Salmo salar Skin and Gill Microbiome during Piscirickettsia salmonis Infection Marcos Godoy, Yoandy Coca, Rudy Suárez, Marco Montes de Oca, Jacob W. Bledsoe, et al. Animals, 2024 Maintaining the high overall health of farmed animals is a central tenant of their well-being and care. Intense animal crowding in aquaculture promotes animal morbidity especially in the absence of straightforward methods for monitoring their health. Here, we used bacterial 16S ribosomal RNA gene sequencing to measure bacterial population dynamics during P. salmonis infection. We observed a complex bacterial community consisting of a previously undescribed core pathobiome. Notably, we detected Aliivibrio wodanis and Tenacibaculum dicentrarchi on the skin ulcers of salmon infected with P. salmonis, while Vibrio spp. were enriched on infected gills. The prevalence of these co-occurring networks indicated that coinfection with other pathogens may enhance P. salmonis pathogenicity.
Bacterial networks in Atlantic salmon with Piscirickettsiosis Yoandy Coca, Marcos Godoy, Juan Pablo Pontigo, Diego Caro, Vinicius Maracaja-Coutinho, et al. Scientific Reports, 2023 An unbalanced composition of gut microbiota in fish is hypothesized to play a role in promoting bacterial infections, but the synergistic or antagonistic interactions between bacterial groups in relation to fish health are not well understood. We report that pathogenic species in the Piscirickettsia, Aeromonas, Renibacterium and Tenacibaculum genera were all detected in the digesta and gut mucosa of healthy Atlantic salmon without clinical signs of disease. Although Piscirickettsia salmonis (and other pathogens) occurred in greater frequencies of fish with clinical Salmonid Rickettsial Septicemia (SRS), the relative abundance was about the same as that observed in healthy fish. Remarkably, the SRS-positive fish presented with a generalized mid-gut dysbiosis and positive growth associations between Piscirickettsiaceae and members of other taxonomic families containing known pathogens. The reconstruction of metabolic phenotypes based on the bacterial networks detected in the gut and mucosa indicated the synthesis of Gram-negative virulence factors such as colanic acid and O-antigen were over-represented in SRS positive fish. This evidence indicates that cooperative interactions between organisms of different taxonomic families within localized bacterial networks might promote an opportunity for P. salmonis to cause clinical SRS in the farm environment.
Differences in Bacterial Small RNAs in Stool Samples from Hypercholesterolemic and Normocholesterolemic Subjects Cristian Morales, Raul Arias-Carrasco, Vinicius Maracaja-Coutinho, Pamela Seron, Fernando Lanas, et al. International Journal of Molecular Sciences, 2023 Cholesterol metabolism is important at the physiological level as well as in several diseases, with small RNA being an element to consider in terms of its epigenetic control. Thus, the aim of this study was to identify differences between bacterial small RNAs present at the gut level in hypercholesterolemic and normocholesterolemic individuals. Twenty stool samples were collected from hypercholesterolemic and normocholesterolemic subjects. RNA extraction and small RNA sequencing were performed, followed by bioinformatics analyses with BrumiR, Bowtie 2, BLASTn, DESeq2, and IntaRNA, after the filtering of the reads with fastp. In addition, the prediction of secondary structures was obtained with RNAfold WebServer. Most of the small RNAs were of bacterial origin and presented a greater number of readings in normocholesterolemic participants. The upregulation of small RNA ID 2909606 associated with Coprococcus eutactus (family Lachnospiraceae) was presented in hypercholesterolemic subjects. In addition, a positive correlation was established between small RNA ID 2149569 from the species Blautia wexlerae and hypercholesterolemic subjects. Other bacterial and archaeal small RNAs that interacted with the LDL receptor (LDLR) were identified. For these sequences, the prediction of secondary structures was also obtained. There were significant differences in bacterial small RNAs associated with cholesterol metabolism in hypercholesterolemic and normocholesterolemic participants.
Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects Cristian Morales, Gabriel Rojas, Camilo Rebolledo, Marcelo Rojas-Herrera, Raúl Arias-Carrasco, et al. Frontiers in Cellular and Infection Microbiology, 2022 IntroductionIn recent years, several studies have evidenced the importance of the microbiome to host physiology as metabolism regulator, along with its potential role in triggering various diseases. In this study, we analyzed the gut microbiota in hypercholesterolemic (cases) and normocholesterolemic (controls) individuals to identify characteristic microbial signature for each condition.MethodsStool samples were obtained from 57 adult volunteers (27 hypercholesterolemic and 30 controls). The taxonomic profiling of microbial communities was performed using high-throughput sequencing of 16S rRNA V3-V4 amplicons, followed by data analysis using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and linear discriminant analysis (LDA) effect size (LEfSe).ResultsSignificant differences were observed in weight, height, body mass index (BMI) and serum levels of triglycerides, total cholesterol and low-density lipoprotein cholesterol (LDL-C) between the groups (p<0.05). LEfSe showed differentially abundant prokaryotic taxa (α=0.05, LDA score > 2.0) in the group of hypercholesterolemic individuals (Methanosphaera, Rothia, Chromatiales, Clostridiales, Bacillaceae and Coriobacteriaceae) and controls (Faecalibacterium, Victivallis and Selenomonas) at various taxonomic levels. In addition, through the application of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2), the predominance of pathways related to biosynthesis in hypercholesterolemic patients was established, compared to controls in which degradation pathways were predominant. Finally, in the analysis of co-occurrence networks, it was possible to identify associations between the microorganisms present in both studied groups.ConclusionOur results point out to unique microbial signatures, which likely play a role on the cholesterol metabolism in the studied population.
OUTBREAK: a user-friendly georeferencing online tool for disease surveillance Raúl Arias-Carrasco, Jeevan Giddaluru, Lucas E. Cardozo, Felipe Martins, Vinicius Maracaja-Coutinho, et al. Biological Research, 2021 The current COVID-19 pandemic has already claimed more than 3.7 million victims and it will cause more deaths in the coming months. Tools that track the number and locations of cases are critical for surveillance and help in making policy decisions for controlling the outbreak. However, the current surveillance web-based dashboards run on proprietary platforms, which are often expensive and require specific computational knowledge. We developed a user-friendly web tool, named OUTBREAK, that facilitates epidemic surveillance by showing in an animated graph the timeline and geolocations of cases of an outbreak. It permits even non-specialist users to input data most conveniently and track outbreaks in real-time. We applied our tool to visualize the SARS 2003, MERS, and COVID19 epidemics, and provided them as examples on the website. Through the zoom feature, it is also possible to visualize cases at city and even neighborhood levels. We made the tool freely available at https://outbreak.sysbio.tools/. OUTBREAK has the potential to guide and help health authorities to intervene and minimize the effects of outbreaks.
The Single Cell Notebooks for inclusive and accessible training in single-cell and spatial omics A Rojas-Hidalgo, R Arias-Carrasco, J Karoline Silva, E Armingol, ... Nature Genetics , 2026 2026.0
The multifaceted roles of non-coding RNAs in cell-cell communication in cardiovascular health and disease D Jimenez-Gallegos, F Sigcho, E Vicencio, R Arias-Carrasco, ... Cell & Bioscience 15 (1), 154 , 2025 2025.0 Citations: 1
The repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation R Arias-Carrasco, V Aliaga-Tobar, S Abades, V Maracaja-Coutinho BioSystems 254, 105519 , 2025 2025.0 Citations: 1
Exploring the regulatory landscape of non-coding RNAs in aquaculture bacterial pathogens: Piscirickettsia salmonis and Francisella noatunensis V Aliaga-Tobar, R Arias-Carrasco, A Isla, J Santander, ... Aquaculture 594, 741356 , 2025 2025.0 Citations: 6
Salmo salar Skin and Gill Microbiome during Piscirickettsia salmonis Infection M Godoy, Y Coca, R Suárez, M Montes de Oca, JW Bledsoe, I Burbulis, ... Animals 14 (1), 97 , 2023 2023.0 Citations: 12
Bacterial networks in Atlantic salmon with piscirickettsiosis Y Coca, M Godoy, JP Pontigo, D Caro, V Maracaja-Coutinho, ... Scientific Reports 13 (1), 17321 , 2023 2023.0 Citations: 11
Differences in bacterial small RNAs in stool samples from hypercholesterolemic and normocholesterolemic subjects C Morales, R Arias-Carrasco, V Maracaja-Coutinho, P Seron, F Lanas, ... International Journal of Molecular Sciences 24 (8), 7213 , 2023 2023.0 Citations: 6
Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects C Morales, G Rojas, C Rebolledo, M Rojas-Herrera, R Arias-Carrasco, ... Frontiers in Cellular and Infection Microbiology, 1723 , 2022 2022.0 Citations: 15
Novel molecular insights and public omics data in pulmonary hypertension C Lopez-Crisosto, R Arias-Carrasco, P Sepulveda, L Garrido-Olivares, ... Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease 1867 (10), 166200 , 2021 2021.0 Citations: 9
OUTBREAK: a user-friendly georeferencing online tool for disease surveillance R Arias-Carrasco, J Giddaluru, LE Cardozo, F Martins, ... Biological Research 54 (1), 20 , 2021 2021.0 Citations: 14
RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction TAR Ramos, NRO Galindo, R Arias-Carrasco, CF da Silva, ... F1000Research 10, 323 , 2021 2021.0 Citations: 15
Predicting RNA families in nucleotide sequences using structrnafinder V Maracaja-Coutinho, R Arias-Carrasco, HI Nakaya, V Aliaga-Tobar Gene Prediction: Methods and Protocols, 15-27 , 2019 2019.0 Citations: 3
Core non-coding RNAs of Piscirickettsia salmonis C Segovia, R Arias-Carrasco, AJ Yanez, V Maracaja-Coutinho, ... PLoS One 13 (5), e0197206 , 2018 2018.0 Citations: 12
Genome-wide circulating microRNA expression profiling reveals potential biomarkers for amyotrophic lateral sclerosis JM Matamala, R Arias-Carrasco, C Sanchez, M Uhrig, L Bargsted, ... Neurobiology of Aging 64, 123-138 , 2018 2018.0 Citations: 79
Long non-coding RNAs responsive to salt and boron stress in the hyper-arid Lluteno maize from Atacama Desert W Huanca-Mamani, R Arias-Carrasco, S Cardenas-Ninasivincha, ... Genes 9 (3), 170 , 2018 2018.0 Citations: 83
Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci PP Amaral, T Leonardi, N Han, E Viré, DK Gascoigne, R Arias-Carrasco, ... Genome biology 19 (1), 32 , 2018 2018.0 Citations: 157
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses PST Russo, GR Ferreira, LE Cardozo, MC Bürger, R Arias-Carrasco, ... BMC bioinformatics 19 (1), 56 , 2018 2018.0 Citations: 365
StructRNAfinder: an automated pipeline and web server for RNA families prediction R Arias-Carrasco, Y Vásquez-Morán, HI Nakaya, V Maracaja-Coutinho BMC bioinformatics 19 (1), 55 , 2018 2018.0 Citations: 60
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis F Torres, R Arias-Carrasco, JC Caris-Maldonado, A Barral, ... Database 2017, bax047 , 2017 2017.0 Citations: 29
Transcriptomic analysis reveals heart failure-related lncRNA LINC00670 as a regulator of colon cancer mesenchymal genes D Jimenez-Gallegos, WA Corrales, A Peñaloza-Otarola, ... Available at SSRN 5741367 , 0
MOST CITED SCHOLAR PUBLICATIONS
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses PST Russo, GR Ferreira, LE Cardozo, MC Bürger, R Arias-Carrasco, ... BMC bioinformatics 19 (1), 56 , 2018 2018.0 Citations: 365
Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci PP Amaral, T Leonardi, N Han, E Viré, DK Gascoigne, R Arias-Carrasco, ... Genome biology 19 (1), 32 , 2018 2018.0 Citations: 157
Long non-coding RNAs responsive to salt and boron stress in the hyper-arid Lluteno maize from Atacama Desert W Huanca-Mamani, R Arias-Carrasco, S Cardenas-Ninasivincha, ... Genes 9 (3), 170 , 2018 2018.0 Citations: 83
Genome-wide circulating microRNA expression profiling reveals potential biomarkers for amyotrophic lateral sclerosis JM Matamala, R Arias-Carrasco, C Sanchez, M Uhrig, L Bargsted, ... Neurobiology of Aging 64, 123-138 , 2018 2018.0 Citations: 79
StructRNAfinder: an automated pipeline and web server for RNA families prediction R Arias-Carrasco, Y Vásquez-Morán, HI Nakaya, V Maracaja-Coutinho BMC bioinformatics 19 (1), 55 , 2018 2018.0 Citations: 60
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis F Torres, R Arias-Carrasco, JC Caris-Maldonado, A Barral, ... Database 2017, bax047 , 2017 2017.0 Citations: 29
Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects C Morales, G Rojas, C Rebolledo, M Rojas-Herrera, R Arias-Carrasco, ... Frontiers in Cellular and Infection Microbiology, 1723 , 2022 2022.0 Citations: 15
RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction TAR Ramos, NRO Galindo, R Arias-Carrasco, CF da Silva, ... F1000Research 10, 323 , 2021 2021.0 Citations: 15
OUTBREAK: a user-friendly georeferencing online tool for disease surveillance R Arias-Carrasco, J Giddaluru, LE Cardozo, F Martins, ... Biological Research 54 (1), 20 , 2021 2021.0 Citations: 14
Salmo salar Skin and Gill Microbiome during Piscirickettsia salmonis Infection M Godoy, Y Coca, R Suárez, M Montes de Oca, JW Bledsoe, I Burbulis, ... Animals 14 (1), 97 , 2023 2023.0 Citations: 12
Core non-coding RNAs of Piscirickettsia salmonis C Segovia, R Arias-Carrasco, AJ Yanez, V Maracaja-Coutinho, ... PLoS One 13 (5), e0197206 , 2018 2018.0 Citations: 12
Bacterial networks in Atlantic salmon with piscirickettsiosis Y Coca, M Godoy, JP Pontigo, D Caro, V Maracaja-Coutinho, ... Scientific Reports 13 (1), 17321 , 2023 2023.0 Citations: 11
Novel molecular insights and public omics data in pulmonary hypertension C Lopez-Crisosto, R Arias-Carrasco, P Sepulveda, L Garrido-Olivares, ... Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease 1867 (10), 166200 , 2021 2021.0 Citations: 9
Exploring the regulatory landscape of non-coding RNAs in aquaculture bacterial pathogens: Piscirickettsia salmonis and Francisella noatunensis V Aliaga-Tobar, R Arias-Carrasco, A Isla, J Santander, ... Aquaculture 594, 741356 , 2025 2025.0 Citations: 6
Differences in bacterial small RNAs in stool samples from hypercholesterolemic and normocholesterolemic subjects C Morales, R Arias-Carrasco, V Maracaja-Coutinho, P Seron, F Lanas, ... International Journal of Molecular Sciences 24 (8), 7213 , 2023 2023.0 Citations: 6
Predicting RNA families in nucleotide sequences using structrnafinder V Maracaja-Coutinho, R Arias-Carrasco, HI Nakaya, V Aliaga-Tobar Gene Prediction: Methods and Protocols, 15-27 , 2019 2019.0 Citations: 3
The multifaceted roles of non-coding RNAs in cell-cell communication in cardiovascular health and disease D Jimenez-Gallegos, F Sigcho, E Vicencio, R Arias-Carrasco, ... Cell & Bioscience 15 (1), 154 , 2025 2025.0 Citations: 1
The repertoire of candidate archaeal noncoding RNAs and their association with temperature adaptation R Arias-Carrasco, V Aliaga-Tobar, S Abades, V Maracaja-Coutinho BioSystems 254, 105519 , 2025 2025.0 Citations: 1
The Single Cell Notebooks for inclusive and accessible training in single-cell and spatial omics A Rojas-Hidalgo, R Arias-Carrasco, J Karoline Silva, E Armingol, ... Nature Genetics , 2026 2026.0
Transcriptomic analysis reveals heart failure-related lncRNA LINC00670 as a regulator of colon cancer mesenchymal genes D Jimenez-Gallegos, WA Corrales, A Peñaloza-Otarola, ... Available at SSRN 5741367 , 0
