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Gomez-Chavarria DA, Rua-Giraldo AL, Alzate JF. An evolutionary view of the Fusarium core genome. BMC Genomics 2024; 25:304. [PMID: 38519886 PMCID: PMC10958916 DOI: 10.1186/s12864-024-10200-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
Fusarium, a member of the Ascomycota fungi, encompasses several pathogenic species significant to plants and animals. Some phytopathogenic species have received special attention due to their negative economic impact on the agricultural industry around the world. Traditionally, identification and taxonomic analysis of Fusarium have relied on morphological and phenotypic features, including the fungal host, leading to taxonomic conflicts that have been solved using molecular systematic technologies. In this work, we applied a phylogenomic approach that allowed us to resolve the evolutionary history of the species complexes of the genus and present evidence that supports the F. ventricosum species complex as the most basal lineage of the genus. Additionally, we present evidence that proposes modifications to the previous hypothesis of the evolutionary history of the F. staphyleae, F. newnesense, F. nisikadoi, F. oxysporum, and F. fujikuroi species complexes. Evolutionary analysis showed that the genome GC content tends to be lower in more modern lineages, in both, the whole-genome and core-genome coding DNA sequences. In contrast, genome size gain and losses are present during the evolution of the genus. Interestingly, core genome duplication events positively correlate with genome size. Evolutionary and genome conservation analysis supports the F3 hypothesis of Fusarium as a more compact and conserved group in terms of genome conservation. By contrast, outside of the F3 hypothesis, the most basal clades only share 8.8% of its genomic sequences with the F3 clade.
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Affiliation(s)
- Daniel A Gomez-Chavarria
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria (SIU), Universidad de Antioquia, Carrera 53 No. 61-30 Lab. 510, Medellín, Colombia
| | | | - Juan F Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria (SIU), Universidad de Antioquia, Carrera 53 No. 61-30 Lab. 510, Medellín, Colombia.
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2
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Bedoya-Urrego K, Alzate JF. Phylogenomic discernments into Anaerolineaceae thermal adaptations and the proposal of a candidate genus Mesolinea. Front Microbiol 2024; 15:1349453. [PMID: 38486696 PMCID: PMC10937449 DOI: 10.3389/fmicb.2024.1349453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
This study delves into the evolutionary history of Anaerolineaceae, a diverse bacterial family within the Chloroflexota phylum. Employing a multi-faceted approach, including phylogenetic analyses, genomic comparisons, and exploration of adaptive features, the research unveils novel insights into the family's taxonomy and evolutionary dynamics. The investigation employs metagenome-assembled genomes (MAGs), emphasizing their prevalence in anaerobic environments. Notably, a novel mesophilic lineage, tentatively named Mesolinea, emerges within Anaerolineaceae, showcasing a distinctive genomic profile and apparent adaptation to a mesophilic lifestyle. The comprehensive genomic analyses shed light on the family's complex evolutionary patterns, including the conservation of key operons in thermophiles, providing a foundation for understanding the diverse ecological roles and adaptive strategies of Anaerolineaceae members.
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Affiliation(s)
- Katherine Bedoya-Urrego
- Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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3
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Rozo-Montoya N, Bedoya-Urrego K, Alzate JF. Monitoring potentially pathogenic protists in sewage sludge using Metataxonomics. Food Waterborne Parasitol 2023; 33:e00210. [PMID: 37808003 PMCID: PMC10558727 DOI: 10.1016/j.fawpar.2023.e00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023] Open
Abstract
Intestinal parasites continue to pose a significant threat to human health worldwide, particularly among children. Contaminated water and soil serve as major transmission vehicles for these parasites and intestinal protists are among the most prevalent parasites in both developed and developing nations. Traditionally, parasites have been studied using human or animal fecal samples, while studying them in environmental samples has been challenging due to technical limitations. However, advancements in Next-Generation Sequencing (NGS) and bioinformatic approaches now enable the detection of parasite DNA in environmental samples. In this study, we applied a metataxonomic and phylogenetic strategy to detect and classify DNA of protists present in sewage sludge from two major cities in Colombia: Medellin and Cali. We successfully detected several human pathogenic parasites including Giardia intestinalis, Entamoeba histolytica, and Blastocystis sp., among other protists, in all sludge samples examined. We also investigated the entry and exit of parasite DNA from the San Fernando wastewater treatment plant (WWTP). We observed a higher number of parasite DNA sequences in the plant's influent wastewater, but we also detected the discharge of DNA from pathogenic parasites in both effluent waters and biosolids.
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Affiliation(s)
- Nicolas Rozo-Montoya
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Katherine Bedoya-Urrego
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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Lopez-Jimenez J, Herrera J, Alzate JF. Expanding the knowledge frontier of mitoviruses in Cannabis sativa. Infect Genet Evol 2023; 116:105523. [PMID: 37940011 DOI: 10.1016/j.meegid.2023.105523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/25/2023] [Accepted: 11/04/2023] [Indexed: 11/10/2023]
Abstract
Mitoviruses were initially known for their presence in the mitochondria of fungi and were considered exclusive to these organisms. However, recent studies have shown that they are also present in a large number of plant species. Despite the potential impact that mitoviruses might have on the mitochondria of plant cells, there is a lack of information about these ancient RNA viruses, especially within the Cannabaceae family. Cannabis sativa has been in the spotlight in recent years due to the growing industrial applications of plant derivatives, such as fiber and secondary metabolites. Given the importance of Cannabis in today's agriculture, our study aimed to expand the knowledge frontier of Mitoviruses in C. sativa by increasing the number of reference genomes of CasaMV1 available in public databases and representing a larger number of crops in countries where its industrial-scale growth is legalized. To achieve this goal, we used transcriptomics to sequence the first mitoviral genomes of Colombian crops and analyzed RNA-seq datasets available in the SRA databank. Additionally, the evolutionary analysis performed using the mitovirus genomes revealed two main lineages of CasaMV1, termed CasaMV1_L1 and CasaMV1_L2. These mitoviral lineages showed strong clustering based on the geographic location of the crops and differential expression intensities.
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Affiliation(s)
- Juliana Lopez-Jimenez
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Jorge Herrera
- Fábrica de Plantas y Semillas de Antioquia S.A.S. - FASPLAN, El Carmen de Viboral, Antioquia, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia; Fábrica de Plantas y Semillas de Antioquia S.A.S. - FASPLAN, El Carmen de Viboral, Antioquia, Colombia; Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
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Ocampo JC, Alzate JF, Barrera LF, Baena A. Tuberculosis Severity Predictive Model Using Mtb Variants and Serum Biomarkers in a Colombian Cohort of APTB Patients. Biomedicines 2023; 11:3110. [PMID: 38137331 PMCID: PMC10740695 DOI: 10.3390/biomedicines11123110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/27/2023] [Accepted: 11/04/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, tuberculosis (TB) is a bacterial infection caused by Mycobacterium tuberculosis (Mtb) that primarily affects the lungs. The severity of active pulmonary TB (APTB) is an important determinant of transmission, morbidity, mortality, disease experience, and treatment outcomes. Several publications have shown a high prevalence of disabling complications in individuals who have had severe APTB. Furthermore, certain strains of Mtb were associated with more severe disease outcomes. The use of biomarkers to predict severe APTB patients who are candidates for host-directed therapies, due to the high risk of developing post-tuberculous lung disease (PTLD), has not yet been implemented in the management of TB patients. We followed 108 individuals with APTB for 6 months using clinical tools, flow cytometry, and whole-genome sequencing (WGS). The median age of the study population was 26.5 years, and the frequency of women was 53.7%. In this study, we aimed to identify biomarkers that could help us to recognize individuals with APTB and improve our understanding of the immunopathology in these individuals. In this study, we conducted a follow-up on the treatment progress of 121 cases of APTB. The follow-up process commenced at the time of diagnosis (T0), continued with a control visit at 2 months (T2), and culminated in an exit appointment at 6 months following the completion of medical treatment (T6). People classified with severe APTB showed significantly higher levels of IL-6 (14.7 pg/mL; p < 0.05) compared to those with mild APTB (7.7 pg/mL) at T0. The AUCs for the ROC curves and the Matthews correlation coefficient values (MCC) demonstrate correlations ranging from moderate to very strong. We conducted WGS on 88 clinical isolates of Mtb, and our analysis revealed a total of 325 genes with insertions and deletions (Indels) within their coding regions when compared to the Mtb H37Rv reference genome. The pattern of association was found between serum levels of CHIT1 and the presence of Indels in Mtb isolates from patients with severe APTB. A key finding in our study was the high levels of CHIT1 in severe APTB patients. We identified a biomarker profile (IL-6, IFN-γ, IL-33, and CHIT1) that allows us to identify individuals with severe APTB, as well as the identification of a panel of polymorphisms (125) in clinical isolates of Mtb from individuals with severe APTB. Integrating these findings into a predictive model of severity would show promise for the management of APTB patients in the future, to guide host-directed therapy and reduce the prevalence of PTLD.
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Affiliation(s)
- Juan C. Ocampo
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
| | - Juan F. Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia;
- Centro Nacional de Secuenciación Genómica (CNSG), Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
- Instituto de Investigaciones Médicas, Universidad de Antioquia (UdeA), Medellín 050010, Colombia
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia;
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Suárez-Baron H, Alzate JF, Ambrose BA, Pelaz S, González F, Pabón-Mora N. Comparative morphoanatomy and transcriptomic analyses reveal key factors controlling floral trichome development in Aristolochia (Aristolochiaceae). J Exp Bot 2023; 74:6588-6607. [PMID: 37656729 DOI: 10.1093/jxb/erad345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023]
Abstract
Trichomes are specialized epidermal cells in aerial plant parts. Trichome development proceeds in three stages, determination of cell fate, specification, and morphogenesis. Most genes responsible for these processes have been identified in the unicellular branched leaf trichomes from the model Arabidopsis thaliana. Less is known about the molecular basis of multicellular trichome formation across flowering plants, especially those formed in floral organs of early diverging angiosperms. Here, we aim to identify the genetic regulatory network (GRN) underlying multicellular trichome development in the kettle-shaped trap flowers of Aristolochia (Aristolochiaceae). We selected two taxa for comparison, A. fimbriata, with trichomes inside the perianth, which play critical roles in pollination, and A. macrophylla, lacking specialized trichomes in the perianth. A detailed morphoanatomical characterization of floral epidermis is presented for the two species. We compared transcriptomic profiling at two different developmental stages in the different perianth portions (limb, tube, and utricle) of the two species. Moreover, we present a comprehensive expression map for positive regulators and repressors of trichome development, as well as cell cycle regulators. Our data point to extensive modifications in gene composition, expression, and putative roles in all functional categories when compared with model species. We also record novel differentially expressed genes (DEGs) linked to epidermis patterning and trichome development. We thus propose the first hypothetical genetic regulatory network (GRN) underlying floral multicellular trichome development in Aristolochia, and pinpoint key factors responsible for the presence and specialization of floral trichomes in phylogenetically distant species of the genus.
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Affiliation(s)
- Harold Suárez-Baron
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cali, Colombia
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica (CNSG), Sede de Investigación Universitaria, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | | | - Soraya Pelaz
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
- ICREA (Institució Catalana de Recerca i Estudis Avançats), Barcelona, Spain
| | - Favio González
- Universidad Nacional de Colombia, Sede Bogotá Facultad de Ciencias, Instituto de Ciencias Naturales, Bogotá, Colombia
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Coltell O, Asensio EM, Sorlí JV, Ortega-Azorín C, Fernández-Carrión R, Pascual EC, Barragán R, González JI, Estruch R, Alzate JF, Pérez-Fidalgo A, Portolés O, Ordovas JM, Corella D. Associations between the New DNA-Methylation-Based Telomere Length Estimator, the Mediterranean Diet and Genetics in a Spanish Population at High Cardiovascular Risk. Antioxidants (Basel) 2023; 12:2004. [PMID: 38001857 PMCID: PMC10669035 DOI: 10.3390/antiox12112004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Biological aging is a relevant risk factor for chronic diseases, and several indicators for measuring this factor have been proposed, with telomere length (TL) among the most studied. Oxidative stress may regulate telomere shortening, which is implicated in the increased risk. Using a novel estimator for TL, we examined whether adherence to the Mediterranean diet (MedDiet), a highly antioxidant-rich dietary pattern, is associated with longer TL. We determined TL using DNA methylation algorithms (DNAmTL) in 414 subjects at high cardiovascular risk from Spain. Adherence to the MedDiet was assessed by a validated score, and genetic variants in candidate genes and at the genome-wide level were analyzed. We observed several significant associations (p < 0.05) between DNAmTL and candidate genes (TERT, TERF2, RTEL1, and DCAF4), contributing to the validity of DNAmTL as a biomarker in this population. Higher adherence to the MedDiet was associated with lower odds of having a shorter TL in the whole sample (OR = 0.93; 95% CI: 0.85-0.99; p = 0.049 after fully multivariate adjustment). Nevertheless, this association was stronger in women than in men. Likewise, in women, we observed a direct association between adherence to the MedDiet score and DNAmTL as a continuous variable (beta = 0.015; SE: 0.005; p = 0.003), indicating that a one-point increase in adherence was related to an average increase of 0.015 ± 0.005 kb in TL. Upon examination of specific dietary items within the global score, we found that fruits, fish, "sofrito", and whole grains exhibited the strongest associations in women. The novel score combining these items was significantly associated in the whole population. In the genome-wide association study (GWAS), we identified ten polymorphisms at the suggestive level of significance (p < 1 × 10-5) for DNAmTL (intergenics, in the IQSEC1, NCAPG2, and ABI3BP genes) and detected some gene-MedDiet modulations on DNAmTL. As this is the first study analyzing the DNAmTL estimator, genetics, and modulation by the MedDiet, more studies are needed to confirm these findings.
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Affiliation(s)
- Oscar Coltell
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
| | - Eva M. Asensio
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - José V. Sorlí
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Carolina Ortega-Azorín
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Rebeca Fernández-Carrión
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Rocío Barragán
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - José I. González
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Ramon Estruch
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Internal Medicine, Institut d’Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain
| | - Juan F. Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica—CNSG, Sede de Investigación Universitaria—SIU, Universidad de Antioquia, Medellín 050010, Colombia
| | - Alejandro Pérez-Fidalgo
- Department of Medical Oncology, University Clinic Hospital of Valencia, 46010 Valencia, Spain; (A.P.-F.)
- Biomedical Research Networking Centre on Cancer (CIBERONC), Health Institute Carlos III, 28029 Madrid, Spain
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Olga Portolés
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Jose M. Ordovas
- Department of Medical Oncology, University Clinic Hospital of Valencia, 46010 Valencia, Spain; (A.P.-F.)
- Nutrition and Genomics, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA
- Nutritional Control of the Epigenome Group, Precision Nutrition and Obesity Program, IMDEA Food, UAM + CSIC, 28049 Madrid, Spain
| | - Dolores Corella
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
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Madrigal Y, Alzate JF, Pabón-Mora N. Evolution of major flowering pathway integrators in Orchidaceae. Plant Reprod 2023:10.1007/s00497-023-00482-7. [PMID: 37823912 DOI: 10.1007/s00497-023-00482-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/10/2023] [Indexed: 10/13/2023]
Abstract
The Orchidaceae is a mega-diverse plant family with ca. 29,000 species with a large variety of life forms that can colonize transitory habitats. Despite this diversity, little is known about their flowering integrators in response to specific environmental factors. During the reproductive transition in flowering plants a vegetative apical meristem (SAM) transforms into an inflorescence meristem (IM) that forms bracts and flowers. In model grasses, like rice, a flowering genetic regulatory network (FGRN) controlling reproductive transitions has been identified, but little is known in the Orchidaceae. In order to analyze the players of the FRGN in orchids, we performed comprehensive phylogenetic analyses of CONSTANS-like/CONSTANS-like 4 (COL/COL4), FLOWERING LOCUS D (FD), FLOWERING LOCUS C/FRUITFULL (FLC/FUL) and SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) gene lineages. In addition to PEBP and AGL24/SVP genes previously analyzed, here we identify an increase of orchid homologs belonging to COL4, and FUL gene lineages in comparison with other monocots, including grasses, due to orchid-specific gene lineage duplications. Contrariwise, local duplications in Orchidaceae are less frequent in the COL, FD and SOC1 gene lineages, which points to a retention of key functions under strong purifying selection in essential signaling factors. We also identified changes in the protein sequences after such duplications, variation in the evolutionary rates of resulting paralogous clades and targeted expression of isolated homologs in different orchids. Interestingly, vernalization-response genes like VERNALIZATION1 (VRN1) and FLOWERING LOCUS C (FLC) are completely lacking in orchids, or alternatively are reduced in number, as is the case of VERNALIZATION2/GHD7 (VRN2). Our findings point to non-canonical factors sensing temperature changes in orchids during reproductive transition. Expression data of key factors gathered from Elleanthus auratiacus, a terrestrial orchid in high Andean mountains allow us to characterize which copies are actually active during flowering. Altogether, our data lays down a comprehensive framework to assess gene function of a restricted number of homologs identified more likely playing key roles during the flowering transition, and the changes of the FGRN in neotropical orchids in comparison with temperate grasses.
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Affiliation(s)
- Yesenia Madrigal
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
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Melo-Bolívar JF, Ruiz Pardo RY, Quintanilla-Carvajal MX, Díaz LE, Alzate JF, Junca H, Rodríguez Orjuela JA, Villamil Diaz LM. Evaluation of dietary single probiotic isolates and probiotic multistrain consortia in growth performance, gut histology, gut microbiota, immune regulation, and infection resistance of Nile tilapia, Oreochromis niloticus, shows superior monostrain performance. Fish Shellfish Immunol 2023; 140:108928. [PMID: 37423403 DOI: 10.1016/j.fsi.2023.108928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 05/15/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
The probiotic potential of a designed bacterial consortia isolated from a competitive exclusion culture originally obtained from the intestinal contents of tilapia juveniles were evaluated on Nile tilapia alevins. The growth performance, intestinal histology, microbiota effects, resistance to Streptococcus agalactiae challenge, and immune response were assessed. In addition, the following treatments were included in a commercial feed: A12+M4+M10 (Lactococcus lactis A12, Priestia megaterium M4, and Priestia sp. M10), M4+M10 (P. megaterium M4, and Priestia sp. M10) and the single bacteria as controls; A12 (L. lactis A12), M4 (P. megaterium M4), M10 (Priestia sp. M10), also a commercial feed without any probiotic addition was included as a control. The results showed that all probiotic treatments improved the growth performance, intestinal histology, and resistance during experimental infection with S. agalactiae in comparison to the control fish. Also, the administration of probiotics resulted in the modulation of genes associated with the innate and adaptive immune systems that were non-dependent on microbial colonization. Surprisingly, L. lactis A12 alone induced benefits in fish compared to the microbial consortia, showing the highest increase in growth rate, survival during experimental infection with S. agalactiae, increased intestinal fold length, and the number of differentially expressed genes. Lastly, we conclude that a competitive exclusion culture is a reliable source of probiotics, and monostrain L. lactis A12 has comparable or even greater probiotic potential than the bacterial consortia.
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Affiliation(s)
- Javier Fernando Melo-Bolívar
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Ruth Yolanda Ruiz Pardo
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - María Ximena Quintanilla-Carvajal
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Luis Eduardo Díaz
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica- CNSG, Sede de Investigación Universitaria SIU, Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Howard Junca
- Microbiomas Foundation, Div. Ecogenomics & Holobionts, RG Microbial Ecology: Metabolism, Genomics & Evolution, Chía, Colombia
| | - Jorge Alberto Rodríguez Orjuela
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Luisa Marcela Villamil Diaz
- Universidad de La Sabana, Doctorado en Biociencias, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia.
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10
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Garcia-Montoya GM, Galvan-Diaz AL, Alzate JF. Metataxomics reveals Blastocystis subtypes mixed infections in Colombian children. Infect Genet Evol 2023; 113:105478. [PMID: 37406785 DOI: 10.1016/j.meegid.2023.105478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Blastocystis sp., is an intestinal protist with a broad host range and a high prevalence in human populations worldwide, even in developed Western countries. The publication of conflicting evidence has divided the scientific community about the pathogenic role of this parasite. Even though, genetic studies on Blastocystis sp. revealed associations between genotypes and different pathogenic profiles. Conventionally, the detection of this parasite is based on microscopic or PCR methods, which offer meager or null performance in detecting mixed infections. In this work, we applied a metataxonomic NGS approach targeting the V4 region of the eukaryotic SSU-rRNA gene and classical phylogenetic methods. This approach allowed us to detect Blastocystis sp. in stool samples from infected children living in an urban setting in the city of Medellin attending the same daycare center. Phylogenetic analysis identified the subtypes present in the children as ST1, ST2, and ST3. Besides, mixed infections of subtypes ST1 + ST3 were spotted in 16% of the analyzed stool samples.
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Affiliation(s)
- Gisela M Garcia-Montoya
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Medellín, Colombia; Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia; Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Ana L Galvan-Diaz
- Grupo de Microbiología ambiental, Escuela de Microbiología, Universidad de Antioquia, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Medellín, Colombia; Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia; Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
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11
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Ramírez DS, Alzate JF, Simone Y, van der Meijden A, Guevara G, Franco Pérez LM, González-Gómez JC, Prada Quiroga CF. Intersexual Differences in the Gene Expression of Phoneutria depilata (Araneae, Ctenidae) Toxins Revealed by Venom Gland Transcriptome Analyses. Toxins (Basel) 2023; 15:429. [PMID: 37505698 PMCID: PMC10467060 DOI: 10.3390/toxins15070429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/17/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
The wandering spider, Phoneutria depilata, is one of Colombia's most active nocturnal arthropod predators of vertebrates and invertebrates. Its venom has been a relevant subject of study in the last two decades. However, the scarcity of transcriptomic data for the species limits our knowledge of the distinct components present in its venom for linking the mainly neurotoxic effects of the spider venom to a particular molecular target. The transcriptome of the P. depilata venom gland was analyzed to understand the effect of different diets or sex and the impact of these variables on the composition of the venom. We sequenced venom glands obtained from ten males and ten females from three diet treatments: (i) invertebrate: Tenebrio molitor, (ii) vertebrate: Hemidactylus frenatus, and (iii) mixed (T. molitor + H. frenatus). Of 17,354 assembled transcripts from all samples, 65 transcripts relating to venom production differed between males and females. Among them, 36 were classified as neurotoxins, 14 as serine endopeptidases, 11 as other proteins related to venom production, three as metalloprotease toxins, and one as a venom potentiator. There were no differences in transcripts across the analyzed diets, but when considering the effect of diets on differences between the sexes, 59 transcripts were differentially expressed. Our findings provide essential information on toxins differentially expressed that can be related to sex and the plasticity of the diet of P. depilata and thus can be used as a reference for venomics of other wandering spider species.
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Affiliation(s)
- Diego Sierra Ramírez
- Grupo de Investigación Biología y Ecología de Artrópodos (BEA), Facultad de Ciencias, Universidad del Tolima, Altos de Santa Helena, Ibagué 730001, Colombia; (D.S.R.); (J.C.G.-G.)
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica (CNSG), Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia
| | - Yuri Simone
- CIBIO/InBIO/Biopolis, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vila do Conde, Portugal; (Y.S.); (A.v.d.M.)
| | - Arie van der Meijden
- CIBIO/InBIO/Biopolis, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vila do Conde, Portugal; (Y.S.); (A.v.d.M.)
| | - Giovany Guevara
- Grupo de Investigación en Zoología (GIZ), Facultad de Ciencias, Universidad del Tolima, Altos de Santa Helena, Ibagué 730001, Colombia;
| | - Lida Marcela Franco Pérez
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 Calle 67, Ibagué 730001, Colombia;
| | - Julio César González-Gómez
- Grupo de Investigación Biología y Ecología de Artrópodos (BEA), Facultad de Ciencias, Universidad del Tolima, Altos de Santa Helena, Ibagué 730001, Colombia; (D.S.R.); (J.C.G.-G.)
| | - Carlos F. Prada Quiroga
- Grupo de Investigación Biología y Ecología de Artrópodos (BEA), Facultad de Ciencias, Universidad del Tolima, Altos de Santa Helena, Ibagué 730001, Colombia; (D.S.R.); (J.C.G.-G.)
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12
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Baena A, Cabarcas F, Ocampo JC, Barrera LF, Alzate JF. Large genomic deletions delineate Mycobacterium tuberculosis L4 sublineages in South American countries. PLoS One 2023; 18:e0285417. [PMID: 37205685 PMCID: PMC10198500 DOI: 10.1371/journal.pone.0285417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/24/2023] [Indexed: 05/21/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is still one of the primary pathogens of humans causing tuberculosis (TB) disease. Mtb embraces nine well-defined phylogenetic lineages with biological and geographical disparities. The lineage L4 is the most globally widespread of all lineages and was introduced to America with European colonization. Taking advantage of many genome projects available in public repositories, we undertake an evolutionary and comparative genomic analysis of 522 L4 Latin American Mtb genomes. Initially, we performed careful quality control of public read datasets and applied several thresholds to filter out low-quality data. Using a genome de novo assembly strategy and phylogenomic methods, we spotted novel south American clades that have not been revealed yet. Additionally, we describe genomic deletion profiles of these strains from an evolutionary perspective and report Mycobacterium tuberculosis L4 sublineages signature-like gene deletions, some of the novel. One is a specific deletion of 6.5 kbp that is only present in sublineage 4.1.2.1. This deletion affects a complex group of 10 genes with putative products annotated, among others, as a lipoprotein, transmembrane protein, and toxin/antitoxin system proteins. The second novel deletion spans for 4.9 kbp and specific of a particular clade of the 4.8 sublineage and affects 7 genes. The last novel deletion affects 4 genes, extends for 4.8 kbp., and is specific to some strains within the 4.1.2.1 sublineage that are present in Colombia, Peru and Brasil.
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Affiliation(s)
- Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Felipe Cabarcas
- Centro Nacional de Secuenciación Genómica—CNSG, Universidad de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan C. Ocampo
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
- Instituto de Investigaciones médicas, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
- Centro Nacional de Secuenciación Genómica—CNSG, Universidad de Antioquia, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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13
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Pabón-Mora N, Suárez-Baron H, Madrigal Y, Alzate JF, González F. Expression and Functional Studies of Leaf, Floral, and Fruit Developmental Genes in Non-model Species. Methods Mol Biol 2023; 2686:365-401. [PMID: 37540370 DOI: 10.1007/978-1-0716-3299-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Researchers working on evolutionary developmental plant biology are inclined to choose non-model taxa to address how specific features have been acquired during ontogeny and fixed during phylogeny. In this chapter we describe methods to extract RNA, to assemble de-novo transcriptomes, to isolate orthologous genes within gene families, and to evaluate expression and function of target genes. We have successfully optimized these protocols for non-model plant species including ferns, gymnosperms, and a large assortment of angiosperms. In the latter, we have ranged a large number of families including Aristolochiaceae, Apodanthaceae, Chloranthaceae, Orchidaceae, Papaveraceae, Rubiaceae, Solanaceae, and Tropaeolaceae.
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Affiliation(s)
| | - Harold Suárez-Baron
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
- Departamento de Ciencias Naturales y Matemáticas, Pontificia Universidad Javeriana, Cali, Colombia
| | - Yesenia Madrigal
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Medellín, Antioquia, Colombia
| | - Favio González
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
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14
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Mesa-Arango JA, Olave-Velandia AM, García-Montoya GM, Isaza-Agudelo JP, Jiménez-Ruiz A, Alzate JF. Evaluation of new Toxocara canis chimeric antigens as an alternative to conventional TES-Ag for anti- Toxocara antibodies detection. Heliyon 2022; 8:e11144. [PMID: 36299519 PMCID: PMC9589186 DOI: 10.1016/j.heliyon.2022.e11144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/01/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Human toxocariasis is one of the neglected helminthiases and it is caused by the zoonotic roundworm species Toxocara canis and Toxocara cati. Diagnosis of human toxocariasis is based on the combination of clinical, parasitological, and epidemiological criteria, as well as serology tests that detect anti-Toxocara antibodies. Notwithstanding, due to the absence of pathognomonic symptoms and signs of the disease, serology is the key evidence to support a conclusive diagnosis. TES-ELISA is the most widely used serological test for diagnosis. However, cross-reaction of TES antigens with antibodies produced to other helminth antigens is a major drawback for its application in countries with high parasitic prevalence. T. canis recombinant antigens have been described as an alternative to native TES for diagnosis. Nevertheless, the selection of antigenic proteins is a complex process that requires validation. In this paper, we developed an eGFP carrier-based system to express and purify blocks of recombinant polypeptides of T. canis antigenic proteins. Intense cross-reaction polypeptides were detected by Immunoblot and avoided to finally produce a chimeric prototype protein. Additionally, a control chimeric protein that harbors the complete tested proteins was produced. Purified chimeric antigens were tested in ELISA and Immunoblot assays with 310 sera samples of negative and positive control individuals. Our results showed that chimeric rCHITC0 and rCHITC1 antigens (with sensitivities of 62% 58%, 38% and 16% in IB-rCHITC0, ELISA-rCHITC0, ELISA-rCHITC1 and IB-rCHITC1 respectively for OLMS) can perform better in terms of specificity (being 91%, 89%, 87% and 76% for ELISA-rCHITC1, IB-rCHITC1, ELISA-rCHITC0 and IB-rCHITC0 respectively for OLMS) than T. canis TES-ELISA (with 61% specificity), giving a higher signal with serum samples of infected individuals as well the possibility to discriminate false positive cases with other parasitic infections. Our data suggest that T. canis chimeric proteins, represent candidate antigens for phase II studies.
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Affiliation(s)
- Jairo A. Mesa-Arango
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Colombia,Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia, Colombia
| | - Ana M. Olave-Velandia
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Colombia
| | - Gisela M. García-Montoya
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Colombia,Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia, Colombia
| | - Juan P. Isaza-Agudelo
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Colombia,Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia, Colombia
| | - Antonio Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Colombia,Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia, Colombia,Corresponding author.
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15
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Uran-Velasquez J, Alzate JF, Farfan-Garcia AE, Gomez-Duarte OG, Martinez-Rosado LL, Dominguez-Hernandez DD, Rojas W, Galvan-Diaz AL, Garcia-Montoya GM. Multilocus Sequence Typing helps understand the genetic diversity of Cryptosporidium hominis and Cryptosporidium parvum isolated from Colombian patients. PLoS One 2022; 17:e0270995. [PMID: 35802653 PMCID: PMC9269747 DOI: 10.1371/journal.pone.0270995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
Multilocus Sequence Typing has become a useful tool for the study of the genetic diversity and population structure of different organisms. In this study, a MLST approach with seven loci (CP47, MS5, MS9, MSC6-7, TP14, and gp60) was used to analyze the genetic diversity of Cryptosporidium hominis and Cryptosporidium parvum isolated from 28 Colombian patients. Five Cryptosporidium species were identified: C. hominis, C. parvum, Cryptosporidium felis, Cryptosporidium meleagridis, and Cryptosporidium suis. Unilocus gp60 analysis identified four allelic families for C. hominis (Ia, Ib, Id, and Ie) and two for C. parvum (IIa and IIc). There was polymorphic behavior of all markers evaluated for both C. hominis and C. parvum, particularly with the CP47, MS5, and gp60 markers. Phylogenetic analysis with consensus sequences (CS) of the markers showed a taxonomic agreement with the results obtained with the 18S rRNA and gp60 gene. Additionally, two monophyletic clades that clustered the species C. hominis and C. parvum were detected, with a higher number of subclades within the monophyletic groups compared to those with the gp60 gene. Thirteen MLG were identified for C. hominis and eight for C. parvum. Haplotypic and nucleotide diversity were detected, but only the latter was affected by the gp60 exclusion from the CS analysis. The gene fixation index showed an evolutionary closeness between the C. hominis samples and a less evolutionary closeness and greater sequence divergence in the C. parvum samples. Data obtained in this work support the implementation of MLST analysis in the study of the genetic diversity of Cryptosporidium, considering the more detailed information that it provides, which may explain some genetic events that with an unilocus approach could not be established. This is the first multilocus analysis of the intra-specific variability of Cryptosporidium from humans in South America.
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Affiliation(s)
- Johanna Uran-Velasquez
- Centro Nacional de Secuenciación Genómica–CNSG, Sede de Investigación Universitaria–SIU, Medellín, Antioquia, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica–CNSG, Sede de Investigación Universitaria–SIU, Medellín, Antioquia, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
- Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Ana E. Farfan-Garcia
- Universidad de Santander, Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Bucaramanga, Colombia
| | - Oscar G. Gomez-Duarte
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States of America
- John R. Oishei Children’s Hospital, Buffalo, NY, United States of America
| | - Larry L. Martinez-Rosado
- Equipo Latinoamericano de Investigación en Infectología y Salud Pública (ELISAP), E.S.E. Hospital La María, Medellín, Colombia
| | - Diego D. Dominguez-Hernandez
- Equipo Latinoamericano de Investigación en Infectología y Salud Pública (ELISAP), E.S.E. Hospital La María, Medellín, Colombia
| | - Winston Rojas
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Ana Luz Galvan-Diaz
- Grupo de Microbiología Ambiental, Escuela de Microbiología, Universidad de Antioquia, Medellín, Antioquia, Colombia
- * E-mail:
| | - Gisela M. Garcia-Montoya
- Centro Nacional de Secuenciación Genómica–CNSG, Sede de Investigación Universitaria–SIU, Medellín, Antioquia, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
- Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
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16
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López-Agudelo VA, Baena A, Barrera V, Cabarcas F, Alzate JF, Beste DJV, Ríos-Estepa R, Barrera LF. Dual RNA Sequencing of Mycobacterium tuberculosis-Infected Human Splenic Macrophages Reveals a Strain-Dependent Host-Pathogen Response to Infection. Int J Mol Sci 2022; 23:ijms23031803. [PMID: 35163725 PMCID: PMC8836425 DOI: 10.3390/ijms23031803] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), leading to pulmonary and extrapulmonary TB, whereby Mtb is disseminated to many other organs and tissues. Dissemination occurs early during the disease, and bacteria can be found first in the lymph nodes adjacent to the lungs and then later in the extrapulmonary organs, including the spleen. The early global gene expression response of human tissue macrophages and intracellular clinical isolates of Mtb has been poorly studied. Using dual RNA-seq, we have explored the mRNA profiles of two closely related clinical strains of the Latin American and Mediterranean (LAM) family of Mtb in infected human splenic macrophages (hSMs). This work shows that these pathogens mediate a distinct host response despite their genetic similarity. Using a genome-scale host–pathogen metabolic reconstruction to analyze the data further, we highlight that the infecting Mtb strain also determines the metabolic response of both the host and pathogen. Thus, macrophage ontogeny and the genetic-derived program of Mtb direct the host–pathogen interaction.
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Affiliation(s)
- Víctor A. López-Agudelo
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia; (V.A.L.-A.); (A.B.)
- Grupo de Bioprocesos, Facultad de Ingeniería, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia; (V.A.L.-A.); (A.B.)
| | - Vianey Barrera
- Programa de Ingeniería Biológica, Universidad Nacional de Colombia, Sede Medellín, Medellín 050010, Colombia;
| | - Felipe Cabarcas
- Grupo Sistemas Embebidos e Inteligencia Computacional (SISTEMIC), Facultad de Ingeniería, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica (CNSG), Sede de Investigación Universitaria (SIU), Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Dany J. V. Beste
- Department of Microbial Sciences, Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7XH, UK;
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Facultad de Ingeniería, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia; (V.A.L.-A.); (A.B.)
- Correspondence:
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17
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Mas A, Martínez-Rodrigo A, Carrión J, Orden JA, Alzate JF, Domínguez-Bernal G, Horcajo P. Transcriptomic Profile of Canine DH82 Macrophages Infected by Leishmania infantum Promastigotes with Different Virulence Behavior. Int J Mol Sci 2022; 23:ijms23031466. [PMID: 35163386 PMCID: PMC8835757 DOI: 10.3390/ijms23031466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 02/07/2023] Open
Abstract
Zoonotic visceral leishmaniosis caused by Leishmania infantum is an endemic disease in the Mediterranean Basin affecting mainly humans and dogs, the main reservoir. The leishmaniosis outbreak declared in the Community of Madrid (Spain) led to a significant increase in human disease incidence without enhancing canine leishmaniosis prevalence, suggesting a better adaptation of the outbreak's isolates by other host species. One of the isolates obtained in the focus, IPER/ES/2012/BOS1FL1 (BOS1FL1), has previously demonstrated a different phenotype than the reference strain MCAN/ES/1996/BCN150 (BCN150), characterized by a lower infectivity when interacting with canine macrophages. Nevertheless, not enough changes in the cell defensive response were found to support their different behavior. Thus, we decided to investigate the molecular mechanisms involved in the interaction of both parasites with DH82 canine macrophages by studying their transcriptomic profiles developed after infection using RNA sequencing. The results showed a common regulation induced by both parasites in the phosphoinositide-3-kinase-protein kinase B/Akt and NOD-like receptor signaling pathways. However, other pathways, such as phagocytosis and signal transduction, including tumor necrosis factor, mitogen-activated kinases and nuclear factor-κB, were only regulated after infection with BOS1FL1. These differences could contribute to the reduced infection ability of the outbreak isolates in canine cells. Our results open a new avenue to investigate the true role of adaptation of L. infantum isolates in their interaction with their different hosts.
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Affiliation(s)
- Alicia Mas
- INMIVET, Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain; (A.M.); (A.M.-R.); (J.C.); (J.A.O.)
| | - Abel Martínez-Rodrigo
- INMIVET, Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain; (A.M.); (A.M.-R.); (J.C.); (J.A.O.)
| | - Javier Carrión
- INMIVET, Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain; (A.M.); (A.M.-R.); (J.C.); (J.A.O.)
| | - José Antonio Orden
- INMIVET, Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain; (A.M.); (A.M.-R.); (J.C.); (J.A.O.)
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Departamento de Microbiología y Parasitología, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Gustavo Domínguez-Bernal
- INMIVET, Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain; (A.M.); (A.M.-R.); (J.C.); (J.A.O.)
- Correspondence: ; Tel.: +34-913943814
| | - Pilar Horcajo
- Animal Health and Zoonoses (SALUVET) Group, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, 28040 Madrid, Spain;
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18
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Alvarez-Eraso KLF, Muñoz-Martínez LM, Alzate JF, Barrera LF, Baena A. Modulatory Impact of the sRNA Mcr11 in Two Clinical Isolates of Mycobacterium tuberculosis. Curr Microbiol 2022; 79:39. [PMID: 34982251 DOI: 10.1007/s00284-021-02733-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/30/2021] [Indexed: 11/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a successful pathogen causing tuberculosis (TB) disease in humans. It has been shown, that some circulating strains of Mtb in TB endemic populations, are more virulent and more transmissible than others, which may be related to their evolved adaptations to modulate the host immune responses. Underlying these adaptations to the stressful conditions, different genetic regulatory networks involved sRNAs that are mostly unknown for Mtb. We have previously shown that Mcr11 is one of the main sRNAs that determine transcriptomic differences among the Colombian clinical isolates UT127 and UT205 compared to the laboratory strain H37Rv. We found that the knock-down of mcr11 using CRISPRi has a major impact on phenotypic traits, especially in the clinical isolate UT205. Through the analysis of RNA-seq during the knock-down of mcr11 in UT205, we found a downregulation of genes mainly involved in lipid synthesis, lipid metabolism, ribosomal proteins, transport systems, respiratory and energy systems, membrane and cell wall components, intermediary metabolism, lipoproteins and virulence genes. One of the most interesting genes showing transcriptomic changes is OprA (encoded by the gene rv0516c), which has been involved in the K+ regulation. Overall, our data may suggest that one of the prominent roles of the sRNA Mcr11 is to regulate genes that control Mtb growth and osmoregulation.
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Affiliation(s)
| | | | - Juan F Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Medellín, Colombia
- Centro Nacional de Secuenciación Genómica-CNSG, Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Medellín, Colombia
| | - Luis F Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Medellín, Colombia
- Instituto de Investigaciones Médicas, Universidad de Antioquia, Medellín, Colombia
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Medellín, Colombia.
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Medellín, Colombia.
- Sede de Investigación Universitaria-SIU, Medellín, Colombia.
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19
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Lopera TJ, Lujan JA, Zurek E, Zapata W, Hernandez JC, Toro MA, Alzate JF, Taborda NA, Rugeles MT, Aguilar-Jimenez W. A specific structure and high richness characterize intestinal microbiota of HIV-exposed seronegative individuals. PLoS One 2021; 16:e0260729. [PMID: 34855852 PMCID: PMC8638974 DOI: 10.1371/journal.pone.0260729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023] Open
Abstract
Intestinal microbiota facilitates food breakdown for energy metabolism and influences the immune response, maintaining mucosal homeostasis. Overall, HIV infection is associated with intestinal dysbiosis and immune activation, which has been related to seroconversion in HIV-exposed individuals. However, it is unclear whether microbiota dysbiosis is the cause or the effect of immune alterations and disease progression or if it could modulate the risk of acquiring the HIV infection. We characterize the intestinal microbiota and determine its association with immune regulation in HIV-exposed seronegative individuals (HESN), HIV-infected progressors (HIV+), and healthy control (HC) subjects. For this, feces and blood were collected. The microbiota composition of HESN showed a significantly higher alpha (p = 0.040) and beta diversity (p = 0.006) compared to HC, but no differences were found compared to HIV+. A lower Treg percentage was observed in HESN (1.77%) than HC (2.98%) and HIV+ (4.02%), with enrichment of the genus Butyrivibrio (p = 0.029) being characteristic of this profile. Moreover, we found that Megasphaera (p = 0.017) and Victivallis (p = 0.0029) also are enriched in the microbiota composition in HESN compared to HC and HIV+ subjects. Interestingly, an increase in Succinivibrio and Prevotella, and a reduction in Bacteroides genus, which is typical of HIV-infected individuals, were observed in both HESN and HIV+, compared to HC. Thus, HESNs have a microbiota profile, similar to that observed in HIV+, most likely because HESN are cohabiting with their HIV+ partners.
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Affiliation(s)
- Tulio J. Lopera
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Jorge A. Lujan
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Eduardo Zurek
- Department of System Engineering, Universidad del Norte, Barranquilla, Colombia
| | - Wildeman Zapata
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
- Facultad de Medicina, Grupo Infettare, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Juan C. Hernandez
- Facultad de Medicina, Grupo Infettare, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Miguel A. Toro
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica -CNSG, Sede de Investigación Universitaria -SIU, Universidad de Antioquia UdeA, Medellin, Colombia
- Facultad de Medicina, Grupo de Parasitología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica -CNSG, Sede de Investigación Universitaria -SIU, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Natalia A. Taborda
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
- Facultad de Ciencias de la Salud, Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Corporación Universitaria Remington, Medellín, Colombia
| | - Maria T. Rugeles
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
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20
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Bedoya K, Niño J, Acero J, Jaimes-Prada R, Cabarcas F, Alzate JF. Metagenomic Analysis of Biocide-Treated Neotropical Oil Reservoir Water Unveils Microdiversity of Thermophile Tepidiphilus. Front Microbiol 2021; 12:741555. [PMID: 34790180 PMCID: PMC8591294 DOI: 10.3389/fmicb.2021.741555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are capable of colonizing extreme environments like deep biosphere and oil reservoirs. The prokaryotes diversity in exploited oil reservoirs is composed of indigenous microbial communities and artificially introduced microbes. In the present work, high throughput sequencing techniques were applied to analyze the microbial community from the injected and produced water in a neotropical hyper-thermophile oil reservoir located in the Orinoquia region of Colombia, South America. Tepidiphilus is the dominant bacteria found in both injection and produced waters. The produced water has a higher microbial richness and exhibits a Tepidiphilus microdiversity. The reservoir injected water is recycled and treated with the biocides glutaraldehyde and tetrakis-hydroxymethyl-phosphonium sulfate (THPS) to reduce microbial load. This process reduces microbial richness and selects a single Tepidiphilus genome (T. sp. UDEAICP_D1) as the dominant isolate. Thermus and Hydrogenobacter were subdominants in both water systems. Phylogenomic analysis of the injection water dominant Tepidiphilus positioned it as an independent branch outside T. succinatimandens and T. thermophilus lineage. Comparative analysis of the Tepidiphilus genomes revealed several genes that might be related to the biocide-resistant phenotype and the tolerance to the stress conditions imposed inside the oil well, like RND efflux pumps and type II toxin-antitoxin systems. Comparing the abundance of Tepidiphilus protein-coding genes in both water systems shows that the biocide selected Tepidiphilus sp. UDEAICP_D1 genome has enriched genes annotated as ABC-2 type transporter, ABC transporter, Methionine biosynthesis protein MetW, Glycosyltransferases, and two-component system NarL.
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Affiliation(s)
- Katherine Bedoya
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia -UdeA, Medellín, Colombia
| | - Jhorman Niño
- Centro de Innovación y Tecnología ICP, Ecopetrol S.A, Gerencia de Operaciones, Bucaramanga, Colombia
| | - Julia Acero
- Centro de Innovación y Tecnología ICP, Ecopetrol S.A, Gerencia de Operaciones, Bucaramanga, Colombia
| | - Ronald Jaimes-Prada
- Centro de Innovación y Tecnología ICP, Ecopetrol S.A, Gerencia de Operaciones, Bucaramanga, Colombia
| | - Felipe Cabarcas
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia -UdeA, Medellín, Colombia.,Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia - UdeA, Medellín, Colombia
| | - Juan F Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia -UdeA, Medellín, Colombia
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21
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Ramírez-Ramírez JA, Madrigal Y, Alzate JF, Pabón-Mora N. Evolution and expression of the MADS-box flowering transition genes AGAMOUS-like 24/SHORT VEGETATIVE PHASE with emphasis in selected Neotropical orchids. Cells Dev 2021; 168:203755. [PMID: 34758403 DOI: 10.1016/j.cdev.2021.203755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 10/24/2021] [Accepted: 10/31/2021] [Indexed: 11/18/2022]
Abstract
In angiosperms the reproductive transition results in the transformation of a vegetative apical meristem (SAM) into an inflorescence meristem (IM), capable of forming floral meristems (FM). Two key players in the flowering transition are AGAMOUS-like 24 (AGL24) and SHORT VEGETATIVE PHASE (SVP). They are eudicot MADS-box paralogs performing opposite roles, as AGL24 positively regulates flowering while SVP represses the reproductive transition in Arabidopsis. We confirm that the Arabidopsis functional reference cannot be readily extrapolated to all eudicots as there are additional duplications of AGL24 in early divergent eudicots and core eudicots with significant sequence variation. In addition, we found that in monocots, two additional independent duplication events have resulted in at least three clades of AGL24/SVP homologs, some only found in Orchidaceae. Protein sequence analyses and comparative evolutionary rates point to higher rates of relaxed negative selection in the Core Eudicot AGL24 B and the Orch SVP-like B clades, in eudicots and monocots respectively. On the other hand, expression data points to plesiomorphic pleiotropic roles of AGL24/SVP genes likely similar to SVP core eudicot genes, and the acquisition of new roles as flowering positive regulators in Core Eudicot AGL24 A genes. Our research presents evidence on the diversification and recruitment of AGL24/SVP homologs in flowering transition in orchids. Although, broad expression of most copies does not allow to determine if they act as flowering repressors or promoters, the restricted expression of some homologs in the SAM suggests putative roles in maintaining the vegetative phase. If so studying in detail the function of AGL24/SVP homologs in orchids is critical to identify putative flowering repressors in a lineage where other canonical repressors remain elusive.
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Affiliation(s)
- Jessica A Ramírez-Ramírez
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
| | - Yesenia Madrigal
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
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Cabarcas F, Galvan-Diaz AL, Arias-Agudelo LM, García-Montoya GM, Daza JM, Alzate JF. Cryptosporidium hominis Phylogenomic Analysis Reveals Separate Lineages With Continental Segregation. Front Genet 2021; 12:740940. [PMID: 34721528 PMCID: PMC8552020 DOI: 10.3389/fgene.2021.740940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Cryptosporidium is a leading cause of waterborne outbreaks globally, and Cryptosporidium hominis and C. parvum are the principal cause of human cryptosporidiosis on the planet. Thanks to the advances in Next-Generation Sequencing (NGS) sequencing and bioinformatic software development, more than 100 genomes have been generated in the last decade using a metagenomic-like strategy. This procedure involves the parasite oocyst enrichment from stool samples of infected individuals, NGS sequencing, metagenomic assembly, parasite genome computational filtering, and comparative genomic analysis. Following this approach, genomes of infected individuals of all continents have been generated, although with striking different quality results. In this study, we performed a thorough comparison, in terms of assembly quality and purity, of 100+ de novo assembled genomes of C. hominis. Remarkably, after quality genome filtering, a comprehensive phylogenomic analysis allowed us to discover that C. hominis encompasses two lineages with continental segregation. These lineages were named based on the observed continental distribution bias as C. hominis Euro-American (EA) and the C. hominis Afro-Asian (AA) lineages.
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Affiliation(s)
- Felipe Cabarcas
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Medellín, Colombia.,Environmental Microbiology Group, School of Microbiology, Universidad de Antioquia, Medellín, Colombia
| | - Ana Luz Galvan-Diaz
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Laura M Arias-Agudelo
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Medellín, Colombia
| | - Gisela María García-Montoya
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Medellín, Colombia.,Grupo SISTEMIC, Departamento de Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia, Medellín, Colombia.,Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan M Daza
- Grupo Herpetológico de Antioquia, Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Medellín, Colombia.,Grupo SISTEMIC, Departamento de Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia, Medellín, Colombia.,Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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23
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Salazar‐Duque H, Alzate JF, Urrea Trujillo A, Ferrándiz C, Pabón‐Mora N. Comparative anatomy and genetic bases of fruit development in selected Rubiaceae (Gentianales). Am J Bot 2021; 108:1838-1860. [PMID: 34699609 PMCID: PMC9298371 DOI: 10.1002/ajb2.1785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The Rubiaceae are ideal for studying the diversity of fruits that develop from flowers with inferior ovary. We aimed to identify morpho-anatomical changes during fruit development that distinguish those derived from the carpel versus the extra-carpellary tissues. In addition, we present the fruit genetic core regulatory network in selected Rubiaceae species and compare it in terms of copy number and expression patterns to model core eudicots in the Brassicaceae and the Solanaceae. METHODS We used light microscopy to follow morphoanatomical changes in four selected species with different fruit types. We generated reference transcriptomes for seven selected Rubiaceae species and isolated homologs of major transcription factors involved in fruit development histogenesis, assessed their homology, identified conserved and new protein motifs, and evaluated their expression in three species with different fruit types. RESULTS Our studies revealed ovary-derived pericarp tissues versus floral-cup-derived epicarp tissues. Gene evolution analyses of FRUITFULL, SHATTERPROOF, ALCATRAZ, INDEHISCENT and REPLUMLESS homologs suggest that the gene complement in Rubiaceae is simpler compared to that in Brassicaceae or Solanaceae. Expression patterns of targeted genes vary in response to the fruit type and the developmental stage evaluated. CONCLUSIONS Morphologically similar fruits can have different anatomies as a result of convergent tissues developed from the epicarps covering the anatomical changes from the pericarps. Expression analyses suggest that the fruit patterning regulatory network established in model core eudicots cannot be extrapolated to asterids with inferior ovaries.
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Affiliation(s)
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica–CNSG, Sede de Investigación Universitaria‐SIUUniversidad de Antioquia MedellínColombia
- Facultad de MedicinaUniversidad de Antioquia MedellínColombia
| | | | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universidad Politécnica de ValenciaValenciaSpain
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Bedoya K, Galeano L, Hincapié MM, Mesa JA, Alzate JF. Bacterial diversity analysis of freshwater sources for human use in rural areas of the tropical Andean region of Colombia. Infect 2021. [DOI: 10.22354/in.v26i1.988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Martínez-Salazar S, González F, Alzate JF, Pabón-Mora N. Molecular framework underlying floral bilateral symmetry and nectar spur development in Tropaeolum, an atypical member of the Brassicales. Am J Bot 2021; 108:1315-1330. [PMID: 34458983 DOI: 10.1002/ajb2.1719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Floral spurs are key innovations associated with elaborate pollination mechanisms that have evolved independently several times across angiosperms. Spur formation can shift the floral symmetry from radial to bilateral, as it is the case in Tropaeolum, the only member of the Brassicales with floral nectar spurs. The genetic mechanisms underlying both spur and bilateral symmetry in the family have not yet been investigated. METHODS We studied flower development and morphoanatomy of Tropaeolum longifolium. We also generated a reference transcriptome and isolated all candidate genes involved in adaxial-abaxial differential growth during spur formation. Finally, we evaluated the evolution of the targeted genes across Brassicales and examined their expression in dissected floral parts. RESULTS Five sepals initiate spirally, followed by five petals alternate to the sepals, five antesepalous stamens, three antepetalous stamens, and three carpels. Intercalary growth at the common base of sepals and petals forms a floral tube. The spur is an outgrowth from the adaxial region of the tube, lined up with the medial sepal. We identified Tropaeolum specific duplications in the TCP3/4L and STM gene lineages, which are critical for spur formation in other taxa. In addition, we found that TM6 (MADS-box), RL2 (RAD-like7), and KN2/6L2 and OSH6L (KNOX1 genes), have been lost in core Brassicales but retained in Tropaeolum. CONCLUSIONS Three genes are pivotal during the extreme adaxial-abaxial asymmetry of the floral tube, namely, TlTCP4L2 restricted to the adaxial side where the spur is formed, and TlTCP12 and TlSTM1 to the abaxial side, lacking a spur.
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Affiliation(s)
| | - Favio González
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Instituto de Ciencias Naturales, AA 7495, Bogotá, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, AA 1226, Medellín, Colombia
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Suárez-Baron H, Alzate JF, González F, Pelaz S, Ambrose BA, Pabón-Mora N. Gene expression underlying floral epidermal specialization in Aristolochia fimbriata (Aristolochiaceae). Ann Bot 2021; 127:749-764. [PMID: 33630993 PMCID: PMC8103811 DOI: 10.1093/aob/mcab033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS The epidermis constitutes the outermost tissue of the plant body. Although it plays major structural, physiological and ecological roles in embryophytes, the molecular mechanisms controlling epidermal cell fate, differentiation and trichome development have been scarcely studied across angiosperms, and remain almost unexplored in floral organs. METHODS In this study, we assess the spatio-temporal expression patterns of GL2, GL3, TTG1, TRY, MYB5, MYB6, HDG2, MYB106-like, WIN1 and RAV1-like homologues in the magnoliid Aristolochia fimbriata (Aristolochiaceae) by using comparative RNA-sequencing and in situ hybridization assays. KEY RESULTS Genes involved in Aristolochia fimbriata trichome development vary depending on the organ where they are formed. Stem, leaf and pedicel trichomes recruit most of the transcription factors (TFs) described above. Conversely, floral trichomes only use a small subset of genes including AfimGL2, AfimRAV1-like, AfimWIN1, AfimMYB106-like and AfimHDG2. The remaining TFs, AfimTTG1, AfimGL3, AfimTRY, AfimMYB5 and AfimMYB6, are restricted to the abaxial (outer) and the adaxial (inner) pavement epidermal cells. CONCLUSIONS We re-evaluate the core genetic network shaping trichome fate in flowers of an early-divergent angiosperm lineage and show a morphologically diverse output with a simpler genetic mechanism in place when compared to the models Arabidopsis thaliana and Cucumis sativus. In turn, our results strongly suggest that the canonical trichome gene expression appears to be more conserved in vegetative than in floral tissues across angiosperms.
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Affiliation(s)
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica (CNSG), Sede de Investigación Universitaria, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Favio González
- Universidad Nacional de Colombia, Facultad de Ciencias, Instituto de Ciencias Naturales, Bogotá, Colombia
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
- ICREA (Institució Catalana de Recerca i Estudis Avançats), Barcelona, Spain
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Cepeda AS, Andreína Pacheco M, Escalante AA, Alzate JF, Matta NE. The apicoplast of Haemoproteus columbae: A comparative study of this organelle genome in Haemosporida. Mol Phylogenet Evol 2021; 161:107185. [PMID: 33932614 DOI: 10.1016/j.ympev.2021.107185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/01/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Apicomplexa is a phylum of parasitic protozoa; among them are the order Haemosporida, vector-borne parasites that include those that cause malaria (genus Plasmodium). Most Apicomplexa species have a non-photosynthetic plastid or apicoplast. Given its unique metabolic pathways, this organelle is considered a target for malaria therapeutics. Regardless of its importance, there is a paucity of complete apicoplast genome data hindering comparative studies. Here, the Haemoproteus (Haemoproteus) columbae apicoplast genome (lineage HAECOL1) was obtained using next-generation sequencing. This genome was included in a comparative analysis with other plastids. This 29.8 kb circular genome shares the same structure found in Plasmodium parasites. It is A + T rich (87.7%), comparable but at the higher end of A + T content observed in Plasmodium species (85.5-87.2%). As expected, considering its high A + T content, the synonymous codon usage (RSCU) and the effective number of codons (ENc) showed a moderate codon bias. Several apicoplast genes have a phylogenetic signal. However, unlike mitochondrial genes, single-gene phylogenies have low support in haemosporidian clades that diverged recently. The H. columbae apicoplast genome suggests that the apicoplast function may be conserved across Haemosporida. This parasite could be a model to study this organelle in a non-mammalian system.
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Affiliation(s)
- Axl S Cepeda
- Departamento de Biología, Grupo de Investigación Caracterización Genética e Inmunología, Sede Bogotá-Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia; Department of Biology, Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, United States.
| | - M Andreína Pacheco
- Department of Biology, Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, United States
| | - Ananías A Escalante
- Department of Biology, Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, United States
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica - CNSG, SIU, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Nubia E Matta
- Departamento de Biología, Grupo de Investigación Caracterización Genética e Inmunología, Sede Bogotá-Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.
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Muñoz-Gómez S, Suárez-Baron H, Alzate JF, González F, Pabón-Mora N. Evolution of the Subgroup 6 R2R3-MYB Genes and Their Contribution to Floral Color in the Perianth-Bearing Piperales. Front Plant Sci 2021; 12:633227. [PMID: 33897722 PMCID: PMC8063865 DOI: 10.3389/fpls.2021.633227] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/08/2021] [Indexed: 05/27/2023]
Abstract
Flavonoids, carotenoids, betalains, and chlorophylls are the plant pigments responsible for floral color. Anthocyanins, a class of flavonoids, are largely responsible for the red, purple, pink, and blue colors. R2R3-MYB genes belonging to subgroup 6 (SG6) are the upstream regulatory factors of the anthocyanin biosynthetic pathway. The canonical members of these genes in Arabidopsis include AtMYB75, AtMYB90, AtMYB113, and AtMYB114. The Aristolochiaceae is an angiosperm lineage with diverse floral groundplans and perianth colors. Saruma henryi exhibits a biseriate perianth with green sepals and yellow petals. All other genera have sepals only, with colors ranging from green (in Lactoris) to a plethora of yellow to red and purple mixtures. Here, we isolated and reconstructed the SG6 R2R3-MYB gene lineage evolution in angiosperms with sampling emphasis in Aristolochiaceae. We found numerous species-specific duplications of this gene lineage in core eudicots and local duplications in Aristolochiaceae for Saruma and Asarum. Expression of SG6 R2R3-MYB genes examined in different developmental stages and plant organs of four Aristolochiaceae species, largely overlaps with red and purple pigments, suggesting a role in anthocyanin and flavonoid synthesis and accumulation. A directed RNA-seq analysis corroborated our RT-PCR analyses, by showing that these structural enzymes activate during perianth development in Aristolochia fimbriata and that the regulatory genes are expressed in correlation with color phenotype. Finally, the reconstruction of the flavonoid and anthocyanin metabolic pathways using predicted peptides from transcriptomic data show that all pivotal enzymes are present in the analyzed species. We conclude that the regulatory genes as well as the biosynthetic pathway are largely conserved across angiosperms. In addition, the Aristolochiaceae emerges as a remarkable group to study the genetic regulatory network for floral color, as their members exhibit an outstanding floral diversity with elaborate color patterns and the genetic complement for SG6 R2R3-MYB genes is simpler than in core eudicot model species.
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Affiliation(s)
- Sarita Muñoz-Gómez
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Harold Suárez-Baron
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica – CNSG, Sede de Investigación Universitaria, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Favio González
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Instituto de Ciencias Naturales, Bogotá, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
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Arias-Agudelo LM, Garcia-Montoya G, Cabarcas F, Galvan-Diaz AL, Alzate JF. Comparative genomic analysis of the principal Cryptosporidium species that infect humans. PeerJ 2020; 8:e10478. [PMID: 33344091 PMCID: PMC7718795 DOI: 10.7717/peerj.10478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/11/2020] [Indexed: 11/25/2022] Open
Abstract
Cryptosporidium parasites are ubiquitous and can infect a broad range of vertebrates and are considered the most frequent protozoa associated with waterborne parasitic outbreaks. The intestine is the target of three of the species most frequently found in humans: C. hominis, C. parvum, and. C. meleagridis. Despite the recent advance in genome sequencing projects for this apicomplexan, a broad genomic comparison including the three species most prevalent in humans have not been published so far. In this work, we downloaded raw NGS data, assembled it under normalized conditions, and compared 23 publicly available genomes of C. hominis, C. parvum, and C. meleagridis. Although few genomes showed highly fragmented assemblies, most of them had less than 500 scaffolds and mean coverage that ranged between 35X and 511X. Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed. Furthermore, deleterious nucleotide substitutions common to all three species were more common in genes associated with DNA repair, recombination, and chromosome-associated proteins. Indel events were observed in the 23 studied isolates that spanned up to 500 bases. The highest number of deletions was observed in C. meleagridis, followed by C. hominis, with more than 60 species-specific deletions found in some isolates of these two species. Although several genes with indel events have been partially annotated, most of them remain to encode uncharacterized proteins.
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Affiliation(s)
- Laura M Arias-Agudelo
- Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | - Gisela Garcia-Montoya
- Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | - Felipe Cabarcas
- Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellin, Antioquia, Colombia.,Grupo SISTEMIC, Departamento de Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | - Ana L Galvan-Diaz
- Grupo de Microbiología ambiental. Escuela de Microbiología, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellin, Antioquia, Colombia
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López-Legarda X, Arboleda-Echavarría C, Parra-Saldívar R, Rostro-Alanis M, Alzate JF, Villa-Pulgarín JA, Segura-Sánchez F. Biotechnological production, characterization and in vitro antitumor activity of polysaccharides from a native strain of Lentinus crinitus. Int J Biol Macromol 2020; 164:3133-3144. [DOI: 10.1016/j.ijbiomac.2020.08.191] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
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Sánchez de la Nieta R, Antoraz S, Alzate JF, Santamaría RI, Díaz M. Antibiotic Production and Antibiotic Resistance: The Two Sides of AbrB1/B2, a Two-Component System of Streptomyces coelicolor. Front Microbiol 2020; 11:587750. [PMID: 33162964 PMCID: PMC7581861 DOI: 10.3389/fmicb.2020.587750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/22/2020] [Indexed: 11/13/2022] Open
Abstract
Antibiotic resistance currently presents one of the biggest threats to humans. The development and implementation of strategies against the spread of superbugs is a priority for public health. In addition to raising social awareness, approaches such as the discovery of new antibiotic molecules and the elucidation of resistance mechanisms are common measures. Accordingly, the two-component system (TCS) of Streptomyces coelicolor AbrB1/B2, offer amenable ways to study both antibiotic production and resistance. Global transcriptomic comparisons between the wild-type strain S. coelicolor M145 and the mutant ΔabrB, using RNA-Seq, showed that the AbrB1/B2 TCS is implicated in the regulation of different biological processes associated with stress responses, primary and secondary metabolism, and development and differentiation. The ΔabrB mutant showed the up-regulation of antibiotic biosynthetic gene clusters and the down-regulation of the vancomycin resistance gene cluster, according to the phenotypic observations of increased antibiotic production of actinorhodin and undecylprodigiosin, and greater susceptibility to vancomycin. The role of AbrB1/B2 in vancomycin resistance has also been shown by an in silico analysis, which strongly indicates that AbrB1/B2 is a homolog of VraR/S from Staphylococcus aureus and LiaR/S from Enterococcus faecium/Enterococcus faecalis, both of which are implied in vancomycin resistance in these pathogenic organisms that present a serious threat to public health. The results obtained are interesting from a biotechnological perspective since, on one hand, this TCS is a negative regulator of antibiotic production and its high degree of conservation throughout Streptomyces spp. makes it a valuable tool for improving antibiotic production and the discovery of cryptic metabolites with antibiotic action. On the other hand, AbrB1/B2 contributes to vancomycin resistance and is a homolog of VraR/S and LiaR/S, important regulators in clinically relevant antibiotic-resistant bacteria. Therefore, the study of AbrB1/B2 could provide new insight into the mechanism of this type of resistance.
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Affiliation(s)
- Ricardo Sánchez de la Nieta
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
| | - Sergio Antoraz
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
| | - Juan F Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Ramón I Santamaría
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
| | - Margarita Díaz
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
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Baena A, Vasco E, Pastrana M, Alzate JF, Barrera LF, Martínez A. New Conjugated Compound T5 Epidioxy-Sterol-ANB Inhibits the Growth of Mycobacterium tuberculosis Affecting the Cholesterol and Folate Pathways. Front Microbiol 2020; 11:537935. [PMID: 33072006 PMCID: PMC7533559 DOI: 10.3389/fmicb.2020.537935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/13/2020] [Indexed: 11/13/2022] Open
Abstract
The upsurge and persistence of drug resistant strains of Mycobacterium tuberculosis (Mtb) is an important limitant to the battery of drugs available for the elimination of tuberculosis (TB). To avoid future scarcity of antibiotics against Mtb, it is important to discover new effective anti-mycobacterial agents. In this study, we present data from a series of experiments to determine in vitro and in vivo anti-mycobacterial activity of a library of epidioxy-sterol analogs. We test 15 compounds for their ability to reduce the viability of Mtb. We found that one compound called T5 epidioxy-sterol-ANB display significant potency against Mtb in vitro specifically inside macrophages but without effectivity in axenic cultures. A viability assay confirms that this T5 compound is less toxic for macrophages in vitro as compared to the current Mtb drug Rifampicin at higher concentrations. We use a transcriptomic analysis of Mtb inside macrophages after T5 epidioxy-sterol-ANB treatment, and we found a significant down-regulation of enzymes involved in the cholesterol and folic acid pathways. In vivo, significant differences were found in the lungs and spleen CFUs of Mtb infected mice treated with the T5 epidioxy-sterol-ANB as compared with the untreated control group, which provides additional evidence of the effectivity of the T5 compound. Altogether these results confirm the potential of this T5 epidioxy-sterol-ANB compound against Mtb.
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Affiliation(s)
- Andres Baena
- Grupo de Inmunología Celular e Inmunogenética, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Emanuel Vasco
- Grupo de Inmunología Celular e Inmunogenética, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Manuel Pastrana
- Grupo de Productos Naturales Marinos, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín, Colombia
| | - Juan F Alzate
- Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.,Centro Nacional de Secuenciación Genómica, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Luis F Barrera
- Grupo de Inmunología Celular e Inmunogenética, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Alejandro Martínez
- Grupo de Productos Naturales Marinos, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín, Colombia
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Pabón-Mora N, Madrigal Y, Alzate JF, Ambrose BA, Ferrándiz C, Wanke S, Neinhuis C, González F. Evolution of Class II TCP genes in perianth bearing Piperales and their contribution to the bilateral calyx in Aristolochia. New Phytol 2020; 228:752-769. [PMID: 32491205 DOI: 10.1111/nph.16719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/20/2020] [Indexed: 05/21/2023]
Abstract
Controlled spatiotemporal cell division and expansion are responsible for floral bilateral symmetry. Genetic studies have pointed to class II TCP genes as major regulators of cell division and floral patterning in model core eudicots. Here we study their evolution in perianth-bearing Piperales and their expression in Aristolochia, a rare occurrence of bilateral perianth outside eudicots and monocots. The evolution of class II TCP genes reveals single-copy CYCLOIDEA-like genes and three paralogs of CINCINNATA (CIN) in early diverging angiosperms. All class II TCP genes have independently duplicated in Aristolochia subgenus Siphisia. Also CIN2 genes duplicated before the diversification of Saruma and Asarum. Sequence analysis shows that CIN1 and CIN3 share motifs with Cyclin proteins and CIN2 genes have lost the miRNA319a binding site. Expression analyses of all paralogs of class II TCP genes in Aristolochia fimbriata point to a role of CYC and CIN genes in maintaining differential perianth expansion during mid- and late flower developmental stages by promoting cell division in the distal and ventral portion of the limb. It is likely that class II TCP genes also contribute to cell division in the leaf, the gynoecium and the ovules in A. fimbriata.
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Affiliation(s)
- Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
- Technische Universität Dresden, Institut für Botanik, Dresden, 01062, Germany
| | - Yesenia Madrigal
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Juan F Alzate
- Facultad de Medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | | | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Valencia, 46022, Spain
| | - Stefan Wanke
- Technische Universität Dresden, Institut für Botanik, Dresden, 01062, Germany
| | - Christoph Neinhuis
- Technische Universität Dresden, Institut für Botanik, Dresden, 01062, Germany
| | - Favio González
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
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Alzate JF, Toro-Londoño M, Cabarcas F, Garcia-Montoya G, Galvan-Diaz A. Contrasting microbiota profiles observed in children carrying either Blastocystis spp. or the commensal amoebas Entamoeba coli or Endolimax nana. Sci Rep 2020; 10:15354. [PMID: 32948808 PMCID: PMC7501860 DOI: 10.1038/s41598-020-72286-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
Recent studies have shown how intestinal parasites can modulate gut microbiota. This observation is not surprising since the human intestinal lumen, like any other niche, is a battlefield of microbial competition, and Eukaryotes can affect bacterial populations. Intestinal pathogenic protist has been associated with reshaping the microbial community structure; however, the interactions between the colonic bacterial communities and parasites like Blastocystis spp., Entamoeba coli, and Endolimax nana have been poorly studied. In this work, we studied the distal intestinal bacterial microbiota of 49 children attending 7 public daycare centers in Medellin, Colombia, and compared the bacterial microbiota structure in the presence or absence of the protists Blastocystis spp., E. coli, and E. nana. Parasite colonization was associated with an increase in bacterial richness. Moreover, Blastocystis spp. presented a positive relationship with Prevotella, since this bacterium was selectively enriched in children carrying it. Remarkably, the E. coli colonized children showed a microbial profile that was closer to uninfected controls, although some bacterial taxa displayed to be enriched. This is the case for Akkermansia, which showed to be favored in E. coli colonized individuals, while notably reduced in the Blastocystis spp. parasitized group.
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Affiliation(s)
- Juan F Alzate
- Departamento de Microbiología Y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
- Facultad de Medicina, Centro Nacional de Secuenciación genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Medellín, Colombia.
| | - Miguel Toro-Londoño
- Facultad de Medicina, Centro Nacional de Secuenciación genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Medellín, Colombia
| | - Felipe Cabarcas
- Facultad de Medicina, Centro Nacional de Secuenciación genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Medellín, Colombia
- Facultad de Ingeniería, Grupo Sistemic, Universidad de Antioquia, Medellín, Colombia
| | - Gisela Garcia-Montoya
- Departamento de Microbiología Y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Ana Galvan-Diaz
- Grupo de Microbiología Ambiental, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
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Benavides A, Sanchez F, Alzate JF, Cabarcas F. DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework. PeerJ 2020; 8:e9762. [PMID: 32953263 PMCID: PMC7474881 DOI: 10.7717/peerj.9762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/28/2020] [Indexed: 11/20/2022] Open
Abstract
Background A prime objective in metagenomics is to classify DNA sequence fragments into taxonomic units. It usually requires several stages: read’s quality control, de novo assembly, contig annotation, gene prediction, etc. These stages need very efficient programs because of the number of reads from the projects. Furthermore, the complexity of metagenomes requires efficient and automatic tools that orchestrate the different stages. Method DATMA is a pipeline for fast metagenomic analysis that orchestrates the following: sequencing quality control, 16S rRNA-identification, reads binning, de novo assembly and evaluation, gene prediction, and taxonomic annotation. Its distributed computing model can use multiple computing resources to reduce the analysis time. Results We used a controlled experiment to show DATMA functionality. Two pre-annotated metagenomes to compare its accuracy and speed against other metagenomic frameworks. Then, with DATMA we recovered a draft genome of a novel Anaerolineaceae from a biosolid metagenome. Conclusions DATMA is a bioinformatics tool that automatically analyzes complex metagenomes. It is faster than similar tools and, in some cases, it can extract genomes that the other tools do not. DATMA is freely available at https://github.com/andvides/DATMA.
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Affiliation(s)
- Andres Benavides
- Grupo GICEI, Facultad de Ingeniería Electrónica, Institución Universitaria Pascual Bravo, Medellín, Antioquia, Colombia
- Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Friman Sanchez
- Barcelona Supercomputing Center, currently at Smart Variable S.L., Barcelona, Spain
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia UdeA, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Felipe Cabarcas
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia UdeA, Medellín, Colombia
- Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia UdeA, Medellín, Colombia
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Bertel-Sevilla A, Alzate JF, Olivero-Verbel J. De novo assembly and characterization of the liver transcriptome of Mugil incilis (lisa) using next generation sequencing. Sci Rep 2020; 10:13957. [PMID: 32811897 PMCID: PMC7435268 DOI: 10.1038/s41598-020-70902-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 07/24/2020] [Indexed: 11/08/2022] Open
Abstract
Mugil incilis (lisa) is an important commercial fish species in many countries, living along the coasts of the western Atlantic Ocean. It has been used as a model organism for environmental monitoring and ecotoxicological investigations. Nevertheless, available genomic and transcriptomic information for this organism is extremely deficient. The aim of this study was to characterize M. incilis hepatic transcriptome using Illumina paired-end sequencing. A total of 32,082,124 RNA-Seq read pairs were generated utilizing the HiSeq platform and subsequently cleaned and assembled into 93,912 contigs (N50 = 2,019 bp). The analysis of species distribution revealed that M. incilis contigs had the highest number of hits to Stegastes partitus (13.4%). Using a sequence similarity search against the public databases GO and KEGG, a total of 7,301 and 16,967 contigs were annotated, respectively. KEGG database showed genes related to environmental information, metabolism and organismal system pathways were highly annotated. Complete or partial coding DNA sequences for several candidate genes associated with stress responses/detoxification of xenobiotics, as well as housekeeping genes, were employed to design primers that were successfully tested and validated by RT-qPCR. This study presents the first transcriptome resources for Mugil incilis and provides basic information for the development of genomic tools, such as the identification of RNA markers, useful to analyze environmental impacts on this fish Caribbean species.
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Affiliation(s)
- Angela Bertel-Sevilla
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, 130015, Cartagena, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Jesus Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, 130015, Cartagena, Colombia.
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González AD, Pabón-Mora N, Alzate JF, González F. Meristem Genes in the Highly Reduced Endoparasitic Pilostyles boyacensis (Apodanthaceae). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Bedoya K, Hoyos O, Zurek E, Cabarcas F, Alzate JF. Annual microbial community dynamics in a full-scale anaerobic sludge digester from a wastewater treatment plant in Colombia. Sci Total Environ 2020; 726:138479. [PMID: 32305756 DOI: 10.1016/j.scitotenv.2020.138479] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 05/23/2023]
Abstract
Anaerobic digestion is a microbe-driven process widely applied to treat activated sludge from municipal wastewater treatment plants. It is one of the most efficient solutions for sludge reduction along with biogas production. However, the knowledge of the microbial consortium involved in this process is still unknown in full-scale anaerobic digesters from Latin America. This study aimed to elucidate the dynamics of the microbial community of a full-scale anaerobic digester for a year using 16S rDNA amplicon sequencing with the Illumina Miseq platform. The results showed fluctuations in the frequencies of dominant phyla with a decrease of Proteobacteria and Bacteroidetes after a temporary suspension of anaerobic digester. The core community was affiliated with bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Chloroflexi. The core community was represented by 154 OTUs that accounted for 74% of all the processed reads. The Anaerolineaceae family, within Chloroflexi phylum, was the most frequently observed taxonomic group in all samples analyzed. Despite the microbial fluctuations, the biogas production was stable over the studied year (average 66% methane production), which might indicate a functional redundancy in the microbial consortium.
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Affiliation(s)
- Katherine Bedoya
- Centro Nacional de Secuenciación Genómica - CNSG, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Oladier Hoyos
- Empresas Públicas de Medellín-EPM, Medellín, Antioquia, Colombia
| | | | - Felipe Cabarcas
- Centro Nacional de Secuenciación Genómica - CNSG, Universidad de Antioquia, Medellín, Antioquia, Colombia; Sistemas Embebidos e Inteligencia Computacional - SISTEMIC, Facultad de Ingeniería, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica - CNSG, Universidad de Antioquia, Medellín, Antioquia, Colombia.
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Segura JA, Isaza JP, Botero LE, Alzate JF, Gutiérrez LA. Assessment of bacterial diversity of Rhipicephalus microplus ticks from two livestock agroecosystems in Antioquia, Colombia. PLoS One 2020; 15:e0234005. [PMID: 32609768 PMCID: PMC7329104 DOI: 10.1371/journal.pone.0234005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/15/2020] [Indexed: 12/16/2022] Open
Abstract
Rhipicephalus microplus is recognized as a tick species highly prevalent in cattle, with a wide pantropical distribution that seems to continue spreading geographically. However, its role as a biological vector has been scarcely studied in the livestock context. In this study, a 16S rRNA next-generation sequencing analysis was used to determine bacterial diversity in salivary glands and gut of R. microplus from two contrasting livestock agroecosystems in Antioquia, Colombia. Both the culture-independent approach (CI) and the culture-dependent (CD) approach were complementarily adopted in this study. A total of 341 unique OTUs were assigned, the richness showed to be higher in the Northern than in the Middle Magdalena region, and a high diversity was found at the phylum and genus levels in the samples obtained. With the CI approach, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most common phylum of bacteria regardless of the organ, or geographic origin of the specimens analyzed. While the relative abundance of bacteria at a phylum level with the CD approach varied between analyzed samples, the data obtained suggest that a high diversity of species of bacteria occurs in R. microplus from both livestock agroecosystems. Bacterial genera such as Anaplasma, Coxiella, and Ehrlichia, recognized for their implications in tick-borne diseases, were also detected, together with endosymbionts such as Lysinibacillus, previously reported as a potential tool for biological control. This information is useful to deepen the knowledge about microbial diversity regarding the relations between endosymbionts and pathogens and could facilitate the future development of epidemiological surveillance in livestock systems.
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Affiliation(s)
- Juan A. Segura
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Antioquia, Colombia
| | - Juan P. Isaza
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Antioquia, Colombia
| | - Luz E. Botero
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Antioquia, Colombia
| | - Juan F. Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Lina A. Gutiérrez
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Antioquia, Colombia
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Galvan-Diaz AL, Bedoya-Urrego K, Medina-Lozano A, Uran-Velasquez J, Alzate JF, Garcia-Montoya G. Common occurrence of Cryptosporidium hominis in children attending day-care centers in Medellin, Colombia. Parasitol Res 2020; 119:2935-2942. [PMID: 32594239 DOI: 10.1007/s00436-020-06782-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/18/2020] [Indexed: 11/28/2022]
Abstract
Cryptosporidium spp. are apicomplexan protozoa associated with chronic diarrhea in AIDS and other immunocompromised patients, and one of the commonest causes of childhood diarrhea and malnutrition, particularly in low-income settings. In Colombia, there are few molecular epidemiological studies on Cryptosporidium spp.; thereby, the transmission dynamics of this parasite in the country is poorly known. This study evaluated the diversity of Cryptosporidium at species, subtype family, and subtype level in children attending various day-care centers in Medellin, Colombia. Two hundred and ninety stool samples from children < 5 years of age were collected from April to November of 2015. All samples were processed by PCR and sequence analysis of the ssu RNA gene and the gp60 gene. An infection rate of 2.4% was observed, with only two Cryptosporidium species identified: C. hominis (6/7) and C. meleagridis (1/7). Cryptosporidium hominis isolates belonged to the subtypes IbA10G2, IaA13R6 and IaA13R7; IIIbA26G1R1 C. meleagridis subtype was also detected. There is a C. hominis predominance in the children evaluated, suggesting an important role of the anthroponotic transmission cycle in the day-care centers analyzed. Further investigation is required to determine infection sources and susceptible hosts in order to define appropriate management of cryptosporidiosis.
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Affiliation(s)
- Ana Luz Galvan-Diaz
- Grupo de Microbiología ambiental, Escuela de microbiología, Universidad de Antioquia, Ciudad universitaria, Bloque 5-410. Cl. 67 #53-108, Medellín, Antioquia, Colombia.
| | - Katherine Bedoya-Urrego
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Cra 53#61-30 Torre 1 Lab S2-15, Medellín, Antioquia, Colombia
| | - Angelica Medina-Lozano
- Grupo de Parasitología, Facultad de Medicina, Corporación Académica para el Estudio de las Patologías Tropicales, Universidad de Antioquia, Cra. 51d #62-29, Medellín, Antioquia, Colombia
| | - Johanna Uran-Velasquez
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Cra 53#61-30 Torre 1 Lab S2-15, Medellín, Antioquia, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Cra 53#61-30 Torre 1 Lab S2-15, Medellín, Antioquia, Colombia
| | - Gisela Garcia-Montoya
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Cra 53#61-30 Torre 1 Lab S2-15, Medellín, Antioquia, Colombia
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Gómez GF, Isaza JP, Segura JA, Alzate JF, Gutiérrez LA. Metatranscriptomic virome assessment of Rhipicephalus microplus from Colombia. Ticks Tick Borne Dis 2020; 11:101426. [PMID: 32473925 DOI: 10.1016/j.ttbdis.2020.101426] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 03/14/2020] [Accepted: 03/23/2020] [Indexed: 11/17/2022]
Abstract
Ticks (Ixodida) are hematophagous ectoparasites that harbor and transmit diverse species of viruses, some of which cause serious diseases with worldwide veterinary and human health consequences. Rhipicephalus microplus is an important cattle tick in Colombia, where it causes significant economic losses. Despite the importance of this tick, its viral profile is unknown. RNA sequencing was used in this study as a surveillance method for virus detection in R. microplus. Most of the viral origin contigs were assigned to two putative viruses: one chuvirus (Wuhan tick virus 2) and one phlebovirus-like (Lihan tick virus). In addition, viral contigs corresponding to two jingmenviruses previously reported in R. microplus from China and Brazil were detected, as well as a novel putative tymovirus, named here as Antioquia tymovirus-like 1 (ATV-like 1). The presence of some of these viruses across numerous regions in the world could have several explanations, including i) a long-term association between those viruses and R. microplus and ii) a consequence of livestock historical trade. Our results shed new light on the virus diversity of this tick species and provide a basis for further studies on the evolutionary history and pathogenic potential of these interesting viruses.
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Affiliation(s)
- Giovan F Gómez
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Antioquia, Colombia.
| | - Juan P Isaza
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Antioquia, Colombia
| | - Juan A Segura
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Antioquia, Colombia
| | - Juan F Alzate
- Grupo de Parasitología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Lina A Gutiérrez
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Antioquia, Colombia
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Baena A, Cabarcas F, Alvarez-Eraso KLF, Isaza JP, Alzate JF, Barrera LF. Differential determinants of virulence in two Mycobacterium tuberculosis Colombian clinical isolates of the LAM09 family. Virulence 2020; 10:695-710. [PMID: 31291814 PMCID: PMC6650194 DOI: 10.1080/21505594.2019.1642045] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The heterogeneity of the clinical outcome of Mycobacterium tuberculosis (Mtb) infection may be due in part to different strategies used by circulating strains to cause disease. This heterogeneity is one of the main limitations to eradicate tuberculosis disease. In this study, we have compared the transcriptional response of two closely related Colombian clinical isolates (UT127 and UT205) of the LAM family under two axenic media conditions. These clinical isolates are phenotypically different at the level of cell death, cytokine production, growth kinetics upon in vitro infection of human tissue macrophages, and membrane vesicle secretion upon culture in synthetic medium. Using RNA-seq, we have identified different pathways that account for two different strategies to cope with the stressful condition of a carbon-poor media such as Sauton’s. We showed that the clinical isolate UT205 focus mainly in the activation of virulence systems such as the ESX-1, synthesis of diacyl-trehalose, polyacyl-trehalose, and sulfolipids, while UT127 concentrates its efforts mainly in the survival mode by the activation of the DNA replication, cell division, and lipid biosynthesis. This is an example of two Mtb isolates that belong to the same family and lineage, and even though they have a very similar genome, its transcriptional regulation showed important differences. This results in summary highlight the necessity to reach a better understanding of the heterogeneity in the behavior of these circulating Mtb strains which may help us to design better treatments and vaccines and to identify new targets for drugs.
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Affiliation(s)
- Andres Baena
- a Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia.,b Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia
| | - Felipe Cabarcas
- c Centro Nacional de Secuenciación Genómica (CNSG), Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia.,d Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia , Medellín , Colombia
| | - Karen L F Alvarez-Eraso
- a Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia
| | - Juan Pablo Isaza
- c Centro Nacional de Secuenciación Genómica (CNSG), Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia
| | - Juan F Alzate
- b Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia.,c Centro Nacional de Secuenciación Genómica (CNSG), Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia.,e Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia
| | - Luis F Barrera
- a Grupo de Inmunología Celular e Inmunogenética (GICIG), Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia.,f Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia
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Ospina-Zapata DA, Madrigal Y, Alzate JF, Pabón-Mora N. Evolution and Expression of Reproductive Transition Regulatory Genes FT/ TFL1 With Emphasis in Selected Neotropical Orchids. Front Plant Sci 2020; 11:469. [PMID: 32373149 PMCID: PMC7186885 DOI: 10.3389/fpls.2020.00469] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/30/2020] [Indexed: 05/23/2023]
Abstract
Flowering is a rigorously timed and morphologically complex shift in plant development. This change depends on endogenous as well as environmental factors. FLOWERING LOCUS T (FT) integrates several cues from different pathways acting as a flowering promoter. Contrary to the role of FT, its paralog TERMINAL FLOWER 1 (TFL1) delays floral transition. Although FT/TFL1 homologs have been studied in model eudicots and monocots, scarce studies are available in non-model monocots like the Orchidaceae. Orchids are very diverse and their floral complexity is translated into a unique aesthetic display, which appeals the ornamental plant market. Nonetheless, orchid trade faces huge limitations due to their long vegetative phase and intractable indoor flowering seasons. Little is known about the genetic basis that control reproductive transition in orchids and, consequently, manipulating their flowering time remains a challenge. In order to contribute to the understanding of the genetic bases that control flowering in orchids we present here the first broad-scale analysis of FT/TFL1-like genes in monocots with an expanded sampling in Orchidaceae. We also compare expression patterns in three selected species and propose hypotheses on the putative role of these genes in their reproductive transition. Our findings show that FT-like genes are by far more diversified than TFL1-like genes in monocots with six subclades in the former and only one in the latter. Within MonFT1, the comparative protein sequences of MonFT1A and MonFT1B suggest that they could have recruited functional roles in delaying flowering, a role typically assigned to TFL1-like proteins. On the other hand, MonFT2 proteins have retained their canonical motifs and roles in promoting flowering transition. This is also shown by their increased expression levels from the shoot apical meristem (SAM) and leaves to inflorescence meristems (IM) and floral buds (FBs). Finally, TFL1-like genes are retained as single copy and often times are lost. Their loss could be linked to the parallel recruitment of MonFT1A and MonFT1B homologs in delaying flowering and maintaining indeterminacy of the inflorescence meristem. These hypotheses lay the foundation for future functional validation in emerging model orchid species and comparative analyses in orchids with high horticultural potential in the market.
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Affiliation(s)
- Diego A. Ospina-Zapata
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Yesenia Madrigal
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica, Sede de Investigación Universitaria, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Natalia Pabón-Mora
- Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
- *Correspondence: Natalia Pabón-Mora,
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Urrea DA, Triana-Chavez O, Alzate JF. Mitochondrial genomics of human pathogenic parasite Leishmania ( Viannia) panamensis. PeerJ 2019; 7:e7235. [PMID: 31304069 PMCID: PMC6611448 DOI: 10.7717/peerj.7235] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/01/2019] [Indexed: 12/14/2022] Open
Abstract
Background The human parasite Leishmania (V.) panamensis is one of the pathogenic species responsible for cutaneous leishmaniasis in Central and South America. Despite its importance in molecular parasitology, its mitochondrial genome, divided into minicircles and maxicircles, haven’t been described so far. Methods Using NGS-based sequencing (454 and ILLUMINA), and combining de novo genome assembly and mapping strategies, we report the maxicircle kDNA annotated genome of L. (V.) panamensis, the first reference of this molecule for the subgenus Viannia. A comparative genomics approach is performed against other Leishmania and Trypanosoma species. Results The results show synteny of mitochondrial genes of L. (V.) panamensis with other kinetoplastids. It was also possible to identify nucleotide variants within the coding regions of the maxicircle, shared among some of them and others specific to each strain. Furthermore, we compared the minicircles kDNA sequences of two strains and the results show that the conserved and divergent regions of the minicircles exhibit strain-specific associations.
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Affiliation(s)
- Daniel Alfonso Urrea
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Departamento de Biología, Facultad de Ciencias, Universidad del Tolima, Ibague, Tolima, Colombia.,Grupo Biología y Control de Enfermedades Infecciosas (BCEI), Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Omar Triana-Chavez
- Grupo Biología y Control de Enfermedades Infecciosas (BCEI), Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica -CNSG, Sede de Investigación Universitaria -SIU. Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellin, Antioquia, Colombia
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Arias-Agudelo LM, González F, Isaza JP, Alzate JF, Pabón-Mora N. Plastome reduction and gene content in New World Pilostyles (Apodanthaceae) unveils high similarities to African and Australian congeners. Mol Phylogenet Evol 2019; 135:193-202. [DOI: 10.1016/j.ympev.2019.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023]
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Melo-Bolívar JF, Ruiz Pardo RY, Hume ME, Nisbet DJ, Rodríguez-Villamizar F, Alzate JF, Junca H, Villamil Díaz LM. Establishment and characterization of a competitive exclusion bacterial culture derived from Nile tilapia (Oreochromis niloticus) gut microbiomes showing antibacterial activity against pathogenic Streptococcus agalactiae. PLoS One 2019; 14:e0215375. [PMID: 31050668 PMCID: PMC6499431 DOI: 10.1371/journal.pone.0215375] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/01/2019] [Indexed: 12/28/2022] Open
Abstract
This study reports the characterization of the microbial community composition, and the establishment and dynamics of a continuous-flow competitive exclusion culture (CFCEC) derived from gut microbiomes of Nile tilapia (Oreochromis niloticus) specimens reared on aquaculture farms in Colombia. 16S rRNA gene amplicon Illumina sequencing was used to identify taxonomical changes in the CFCEC microbial community over time. The CFCEC was developed from adult tilapia from two farms in Colombia, and CFCEC samples were collected over two months. The pH varied from 6.25 to 6.35 throughout culturing, while anaerobic and aerobic cell counts stabilized at day 9, at 109 CFU mL-1 and were maintained to day 68. A variation in the CFCEC bacterial composition was observed over time. Cetobacterium was the most abundant in the first two days and coincided with a higher CFCEC supernatant antimicrobial effect against the fish pathogen Streptococcus agalactiae. Antimicrobial activity against S. agalactiae disappeared by day 3. Changes in bacterial composition continued to day 33 with Lactococcus spp. becoming the most abundant member of the community. In conclusion, the study of the CFCEC from intestinal tract of Nile tilapia (Oreochromis niloticus) by 16S rRNA gene sequencing allowed identification of predominant bacterial genera in the continuous-flow competitive exclusion culture exhibiting antibacterial activity against the fish pathogen Streptococcus agalactiae.
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Affiliation(s)
- Javier Fernando Melo-Bolívar
- Universidad de La Sabana, Faculty of Engineering, Campus Universitario del Puente del Común, Km 7 Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Ruth Yolanda Ruiz Pardo
- Universidad de La Sabana, Faculty of Engineering, Campus Universitario del Puente del Común, Km 7 Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
- Universidad de La Sabana, Faculty of Engineering, Grupo de Investigación en Procesos Agroindustriales, Campus Universitario del Puente del Común, Km 7 Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
| | - Michael E. Hume
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX, United States of America
| | - David J. Nisbet
- United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX, United States of America
| | - Fernando Rodríguez-Villamizar
- Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Centro de investigación Tibaitatá, Mosquera, Cundinamarca, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica- CNSG, Sede de Investigación Universitaria SIU, Grupo de Parasitología, Facultad de Medicina Universidad de Antioquia, Medellín, Colombia
| | - Howard Junca
- Microbiomas Foundation, Div. Ecogenomics & Holobionts, RG Microbial Ecology: Metabolism, Genomics & Evolution, Chía, Colombia
| | - Luisa Marcela Villamil Díaz
- Universidad de La Sabana, Faculty of Engineering, Campus Universitario del Puente del Común, Km 7 Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
- Universidad de La Sabana, Faculty of Engineering, Grupo de Investigación en Procesos Agroindustriales, Campus Universitario del Puente del Común, Km 7 Autopista Norte de Bogotá, Chía, Cundinamarca, Colombia
- * E-mail:
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47
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Bedoya K, Coltell O, Cabarcas F, Alzate JF. Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia. Sci Total Environ 2019; 648:572-581. [PMID: 30121535 DOI: 10.1016/j.scitotenv.2018.08.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
Abundance and diversity of microbial communities in biosolids are variable and poorly studied in the tropics, and it is known that rainfall is one of the events that could affect the phylogenetic and functional microbial structure. In the present study, using NGS technics, we studied the microbial diversity as well as the methanogenesis pathway in one of the largest WWTP in Colombia. Besides, we sampled and analyzed biosolids from rainy season and dry season. Phylogenetic classification showed a predominance of bacteria in both samples and difference in the dominant groups depending on the rainfall season. Whereas Pseudomonas was the dominant bacteria in the dry season, Coprothermobacter was in the rainy season. Archaea abundance was higher in the rainy season (11.5%) doubling dry season proportion. The bioreactor biogas production and total solids content showed similar results between rainy and dry season at the sampling dates. The most abundant Archaea related with methanogenesis was Methanosaeta, which is a methanogenic microorganism that exclusively uses acetate to produce methane. Moreover, annotation of the methanogenic pathway in the metagenome showed abundance in genes encoding Acetyl-CoA synthetases (ACSS), an enzyme that catalyzes acetate activation. Our results suggest that the microbial diversity was stable among the two time points tested, rainy season and dry season; and, although there were changes in the microbial abundance of dominant bacterial species, anaerobic digester performance is not affected.
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Affiliation(s)
- Katherine Bedoya
- Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia; Centro Nacional de Secuenciación Genómica-CNSG, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Oscar Coltell
- Department of Computer Languages and Systems, School of Technology and Experimental Sciences, Universitat Jaume I, Castellón, Spain; CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Felipe Cabarcas
- Centro Nacional de Secuenciación Genómica-CNSG, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia; Grupo SISTEMIC, Ingeniería Electrónica, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Juan F Alzate
- Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia; Centro Nacional de Secuenciación Genómica-CNSG, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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48
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Toro-Londono MA, Bedoya-Urrego K, Garcia-Montoya GM, Galvan-Diaz AL, Alzate JF. Intestinal parasitic infection alters bacterial gut microbiota in children. PeerJ 2019; 7:e6200. [PMID: 30643702 PMCID: PMC6327884 DOI: 10.7717/peerj.6200] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 12/03/2018] [Indexed: 12/29/2022] Open
Abstract
The study of the burden that parasites can exert upon the bacterial gut microbiota was restricted by the available technologies and their costs. Currently, next-generation sequencing coupled with traditional methodologies allows the study of eukaryotic parasites (protozoa and helminths) and its effects on the human bacterial gut microbiota diversity. This diversity can be altered by a variety of factors such as age, diet, genetics and parasitic infections among others. The disturbances of the gut microbiota have been associated with a variety of illnesses. Children population in developing countries, are especially susceptible to parasitic infections because of the lack of proper sanitation and undernutrition, allowing both, the thriving of intestinal parasites and profound alteration of the gut microbiota. In this work, we have sampled the stool of 23 children from four different children's care-centers in Medellin, Colombia, and we have identified the eukaryotic parasites by traditional and molecular methodologies coupled with microbial profiling using 16S rDNA sequencing. This mixed methodology approach has allowed us to establish an interesting relationship between Giardia intestinalis and helminth infection, having both effects upon the bacterial gut microbiota enterotypes, causing a switch from a type I to a type II enterotype upon infection.
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Affiliation(s)
- Miguel A. Toro-Londono
- Centro Nacional de Secuenciación Genómica—CNSG, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | - Katherine Bedoya-Urrego
- Centro Nacional de Secuenciación Genómica—CNSG, Universidad de Antioquia, Medellin, Antioquia, Colombia
- Parasitology group, School of Medicine, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | | | - Ana L. Galvan-Diaz
- Environmental Microbiology Group, School of Microbiology, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica—CNSG, Universidad de Antioquia, Medellin, Antioquia, Colombia
- Parasitology group, School of Medicine, Universidad de Antioquia, Medellin, Antioquia, Colombia
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49
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Flórez-Muñoz SV, Alzate JF, Mesa-Arango AC. Molecular Identification and Antifungal Susceptibility of Clinical Isolates of Sporothrix schenckii Complex in Medellin, Colombia. Mycopathologia 2018; 184:53-63. [PMID: 30554299 DOI: 10.1007/s11046-018-0310-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 11/27/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Sporotrichosis is a subcutaneous mycosis that affects humans and other animals. Infection prevails in tropical and subtropical countries. Until a few years ago, it was considered that two varieties of Sporothrix schenckii caused this mycosis, but by applying molecular taxonomic markers, it has been demonstrated that there are several cryptic species within S. schenckii complex which varies in susceptibility, virulence, and geographic distribution. OBJECTIVE This study aimed to identify the clinical isolates of Sporothrix spp. from patients with sporotrichosis in Medellin, Colombia, using two markers and to evaluate the in vitro susceptibility to itraconazole. METHODS Thirty-four clinical isolates of Sporothrix spp. from Colombia, three from Mexico, and one from Guatemala were identified through sequencing of the noncoding region ITS-1 + 5.8SDNAr + ITS-2 and of the fragment containing exons 3 and 4 of the β-tubulin gene. Clinical isolate sequences were compared with GenBank reference sequences using the BLASTN tool, and then, phylogenetic analysis was performed. Besides, the in vitro susceptibility to itraconazole was evaluated by determining the minimum inhibitory concentrations according to the CLSI M38-A2 method. RESULTS Clinical isolates were identified by morphology as Sporothrix spp. Using the molecular markers, ITS and β-tubulin, isolates were identified as S. schenckii sensu stricto (25) and Sporothrix globosa (13). Susceptibility to itraconazole was variable among clinical isolates. CONCLUSION This is the first scientific publication that identifies species that cause sporotrichosis in Colombia, along with the antifungal susceptibility to itraconazole.
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Affiliation(s)
- S V Flórez-Muñoz
- Grupo de Investigación Dermatológica, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-29, Oficina 303, Edificio Manuel Uribe Angel, Medellín, Colombia
| | - J F Alzate
- Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.,Centro Nacional de Secuenciación Genómica, CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - A C Mesa-Arango
- Grupo de Investigación Dermatológica, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-29, Oficina 303, Edificio Manuel Uribe Angel, Medellín, Colombia.
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50
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van de Geer A, Nieto-Patlán A, Kuhns DB, Tool AT, Arias AA, Bouaziz M, de Boer M, Franco JL, Gazendam RP, van Hamme JL, van Houdt M, van Leeuwen K, Verkuijlen PJ, van den Berg TK, Alzate JF, Arango-Franco CA, Batura V, Bernasconi AR, Boardman B, Booth C, Burns SO, Cabarcas F, Bensussan NC, Charbit-Henrion F, Corveleyn A, Deswarte C, Azcoiti ME, Foell D, Gallin JI, Garcés C, Guedes M, Hinze CH, Holland SM, Hughes SM, Ibañez P, Malech HL, Meyts I, Moncada-Velez M, Moriya K, Neves E, Oleastro M, Perez L, Rattina V, Oleaga-Quintas C, Warner N, Muise AM, López JS, Trindade E, Vasconcelos J, Vermeire S, Wittkowski H, Worth A, Abel L, Dinauer MC, Arkwright PD, Roos D, Casanova JL, Kuijpers TW, Bustamante J. Inherited p40phox deficiency differs from classic chronic granulomatous disease. J Clin Invest 2018; 128:3957-3975. [PMID: 29969437 PMCID: PMC6118590 DOI: 10.1172/jci97116] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 06/14/2018] [Indexed: 12/23/2022] Open
Abstract
Biallelic loss-of-function (LOF) mutations of the NCF4 gene, encoding the p40phox subunit of the phagocyte NADPH oxidase, have been described in only 1 patient. We report on 24 p40phox-deficient patients from 12 additional families in 8 countries. These patients display 8 different in-frame or out-of-frame mutations of NCF4 that are homozygous in 11 of the families and compound heterozygous in another. When overexpressed in NB4 neutrophil-like cells and EBV-transformed B cells in vitro, the mutant alleles were found to be LOF, with the exception of the p.R58C and c.120_134del alleles, which were hypomorphic. Particle-induced NADPH oxidase activity was severely impaired in the patients' neutrophils, whereas PMA-induced dihydrorhodamine-1,2,3 (DHR) oxidation, which is widely used as a diagnostic test for chronic granulomatous disease (CGD), was normal or mildly impaired in the patients. Moreover, the NADPH oxidase activity of EBV-transformed B cells was also severely impaired, whereas that of mononuclear phagocytes was normal. Finally, the killing of Candida albicans and Aspergillus fumigatus hyphae by neutrophils was conserved in these patients, unlike in patients with CGD. The patients suffer from hyperinflammation and peripheral infections, but they do not have any of the invasive bacterial or fungal infections seen in CGD. Inherited p40phox deficiency underlies a distinctive condition, resembling a mild, atypical form of CGD.
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Affiliation(s)
- Annemarie van de Geer
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Alejandro Nieto-Patlán
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Department of Immunology, National School of Biological Science, National Polytechnic Institute, ENCB - IPN, Mexico
| | - Douglas B Kuhns
- Neutrophil Monitoring Laboratory, Clinical Services Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Anton Tj Tool
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Andrés A Arias
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, and.,School of Microbiology, University of Antioquia, Medellin, Colombia
| | - Matthieu Bouaziz
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Martin de Boer
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - José Luis Franco
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, and
| | - Roel P Gazendam
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - John L van Hamme
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Michel van Houdt
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Karin van Leeuwen
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Jh Verkuijlen
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Timo K van den Berg
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Molecular Cell Biology and Immunology, VU Medical Center, VU University, Amsterdam, Netherlands
| | - Juan F Alzate
- National Center for Genomic Sequencing - CNSG-SIU, School of Medicine, University of Antioquia, Medellin, Colombia
| | - Carlos A Arango-Franco
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, and.,School of Microbiology, University of Antioquia, Medellin, Colombia
| | - Vritika Batura
- Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrea R Bernasconi
- Service of Immunology and Rheumatology, Garrahan National Pediatric Hospital, Buenos Aires, Argentina
| | - Barbara Boardman
- Department of Pediatric Allergy and Immunology, Royal Manchester Children's Hospital, University of Manchester, Manchester, United Kingdom
| | - Claire Booth
- Department of Immunology, Great Ormond Street Hospital, NHS Foundation Trust, London, United Kingdom
| | - Siobhan O Burns
- Institute of Immunity and Transplantation, University College London, London, United Kingdom.,Department of Clinical Immunology, Royal Free London, NHS Foundation Trust, London, United Kingdom
| | - Felipe Cabarcas
- National Center for Genomic Sequencing - CNSG-SIU, School of Medicine, University of Antioquia, Medellin, Colombia.,SISTEMIC Group, Electronic Engineering Department, University of Antioquia, Medellin, Colombia
| | - Nadine Cerf Bensussan
- Laboratory of Intestinal Immunity, INSERM U1163, Imagine Institute, Paris, France.,GENIUS group (GENetically ImmUne-mediated enteropathieS) of the European Society for Pediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN).,Paris Descartes University, Paris, France
| | - Fabienne Charbit-Henrion
- Laboratory of Intestinal Immunity, INSERM U1163, Imagine Institute, Paris, France.,GENIUS group (GENetically ImmUne-mediated enteropathieS) of the European Society for Pediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN).,Paris Descartes University, Paris, France.,Pediatric Gastroenterology, Hepatology and Nutrition Unit, AP-HP, Necker Hospital for Sick Children, Paris, France
| | - Anniek Corveleyn
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - María Esnaola Azcoiti
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Department of Immunology, Ricardo Gutierrez Children's Hospital, Buenos Aires, Argentina
| | - Dirk Foell
- Department of Pediatric Rheumatology and Immunology, Munster University Hospital, Munster, Germany
| | - John I Gallin
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Carlos Garcés
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, and
| | - Margarida Guedes
- Department of Pediatrics, Santo Antonio Hospital, Porto, Portugal
| | - Claas H Hinze
- Department of Pediatric Rheumatology and Immunology, Munster University Hospital, Munster, Germany
| | - Steven M Holland
- Laboratory of Clinical Infectious Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Stephen M Hughes
- Department of Pediatric Allergy and Immunology, Royal Manchester Children's Hospital, University of Manchester, Manchester, United Kingdom
| | - Patricio Ibañez
- Inflammatory Bowel Disease Program, Gastroenterology Department, Clinic Las Condes Medical Center, University of Chile, Santiago de Chile, Chile
| | - Harry L Malech
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Isabelle Meyts
- Department of Pediatric Hematology and Oncology and.,Department of Microbiology and Immunology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Marcela Moncada-Velez
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, and
| | - Kunihiko Moriya
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Esmeralda Neves
- Department of Immunology, Santo Antonio Hospital, Porto, Portugal
| | - Matias Oleastro
- Service of Immunology and Rheumatology, Garrahan National Pediatric Hospital, Buenos Aires, Argentina
| | - Laura Perez
- Service of Immunology and Rheumatology, Garrahan National Pediatric Hospital, Buenos Aires, Argentina
| | - Vimel Rattina
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Neil Warner
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, and
| | - Aleixo M Muise
- Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada.,SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, and.,Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jeanet Serafín López
- Department of Immunology, National School of Biological Science, National Polytechnic Institute, ENCB - IPN, Mexico
| | - Eunice Trindade
- Pediatric Gastroenterology Unit, Sao Joao Hospital, Porto, Portugal
| | | | - Séverine Vermeire
- Division of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium.,Department of Experimental Medicine, KU Leuven, Leuven, Belgium
| | - Helmut Wittkowski
- Department of Pediatric Rheumatology and Immunology, Munster University Hospital, Munster, Germany
| | - Austen Worth
- Department of Immunology, Great Ormond Street Hospital, NHS Foundation Trust, London, United Kingdom
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Mary C Dinauer
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Peter D Arkwright
- Department of Pediatric Allergy and Immunology, Royal Manchester Children's Hospital, University of Manchester, Manchester, United Kingdom
| | - Dirk Roos
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Howard Hughes Medical Institute, New York, New York, USA.,Pediatric Hematology and Immunology Unit, AP-HP, Necker Hospital for Sick Children, Paris, France
| | - Taco W Kuijpers
- Department of Blood Cell Research, Sanquin Research, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam, Netherlands.,Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France
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