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Migueletti MR, García Rey J, Micheloni J, Lomanto C, Martelli E, Sánchez G, Colombo JM, Vallecillo LM, Lamagni F, Giusti T, Acosta F, Villagrán F, Gvozdenovich M, Pricco Frakich A, Pianesi T, Tulin G, Mascali FC, Petitti TD, Torres Manno MA, Fusari CM, Buttigliero L, Giordana MF, Gramajo H, Diacovich L, Espariz M, Mussi MA. Complete genome sequence of the Microbacterium foliorum bacteriophage Garey24. Microbiol Resour Announc 2024; 13:e0121523. [PMID: 38315107 DOI: 10.1128/mra.01215-23] [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: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
In this work, we report the discovery and characterization of Garey24, a bacteriophage that forms medium-size plaques with halo rings isolated from a soil sample in Funes, Argentina. Its 41,522 bp circularly permuted genome contains 63 putative protein-coding genes. Based on gene content similarity, Garey24 was assigned to subcluster EA1.
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Affiliation(s)
- Matías R Migueletti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julieta García Rey
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Josefina Micheloni
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Camila Lomanto
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Elisa Martelli
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gastón Sánchez
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julián M Colombo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luciano M Vallecillo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Francisco Lamagni
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás Giusti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Fabrina Acosta
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Franco Villagrán
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martín Gvozdenovich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Abril Pricco Frakich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tulio Pianesi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gonzalo Tulin
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Florencia C Mascali
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás D Petitti
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariano A Torres Manno
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Corina M Fusari
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | | | - Hugo Gramajo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Martín Espariz
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Alejandra Mussi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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Torres Manno MA, Gizzi FO, Martín M, Espariz M, Magni C, Blancato VS. Metagenomic approach to infer rumen microbiome derived traits of cattle. World J Microbiol Biotechnol 2023; 39:250. [PMID: 37439894 DOI: 10.1007/s11274-023-03694-1] [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] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
Ruminants enable the conversion of indigestible plant material into animal consumables, including dairy products, meat, and valuable fibers. Microbiome research is gaining popularity in livestock species because it aids in the knowledge of illnesses and efficiency processes in animals. In this study, we use WGS metagenomic data to thoroughly characterize the ruminal ecosystem of cows to infer positive and negative livestock traits determined by the microbiome. The rumen of cows from Argentina were described by combining different gene biomarkers, pathways composition and taxonomic information. Taxonomic characterization indicated that the two major phyla were Bacteroidetes and Firmicutes; in third place, Proteobacteria was highly represented followed by Actinobacteria; Prevotella, and Bacteroides were the most abundant genera. Functional profiling of carbohydrate-active enzymes indicated that members of the Glycoside Hydrolase (GH) class accounted for 52.2 to 55.6% of the total CAZymes detected, among them the most abundant were the oligosaccharide degrading enzymes. The diversity of GH families found suggested efficient hydrolysis of complex biomass. Genes of multidrug, macrolides, polymyxins, beta-lactams, rifamycins, tetracyclines, and bacitracin resistance were found below 0.12% of relative abundance. Furthermore, the clustering analysis of genera and genes that correlated to methane emissions or feed efficiency, suggested that the cows analysed could be regarded as low methane emitters and clustered with high feed efficiency reference animals. Finally, the combination of bioinformatic analyses used in this study can be applied to assess cattle traits difficult to measure and guide enhanced nutrition and breeding methods.
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Affiliation(s)
- Mariano A Torres Manno
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Concejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad Nacional de Rosario (UNR), Suipacha 531, 2000, Rosario, Argentina
| | - Fernán O Gizzi
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Concejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad Nacional de Rosario (UNR), Suipacha 531, 2000, Rosario, Argentina
| | - Mariana Martín
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Concejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) - UNR, Rosario, Argentina
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Concejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad Nacional de Rosario (UNR), Suipacha 531, 2000, Rosario, Argentina
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF) - Municipalidad de Granadero Baigorria, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Concejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad Nacional de Rosario (UNR), Suipacha 531, 2000, Rosario, Argentina
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF) - Municipalidad de Granadero Baigorria, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- Biotecnología de los Alimentos, LCTA, FBioyF-UNR, Suipacha 590, Rosario, Argentina
| | - Víctor S Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Concejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad Nacional de Rosario (UNR), Suipacha 531, 2000, Rosario, Argentina.
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF) - Municipalidad de Granadero Baigorria, Universidad Nacional de Rosario (UNR), Rosario, Argentina.
- Biotecnología de los Alimentos, LCTA, FBioyF-UNR, Suipacha 590, Rosario, Argentina.
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Acciarri G, Gizzi FO, Torres Manno MA, Stülke J, Espariz M, Blancato VS, Magni C. Redundant potassium transporter systems guarantee the survival of Enterococcus faecalis under stress conditions. Front Microbiol 2023; 14:1117684. [PMID: 36846772 PMCID: PMC9945522 DOI: 10.3389/fmicb.2023.1117684] [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] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Enterococcus is able to grow in media at pH from 5.0 to 9.0 and a high concentration of NaCl (8%). The ability to respond to these extreme conditions requires the rapid movement of three critical ions: proton (H+), sodium (Na+), and potassium (K+). The activity of the proton F0F1 ATPase and the sodium Na+ V0V1 type ATPase under acidic or alkaline conditions, respectively, is well established in these microorganisms. The potassium uptake transporters KtrI and KtrII were described in Enterococcus hirae, which were associated with growth in acidic and alkaline conditions, respectively. In Enterococcus faecalis, the presence of the Kdp (potassium ATPase) system was early established. However, the homeostasis of potassium in this microorganism is not completely explored. In this study, we demonstrate that Kup and KimA are high-affinity potassium transporters, and the inactivation of these genes in E. faecalis JH2-2 (a Kdp laboratory natural deficient strain) had no effect on the growth parameters. However, in KtrA defective strains (ΔktrA, ΔkupΔktrA) an impaired growth was observed under stress conditions, which was restored to wild type levels by external addition of K+ ions. Among the multiplicity of potassium transporters identify in the genus Enterococcus, Ktr channels (KtrAB and KtrAD), and Kup family symporters (Kup and KimA) are present and may contribute to the particular resistance of these microorganisms to different stress conditions. In addition, we found that the presence of the Kdp system in E. faecalis is strain-dependent, and this transporter is enriched in strains of clinical origin as compared to environmental, commensal, or food isolates.
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Affiliation(s)
- Giuliana Acciarri
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina
| | - Fernán O. Gizzi
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina
| | - Mariano A. Torres Manno
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina,Área Bioinformática, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Jörg Stülke
- Department of General Microbiology, Georg August University, Göttingen, Germany
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina,Área Bioinformática, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Víctor S. Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los Alimentos, FBioyF, UNR–Municipalidad de Granadero Baigorria, Rosario, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los Alimentos, FBioyF, UNR–Municipalidad de Granadero Baigorria, Rosario, Argentina,*Correspondence: Christian Magni, ✉
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Torres Manno MA, Repizo GD, Magni C, Dunlap CA, Espariz M. The assessment of leading traits in the taxonomy of the Bacillus cereus group. Antonie Van Leeuwenhoek 2020; 113:2223-2242. [PMID: 33179199 DOI: 10.1007/s10482-020-01494-3] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022]
Abstract
Bacillus cereus sensu lato strains (B. cereus group) are widely distributed in nature and have received interest for decades due to their importance in insect pest management, food production and their positive and negative repercussions in human health. Consideration of practical uses such as virulence, physiology, morphology, or ill-defined features have been applied to describe and classify species of the group. However, current comparative studies have exposed inconsistencies between evolutionary relatedness and biological significance among genomospecies of the B. cereus group. Here, the combined analyses of core-based phylogeny and all versus all Average Nucleotide Identity values based on 2116 strains were conducted to update the genomospecies circumscriptions within B. cereus group. These analyses suggested the existence of 57 genomospecies, 37 of which are novel, thus indicating that the taxonomic identities of more than 39% of the analyzed strains should be revised or updated. In addition, we found that whole-genome in silico analyses were suitable to differentiate genomospecies such as B. anthracis, B. cereus and B. thuringiensis. The prevalence of toxin and virulence factors coding genes in each of the genomospecies of the B. cereus group was also examined, using phylogeny-aware methods at wide-genome scale. Remarkably, Cry and emetic toxins, commonly assumed to be associated with B. thuringiensis and emetic B. paranthracis, respectively, did not show a positive correlation with those genomospecies. On the other hand, anthrax-like toxin and capsule-biosynthesis coding genes were positively correlated with B. anthracis genomospecies, despite not being present in all strains, and with presumably non-pathogenic genomospecies. Hence, despite these features have been so far considered relevant for industrial or medical classification of related species of the B. cereus group, they were inappropriate for their circumscription. In this study, genomospecies of the group were accurately affiliated and representative strains defined, generating a rational framework that will allow comparative analysis in epidemiological or ecological studies. Based on this classification the role of specific markers such as Type VII secretion system, cytolysin, bacillolysin, and siderophores such as petrobactin were pointed out for further analysis.
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Affiliation(s)
- Mariano A Torres Manno
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina
- Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo D Repizo
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- Laboratorio de Resistencia bacteriana a antimicrobianos, Instituto de Biología Molecular y Celular de Rosario (IBR), sede FCByF - UNR, Rosario, Santa Fe, Argentina
| | - Christian Magni
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina
| | - Christopher A Dunlap
- United States Department of Agriculture, Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, 1815 North University Street, Peoria, IL, 61604, USA
| | - Martín Espariz
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Santa Fe, Argentina.
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), sede FCByF - UNR, Rosario, Santa Fe, Argentina.
- Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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Torres Manno MA, Pizarro MD, Prunello M, Magni C, Daurelio LD, Espariz M. GeM-Pro: a tool for genome functional mining and microbial profiling. Appl Microbiol Biotechnol 2019; 103:3123-3134. [DOI: 10.1007/s00253-019-09648-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 11/30/2022]
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