk, and root samples of Araucaria araucana , plus soil and associated insects, collected along the entirety of its geographic distribution in Chile (January 2017 and 2018).
Article
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Polyextremophilic bacteria can thrive in environments with multiple stressors such as the Salar de Huasco (SH). Microbial communities in SH are exposed to low atmospheric pressure, high UV radiation, wide temperature ranges, salinity gradient and the presence of toxic compounds such as arsenic (As). In this work we focus on arsenic stress as one of...
Article
Repeated reports of microplastic pollution in the marine pinniped diet have emerged in the last years. However, only few studies address the drivers of microplastics presence and the potential implications for monitoring microplastic pollution in the ocean. This study monitored their in the scats (N = 205) of four pinniped species/subspecies at fiv...
Article
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Clostridium difficile B1/NAP1/RT027/ST01 has been responsible for outbreaks of antibiotic-associated diarrhoea in clinical settings worldwide and is associated with severe disease presentations and increased mortality rates. Two fluoroquinolone-resistant (FQR) lineages of the epidemic B1/NAP1/RT027/ST01 strain emerged in the USA in the early 1990s...
Article
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Background: The marine alga Ulva compressa is the dominant species in copper-polluted coastal areas in northern Chile. It has been shown that the alga tolerates micromolar concentrations of copper and accumulates copper at the intracellular level. Transcriptomic analyses were performed using total RNA of the alga cultivated with 10 μ M copper for...
Article
2,4,6-Trinitrotoluene (TNT) is a nitroaromatic explosive, highly toxic and mutagenic for organisms. In this study, we report for the first time the screening and isolation of TNT-degrading bacteria from Antarctic environmental samples with potential use as bioremediation agents. Ten TNT-degrading bacterial strains were isolated from Deception Islan...
Article
Bronchiolitis is the leading cause of hospitalizations among infants in the U.S. Two major respiratory viruses—respiratory syncytial virus (RSV) and rhinovirus (RV)—account for 85% of severe bronchiolitis (bronchiolitis resulting in hospitalization). While bronchiolitis has been considered a single disease entity and currently available management...
Preprint
Phosphate and arsenate are very similar compounds, and there is great interest in studying their relationship and their interaction with biological systems. Despite having no apparent biological function, specific genes regulate arsenic interaction with cells and can be located in regions of the genome called arsenic islands, where phosphate metabo...
Article
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Salmonella Typhimurium, a bacterial pathogen with high metabolic plasticity, can adapt to different environmental conditions; these traits enhance its virulence by enabling bacterial survival. Neutrophils play important roles in the innate immune response, including the production of microbicidal reactive oxygen species (ROS). In addition, the myel...
Article
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Chronic otitis media with effusion (COME) is a common childhood disease characterized by an accumulation of fluid behind the eardrum. COME often requires surgical intervention and can also lead to significant hearing loss and subsequent learning disabilities. Recent characterization of the middle ear fluid (MEF) microbiome in pediatric patients has...
Article
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Antarctic vascular plants such as Deschampsia antarctica (Da) could generate more suitable micro-environmental conditions for the establishment of other plants like Colobanthus quitensis (Cq). Although positive plant–plant interactions have been shown to contribute to plant performance and establishment, little is known about how microorganisms mig...
Article
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Exiguobacterium is a polyextremophile bacterial genus with a physiology that allows it to develop in different adverse environments. The Salar de Huasco is one of these environments due to its altitude, atmospheric pressure, solar radiation, temperature variations, pH, salinity, and the presence of toxic compounds such as arsenic. However, the phys...
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
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Porphyromonas gingivalis has been extensively associated with both the onset and progression of periodontitis. We previously isolated and characterized two P. gingivalis strains, one from a patient exhibiting severe chronic periodontitis (CP3) and another from a periodontally healthy individual (H3). We previously showed that CP3 and H3 exhibit dif...
Article
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We obtained the complete genome sequence of the psychrotolerant extremophile Pseudomonas sp. MPC6, a natural Polyhydroxyalkanoates (PHAs) producing bacterium able to rapidly grow at low temperatures. Genomic and phenotypic analyses allowed us to situate this isolate inside the Pseudomonas fluorescens phylogroup of pseudomonads as well as to reveal...
Article
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Alcaligenes aquatilis QD168 is a marine, aromatic hydrocarbon-degrading bacterium, isolated from an oil-polluted sediment of Quintero Bay, an industrial-coastal zone that has been chronically impacted by diverse pollutants. The aims of this study were to characterize the phylogenomic positions of Alcaligenes spp. and to characterize the genetic det...
Article
Full-text available
Background The marine alga Ulva compressa is the dominant species in coastal areas receiving effluents from copper mines. The alga can accumulate high amounts of copper and possesses a strong antioxidant system. Here, we performed short-term transcriptomic analyses using total RNA of the alga cultivated with 10 μM of copper for 0, 3, 6, 12 and 24 h...
Article
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The antibiotic-resistant bacterium Paenibacillus larvae is the causative agent of American foulbrood (AFB), currently the most destructive bacterial disease in honeybees. Phages that infect P. larvae were isolated as early as the 1950s, but it is only in recent years that P. larvae phage genomes have been sequenced and annotated. In this study we a...
Article
Full-text available
Salmonella Typhimurium is an intracellular pathogen that is capable of generating systemic fever in a murine model. Over the course of the infection, Salmonella faces different kinds of stressors, including harmful reactive oxygen species (ROS). Various defence mechanisms enable Salmonella to successfully complete the infective process in the prese...
Article
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We describe the genome sequence of Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3, the most abundant members of a bacterial community capable of degrading chloroaromatic compounds. The MT1 genome contains open reading frames encoding enzymes responsible for the catabolism of chlorosalicylate, methylsalicylate, chlorophenols, phenol, be...
Article
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The Psychrobacter genus is a cosmopolitan and diverse group of aerobic, cold-adapted, Gram-negative bacteria exhibiting biotechnological potential for low-temperature applications including bioremediation. Here, we present the draft genome sequence of a bacterium from the Psychrobacter genus isolated from a sediment sample from King George Island,...
Preprint
Full-text available
Antarctica is one of the most stressful ecosystems worldwide with few vascular plants, which are limited by abiotic conditions. Here, plants such as Deschampsia antarctica ( Da ) could generate more suitable micro-environmental conditions for the establishment of other plants as Colobanthus quitensis ( Cq ). Although, plant-plant interaction is kno...
Preprint
Full-text available
Antarctica is one of the most stressful ecosystems worldwide with few vascular plants, which are limited by abiotic conditions. Here, plants such as Deschampsia antarctica ( Da ) could generate more suitable micro-environmental conditions for the establishment of other plants as Colobanthus quitensis ( Cq ). Although, plant-plant interaction is kno...
Article
Rhodococcus sp. H-CA8f was isolated from marine sediments obtained from the Comau fjord, located in Northern Chilean Patagonia. Whole-genome sequencing was achieved using PacBio RS II platform, comprising one closed, complete chromosome of 6,19 Mbp with a 62.45% G + C content. The chromosome harbours several metabolic pathways providing a wide cata...