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Simar SR, Tran TT, Rydell KB, Atterstrom RL, Sahasrabhojane PV, Dinh AQ, Schettino MG, Slanis HS, Deyanov AE, DeTranaltes AM, Axell-House DB, Miller WR, Munita JM, Tobys D, Seifert H, Biehl L, Zervos M, Suleyman G, Kaur J, Warzocha V, Cifuentes RO, Abbo LM, Shimose L, Liu C, Nguyen K, Miller A, Shelburne SA, Hanson BM, Arias CA. Clinical and Genomic Characterization of Recalcitrant Enterococcal Bacteremia: A Multicenter Prospective Cohort Study (VENOUS). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.01.645485. [PMID: 40236068 PMCID: PMC11996524 DOI: 10.1101/2025.04.01.645485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Background Patients with recalcitrant enterococcal bloodstream infections are at greater risk of adverse outcomes. We identified patients in the 2016-2022 Vancomycin-Resistant Enterococcal Bacteremia Outcomes Study (VENOUS) cohort experiencing recalcitrant bloodstream infections for further clinical and genomic characterization. Methods Bacteremia episodes were considered "persistent" if there was a lack of clearance on day four while receiving ≥ 48 hours of active therapy and recurrent if there was clearance during hospitalization with a subsequent positive culture (collectively, "recalcitrant" bacteremia). A matched comparison group of non-recalcitrant bacteremia patients was chosen in a 2:1 control:case ratio. Isolates were subjected to short- and long-read whole-genome sequencing. Hybrid assemblies were created using a custom pipeline. Findings. A total of 46 recalcitrant infections from 41 patients were identified. Patients with persistent bacteremia were more often admitted to the ICU upon admission relative to controls. E. faecalis strains causing persistent infections had a significantly higher proportion of genes associated with carbohydrate utilization relative to controls. Representation of functional groups associated with mutated genes was disparate between E. faecium and E. faecalis index and persistent isolates, suggesting species-specific adaptation. Discussion Enterococcal isolates causing recalcitrant bacteremia were genomically diverse, indicating that strain-specific signatures are not drivers of persistence. However, comparisons of index vs. persistent isolates revealed that E. faecium may be genetically pre-adapted to cause persistent infection, and site-specific structural variation during infection suggests the role of differential gene expression in adaptation and persistence. This data lays groundwork for future studies to define signatures of enterococcal adaptation during bacteremia.
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González D, Bruna P, Contreras MJ, Leal K, Urrutia CV, Núñez-Montero K, Barrientos L. Genome Mining of Pseudarthrobacter sp. So.54, a Rhizospheric Bacteria from Colobanthus quitensis Antarctic Plant. Biomolecules 2025; 15:534. [PMID: 40305262 PMCID: PMC12025171 DOI: 10.3390/biom15040534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2025] [Revised: 03/25/2025] [Accepted: 04/01/2025] [Indexed: 05/02/2025] Open
Abstract
Antarctic microorganisms have genomic characteristics and biological functions to ensure survival in complex habitats, potentially representing bioactive compounds of biotechnological interest. Pseudarthrobacter sp. So.54 is an Antarctic bacteria strain isolated from the rhizospheric soil of Colobanthus quitensis. Our work aimed to study its genomic characteristics and metabolic potential, linked to environmental adaptation and the production of secondary metabolites with possible biotechnological applications. Whole-genome sequencing, assembly, phylogenetic analysis, functional annotation, and genomic islands prediction were performed to determine the taxonomic affiliation and differential characteristics of the strain So.54. Additionally, Biosynthetic Gene Clusters (BGCs) responsible for secondary metabolites production were identified. The assembled genome of strain So.54 has 3,871,805 bp with 66.0% G + C content. Phylogenetic analysis confirmed that strain So.54 belongs to the Pseudarthrobacter genus; nevertheless, its nucleotide and amino acid identity values were below the species threshold. The main metabolic pathways and 64 genomic islands associated with stress defense and environmental adaptation, such as heavy metal resistance genes, were identified. AntiSMASH analysis predicted six BGCs with low or no similarity to known clusters, suggesting potential as novel natural products. These findings indicate that strain So.54 could be a novel Pseudarthrobacter species with significant environmental adaptation and biotechnological potential.
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Affiliation(s)
- Dayaimi González
- Programa de Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco 4811230, Chile (C.V.U.)
- Centro de Excelencia en Medicina Traslacional (CEMT), Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile
| | - Pablo Bruna
- Programa de Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco 4811230, Chile (C.V.U.)
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco 4811230, Chile
| | - María J. Contreras
- Facultad de Ciencias de la Salud, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco 4800000, Chile
| | - Karla Leal
- Facultad de Ciencias de la Salud, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco 4800000, Chile
| | - Catherine V. Urrutia
- Programa de Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco 4811230, Chile (C.V.U.)
- Centro de Excelencia en Medicina Traslacional (CEMT), Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile
| | - Kattia Núñez-Montero
- Facultad de Ingeniería, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco 4800000, Chile
| | - Leticia Barrientos
- Facultad de Ingeniería, Instituto de Ciencias Aplicadas, Universidad Autónoma de Chile, Avenida Alemania 1090, Temuco 4800000, Chile
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Bakelli A, Dif G, Djemouai N, Bouri M, Şahin F. Plant Growth-Promoting Pseudomonas sp. TR47 Ameliorates Pepper (Capsicum annuum L. var. conoides Mill) Growth and Tolerance to Salt Stress. Curr Microbiol 2025; 82:231. [PMID: 40184005 DOI: 10.1007/s00284-025-04217-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Accepted: 03/22/2025] [Indexed: 04/05/2025]
Abstract
Pepper plants are susceptible to salt stress conditions, while rhizobacteria are considered auspicious factors for boosting plant growth. In this investigation, the Tamarix gallica L. rhizospheric bacterium TR47 was assessed for its capacity to promote growth under normal and saline conditions in the greenhouse. In addition, the genetic mechanisms were investigated through genome mining. Strain TR47 demonstrated numerous growth-promoting characteristics, such as the production of siderophores, phosphate and potassium solubilization, the ability to generate 1-aminocyclopropane-1-carboxylate deaminase as well as indole-3-acetic acid production. The inoculation of pepper seedlings by strain TR47 subjected to normal and salt conditions resulted in significantly increased germination rates compared to uninoculated seeds. Furthermore, the findings demonstrated that strain TR47 exhibited greater fresh and dry biomass values in comparison to the control group, specifically during salt stress conditions. All of these characteristics may enhance plant growth and development, contribute to salt tolerance, and stress mitigation. The genome sequence of TR47 that is most likely related to Pseudomonas plecoglossicida DSM 15088 T consists of a single circular chromosome that is about 5.55 megabase pairs in length and has a GC content of 61.8%. By doing a comprehensive analysis of the whole-genome sequence, genes linked to the promotion of plant development were identified. Our results open up exciting possibilities for the use of TR47 as a biostimulant that may enhance pepper plants under saline conditions, sparking interest in its potential future applications.
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Affiliation(s)
- Aissa Bakelli
- Département de Biologie, Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre, Université de Ghardaia, BP 455, 47000, Ghardaïa, Algeria
| | - Guendouz Dif
- Département des Sciences Naturelles, École Normale Supérieure Taleb Abderrahmane de Laghouat, BP 4033, 03000, Laghouat, Algeria
| | - Nadjette Djemouai
- Département de Biologie, Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre, Université de Ghardaia, BP 455, 47000, Ghardaïa, Algeria.
- Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure Cheikh Mohamed El Bachir El Ibrahimi, Kouba, BP 92, Algiers, Algeria.
| | - Meriam Bouri
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Kayisdagi St., 34755, Istanbul, Turkey
| | - Fikrettin Şahin
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Kayisdagi St., 34755, Istanbul, Turkey
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204
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Chan V, Holcomb T, Kaspar JR, Shields RC. Characterization of MreCD in Streptococcus mutans. J Oral Microbiol 2025; 17:2487643. [PMID: 40206099 PMCID: PMC11980242 DOI: 10.1080/20002297.2025.2487643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 03/21/2025] [Accepted: 03/25/2025] [Indexed: 04/11/2025] Open
Abstract
Background Activities that control cell shape and division are critical for the survival of bacteria. However, little is known about the circuitry controlling these processes in the dental caries pathogen Streptococcus mutans. Methodology We designed experiments to characterize two genes, mreC and mreD, in S. mutans. Assays included cell morphology imaging, protein interaction analysis, transcriptomics, proteomics, and biofilm studies to generate a comprehensive understanding of the role of MreCD in S. mutans. Results Consistent with mreCD participating in cell elongation, cells lacking these genes were found to be rounder than wild-type cells. Using bacterial two-hybrid assays, interactions between MreCD and several other proteins implicated in cell elongation were observed. Further characterization, using proteomics, revealed that the surface-associated proteome is different in mutants lacking mreCD. Consistent with these changes we observed altered sucrose-mediated biofilm architecture. Loss of mreCD also had a noticeable impact on bacteriocin gene expression, which could account in part for the observation that mreCD mutants had a diminished capacity to compete with commensal streptococci. Conclusion Our results provide evidence that cell elongation proteins are required for normal S. mutans physiology and establish a foundation for additional examination of these and related proteins in this organism.
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Affiliation(s)
- Victor Chan
- Department of Oral Biology, University of Florida, Gainesville, FL, USA
| | - Tessa Holcomb
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Justin R. Kaspar
- Division of Biosciences, Ohio State University, Columbus, OH, USA
| | - Robert C. Shields
- Department of Oral Biology, University of Florida, Gainesville, FL, USA
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
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205
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Gomes AC, Montgomery J, Araujo ALS, Morran S, Cutti L, Patterson E, Marques Hill S, Matzrafi M, Shrestha A, Merotto A, Abdollahi F, Nelson DR, Llaca V, Fengler K, de Pinho CF, Gaines TA. Chromosome-Level Assemblies of the Allohexaploid Genomes of Conyza sumatrensis and Conyza bonariensis. Genome Biol Evol 2025; 17:evaf065. [PMID: 40181513 PMCID: PMC12008746 DOI: 10.1093/gbe/evaf065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/19/2025] [Accepted: 03/24/2025] [Indexed: 04/05/2025] Open
Abstract
Conyza sumatrensis and Conyza bonariensis are two important hexaploid weed species that impact crop production systems across the globe. Here, we report reference genome assemblies for both species. The sequenced accession of C. sumatrensis is resistant to multiple herbicides and was collected from the state of Paraná in Brazil, while the accession of C. bonariensis was collected from California, USA. Genomic long read data was used along with optical mapping data to assemble the C. sumatrensis genome into a single haplome at chromosome-level contiguity. The same approach was used along with chromatin contact mapping data to phase the haplotypes of C. bonariensis and generate two chromosome-level haplome assemblies. Subgenome-specific sequences were identified and used to classify the three subgenomes within each assembly. The assemblies are highly complete based on the presence of conserved single-copy orthologs and telomeres, and the size of these assemblies agrees with previous flow cytometry estimates. Full-length transcript sequencing along with gene models from other Asteraceae members was used to predict gene models within each assembly. The genomic resources reported here will be useful for investigations into evolutionary and ecological questions around weed invasion and management for these two species.
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Affiliation(s)
- Anthony Côrtes Gomes
- Crop Science Department, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jacob Montgomery
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Sarah Morran
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Luan Cutti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Eric Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Sofia Marques Hill
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Maor Matzrafi
- Department of Plant Pathology and Weed Research, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani Institute, Yishay, Israel
| | - Anil Shrestha
- Department of Plant Science, California State University, Fresno, CA, USA
| | - Aldo Merotto
- Department of Crop Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Fatemeh Abdollahi
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Llaca
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Kevin Fengler
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | | | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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206
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Ly T, de Melo Teixeira M, Jofre-Rodriguez G, Blanchet D, Mc Donald S, Alvarado P, da Silva SHM, Sepúlveda VE, Zeb Q, Vreden S, Adenis A, Yegres F, Demar M, Buitrago MJS, Barker B, Nacher M, Matute DR. High genetic diversity of Histoplasma in the Amazon basin, 2006-2017. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.04.01.25324933. [PMID: 40236390 PMCID: PMC11998801 DOI: 10.1101/2025.04.01.25324933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Genome sequencing has revealed that Histoplasma, the etiological agent of histoplasmosis is composed of several phylogenetic species. Nonetheless, the genetic diversity of the pathogen remains largely unknown, especially in the tropics. We sequenced the genome for 91 Histoplasma isolates from the Amazon basin, and used phylogenomics, and population genetic evidence to measure the genetic variation of the genus in South America. We report a previously unidentified clade of Histoplasma endemic to the Amazon basin. The lineage is widespread across the continent and contains five lineages that are sufficiently differentiated to be considered phylogenetic species. We find that the geographic range of these lineages is largely but not completely overlapping. Finally, we find that the patient median age and sex ratio differs among species suggesting differences in the epidemiology of histoplasmosis caused by each Histoplasma lineage.
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Affiliation(s)
- Tani Ly
- UMR TBIP, Université de Guyane, 97300 Cayenne, French Guiana
- CIC INSERM1424, Institut Santé des Populations en Amazonie, Centre Hospitalier de Cayenne, 97306, Cayenne, French Guiana
| | | | | | - Denis Blanchet
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier de Cayenne, 97300 Cayenne, French Guiana
| | - Sigrid Mc Donald
- Department of Medical Microbiology, University of Amsterdam UMC, Amsterdam, Netherlands. Evandro Chagas Institute, Bacteriology and Mycology Section, Mycology Laboratory, Ananindeua, Pará, Brazil
| | - Primavera Alvarado
- Laboratorio de Micología. Instituto de Biomedicina “Dr. Jacinto Convit”. Caracas, Venezuela
- Facultad de Medicina, Universidad Central de Venezuela
| | | | | | - Qandeel Zeb
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen Vreden
- Stichting Wetenschappelijk Onderzoek Suriname, Paramaribo, Suriname. Academisch Ziekenhuis Paramaribo, RRP8+PQ7, Flustraat, Paramaribo, Suriname
| | - Antoine Adenis
- CIC INSERM1424, Institut Santé des Populations en Amazonie, Centre Hospitalier de Cayenne, 97300, Cayenne, French Guiana
| | - Francisco Yegres
- Centro de Investigaciones Biomédicas, Universidad Nacional Experimental Francisco de Miranda, Coro, Estado Falcón, Venezuela
| | - Magalie Demar
- Laboratoire EA3593 Ecosystemes amazoniens et pathologies tropicales, Université de Guyane, 97300 Cayenne, French Guiana; Laboratoire de Parasitologie-Mycologie, Centre Hospitalier de Cayenne, 97300 Cayenne, French Guiana
| | - Maria José Serna Buitrago
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
- CIBERINFEC, ISCIII -CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III
| | - Bridget Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff-AZ, USA
| | - Mathieu Nacher
- UMR TBIP, Université de Guyane, 97300 Cayenne, French Guiana
- CIC INSERM1424, Institut Santé des Populations en Amazonie, Centre Hospitalier de Cayenne, 97306, Cayenne, French Guiana
| | - Daniel R. Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
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207
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Samper-Cativiela C, Torre-Fuentes L, Diéguez-Roda B, Maex M, Ugarte-Ruiz M, Carrizo P, Hernández M, Höfle Ú, Sáez JL, de Frutos C, Agüero M, Moreno MÁ, Domínguez L, Herrera-León S, Alvarez J. Molecular epidemiology of Salmonella Enteritidis in humans and animals in Spain. Antimicrob Agents Chemother 2025; 69:e0073824. [PMID: 40029002 PMCID: PMC11963599 DOI: 10.1128/aac.00738-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 01/11/2025] [Indexed: 03/05/2025] Open
Abstract
Salmonella Enteritidis, the most prevalent serovar-causing human gastroenteritis, has been traditionally linked to poultry sources. Although antimicrobial resistance (AMR) is not common in this serovar, increasing levels of resistance to fluoroquinolones and ampicillin have been reported in the last few years. Here, 298 isolates retrieved from different sources (human, livestock, wildlife, food, and environment) and years (2002-2021) in Spain were analyzed to evaluate their diversity, the distribution of AMR-conferring genes (ARGs), and mutations and reconstruct the epidemiology of infection due to this serovar. Isolates were clustered in two major clades (I and II), with strains in clade I (including 61.5% of all human isolates) displaying a pan-susceptible phenotype and not carrying AMR determinants. In contrast, clade II included 80.7% of isolates from animal/food/environmental sources, with the majority (69.8%) harboring mutations in the quinolone resistance determinant regions (QRDR). ARGs, although rare, were mostly found in clade II strains that also carried plasmid replicons, among which IncX1 was the most common. Although higher levels of phenotypic resistance were found in animal isolates, extended-spectrum beta-lactamase, plasmid-mediated AmpC, and carbapenemase-encoding genes were only found among human isolates. In summary, the majority of human and animal isolates from Spanish sources in our collection were classified in different phylogenetic branches, suggesting that additional sources are contributing to the occurrence of foodborne infections in Spain. Furthermore, the different distributions of virulence factors and ARGs in isolates from different sources and their association with specific plasmids suggest the presence of different dynamics contributing to the selection of resistant strains.
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Affiliation(s)
- Clara Samper-Cativiela
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Laura Torre-Fuentes
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | | | - Margo Maex
- Division of Human Bacterial Diseases, Sciensano, Uccle, Belgium
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Paula Carrizo
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Marta Hernández
- Departamento de Anatomía Patológica, Microbiología, Medicina Preventiva y Salud Pública, Medicina Legal y Forense. Facultad de Medicina, Universidad de Valladolid Facultad de Medicina, Valladolid, Spain
| | - Úrsula Höfle
- IREC, Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Spain
| | - José Luis Sáez
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Dirección General de la Producción Agraria, Ministerio de Agricultura, Pesca y Alimentación, Madrid, Spain
| | - Cristina de Frutos
- Laboratorio Central de Veterinaria, Ministerio de Agricultura, Pesca y Alimentación, Algete, Spain
| | - Montserrat Agüero
- Laboratorio Central de Veterinaria, Ministerio de Agricultura, Pesca y Alimentación, Algete, Spain
| | - Miguel Ángel Moreno
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Silvia Herrera-León
- Laboratorio de Referencia e Investigación en Enfermedades Bacterianas Transmitidas por Alimentos, Instituto de Salud Carlos III, Madrid, Spain
| | - Julio Alvarez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
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Zampieri A, Carraro L, Mohammadpour H, Rovere GD, Milan M, Fasolato L, Cardazzo B. Presence and characterization of the human pathogenic Vibrio species in the microbiota of Manila clams using cultural and molecular methods. Int J Food Microbiol 2025; 433:111113. [PMID: 39987648 DOI: 10.1016/j.ijfoodmicro.2025.111113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Revised: 02/07/2025] [Accepted: 02/15/2025] [Indexed: 02/25/2025]
Abstract
The North Adriatic lagoons and the Po River Delta are important areas for farming Manila clams (Ruditapes philippinarum). These areas have been heavily impacted by climate change, reducing livestock numbers and increasing pathogen spread. Shellfish, particularly clams, are primary vectors for Vibrio pathogens affecting humans. In this study, the occurrence of human pathogenic Vibrio species on Manila clams was investigated using an integrated approach that combined culture-dependent and culture-independent techniques. Samples were collected over three years from farming areas in the northeastern Adriatic lagoons and the Po River Delta, regions seriously impacted by climate change and pollution. In this study, species of the human pathogen Vibrio were analyzed in the clam microbiota and characterized using recA-pyrH metabarcoding and shotgun metagenomics. Human pathogenic Vibrio species were widespread in the clam microbiota, especially in summer, demonstrating that the environmental conditions on the northern Adriatic coasts allowed the growth of these bacteria. V. parahaemolyticus and V. vulnificus were also quantified using qPCR in <50 % of summer samples Shotgun metagenomics revealed the similarity of V. parahaemolyticus strains to other worldwide genomes, enabling improved pathogen identification and tracking. In the future, climate change could cause these conditions to become even more favorable to these bacteria, potentially increasing pathogen spread. Consequently, enhanced monitoring and control of both the environment and seafood products should be planned to ensure food safety.
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Affiliation(s)
- Angela Zampieri
- Department of Comparative Biomedicine and Food Science (University of Padova), University of Padua, Viale Università 16, 35020 Legnaro, Pd, Italy
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science (University of Padova), University of Padua, Viale Università 16, 35020 Legnaro, Pd, Italy
| | - Hooriyeh Mohammadpour
- Department of Comparative Biomedicine and Food Science (University of Padova), University of Padua, Viale Università 16, 35020 Legnaro, Pd, Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science (University of Padova), University of Padua, Viale Università 16, 35020 Legnaro, Pd, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science (University of Padova), University of Padua, Viale Università 16, 35020 Legnaro, Pd, Italy
| | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science (University of Padova), University of Padua, Viale Università 16, 35020 Legnaro, Pd, Italy.
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science (University of Padova), University of Padua, Viale Università 16, 35020 Legnaro, Pd, Italy
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209
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Terra LA, Klepa MS, Nogueira MA, Hungria M. Pangenome analysis indicates evolutionary origins and genetic diversity: emphasis on the role of nodulation in symbiotic Bradyrhizobium. FRONTIERS IN PLANT SCIENCE 2025; 16:1539151. [PMID: 40241821 PMCID: PMC12000093 DOI: 10.3389/fpls.2025.1539151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Accepted: 03/10/2025] [Indexed: 04/18/2025]
Abstract
The Bradyrhizobium genus is widely known for encompassing many species capable of forming nodules and establishing the biological nitrogen fixation process with several legumes, significantly contributing to agriculture and environmental sustainability. Despite its importance, questions about the evolution, pangenome, and symbiotic genes of Bradyrhizobium are still poorly understood. In this study, we analyzed the pangenome of a set of Bradyrhizobium symbiotic species using the Roary and GET_HOMOLOGUES tools in strains originated from the Northern and Southern Hemispheres. We also investigated the presence and correlation of the fix, nif, nod, Type III secretion system (T3SS) and their effector proteins, and T4SS genes, trying to find differences between clades, hosts, and biogeographic origin. Pangenome analysis of Bradyrhizobium species from the Northern and Southern Hemispheres provided valuable insights into their diversity, biogeography, origin, and co-evolution with their legume host plants. The genus possesses a relatively small core genome compared to the expanded accessory genome, a key feature that facilitates genetic exchange and acquisition of new genes, allowing adaptation to a variety of environments. Notably, the presence or absence of T3SS effector proteins varied significantly according to the geographic location, suggesting specific environmental adaptations, as well as a direct relationship with nodulation genes. Comparative analysis indicated that symbiotic Bradyrhizobium species originated in the Northern Hemisphere and present a greater diversity of orthologous groups than those from the Southern Hemisphere. These results contribute to our understanding of the evolutionary history of these symbiotic bacteria.
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Affiliation(s)
| | | | - Marco Antonio Nogueira
- CNPq, Brasília, Brazil
- Soil Biotechnology Laboratory, Embrapa Soja, Londrina, Paraná, Brazil
| | - Mariangela Hungria
- CNPq, Brasília, Brazil
- Soil Biotechnology Laboratory, Embrapa Soja, Londrina, Paraná, Brazil
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Petersen ME, Khamas AB, Østergaard LJ, Jørgensen NP, Meyer RL. Combination therapy delays antimicrobial resistance after adaptive laboratory evolution of Staphylococcus aureus. Antimicrob Agents Chemother 2025; 69:e0148324. [PMID: 40084881 PMCID: PMC11963546 DOI: 10.1128/aac.01483-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Accepted: 02/17/2025] [Indexed: 03/16/2025] Open
Abstract
Antibiotic resistance, driven by misuse and overuse of antibiotics, is one of the greatest threats against human health. The antimicrobial pressure during prolonged antibiotic treatment of chronic bacterial infections selects for resistance. While antibiotic combinations may reduce resistance emergence, antibiotic-tolerant persister cells can serve as a reservoir for resistance development. Therefore, targeting these cells with anti-persister drugs might provide a novel strategy for resistance prevention. In this study, we conducted 42 days of adaptive laboratory evolution using Staphylococcus aureus exposed to rifampicin, ciprofloxacin, daptomycin, and vancomycin, alone or in combination with the anti-persister drug mitomycin C. We monitored antibiotic susceptibility daily and assessed phenotypic changes in growth and biofilm formation in evolved strains. Whole-genome sequencing revealed mutations linked to antibiotic resistance and phenotypic shifts. Rifampicin resistance developed within a few days, while ciprofloxacin and daptomycin emerged in approximately 3 weeks. Treatments with vancomycin or mitomycin C resulted in minimal changes in susceptibility. While combination therapy delayed resistance, it did not fully prevent it. Notably, the combination of rifampicin with mitomycin C maintained rifampicin susceptibility throughout the long-term evolution experiment. Sub-inhibitory antibiotic treatments selected for both previously characterized and novel mutations, including unprecedented alterations in the nucleotide excision repair system and azoreductase following mitomycin C exposure. The delayed resistance development observed with combination therapy, particularly mitomycin C's ability to suppress rifampicin resistance, suggests potential therapeutic applications. Future studies should evaluate the clinical efficacy of anti-persister drugs in preventing resistance across different bacterial pathogens and infection models.
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Affiliation(s)
| | | | | | | | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Department of Biology, Aarhus University, Aarhus, Denmark
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211
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Duchez R, Vingadassalon N, Merda D, Van Nieuwenhuysen T, Byrne B, Kourtis C, Nia Y, Hennekinne JA, Cavaiuolo M. Genetic relatedness of Staphylococcus aureus isolates within food outbreaks by single nucleotide polymorphisms. Int J Food Microbiol 2025; 433:111115. [PMID: 39993362 DOI: 10.1016/j.ijfoodmicro.2025.111115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 02/14/2025] [Accepted: 02/15/2025] [Indexed: 02/26/2025]
Abstract
Investigation of bacterial food outbreaks by whole genome sequencing can rely on the inspection of the genetic relatedness between isolates through the application of single nucleotide polymorphism (SNP) thresholds. However, there is no consensus for Staphylococcus aureus in the context of food outbreaks. In this study, we propose a SNP cut-off by taking into account the mutation rate and the evolution time of this pathogen in food. Through in vitro microevolution, we determined the mutation rate of three S. aureus strains grown under mimicked food stressing conditions. From the mutation rate, we set a cut-off of 28 SNPs considering 30 days as evolution time based on the average shelf-life of foods contaminated by S. aureus and the timeline for identifying this pathogen in outbreaks. The SNP threshold was applied to retrospectively study ten staphylococcal food outbreaks to assess whether isolates from food and/or of human origin from the same outbreak were epidemiologically related. To interpret SNP distances, phylogenetic tree topologies and bootstraps were integrated and showed that isolates differing by up to 28 SNPs were monophyletic. Our suggested cut-off can be used in outbreak management to identify closely related S. aureus strains.
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Affiliation(s)
- Rémi Duchez
- ANSES, Laboratory for Food Safety, SBCL Unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - Noémie Vingadassalon
- ANSES, Laboratory for Food Safety, SBCL Unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - Déborah Merda
- ANSES, Laboratory for Food Safety, Shared Support Service for Data Analysis (SPAAD), F-94706 Maisons-Alfort, France
| | | | - Brian Byrne
- Department of Agriculture, Food and the Marine, Food Microbiology Division, Backweston Laboratory Campus, Kildare, Ireland
| | - Christos Kourtis
- State General Laboratory, Food Microbiology Laboratory, Nicosia, Cyprus
| | - Yacine Nia
- ANSES, Laboratory for Food Safety, SBCL Unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | | | - Marina Cavaiuolo
- ANSES, Laboratory for Food Safety, SBCL Unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France.
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212
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Deng Z, Yang W, Lin T, Wang Y, Hua X, Jiang X, Chen J, Liu D, Ye Z, Zhang Y, Lynch M, Long H, Pan J. Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study. Microbiol Spectr 2025; 13:e0169224. [PMID: 40172189 PMCID: PMC12054067 DOI: 10.1128/spectrum.01692-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 02/11/2025] [Indexed: 04/04/2025] Open
Abstract
Streptomyces, a diverse group of filamentous bacteria found predominantly in soil, play a crucial role in nutrient cycling and produce many valuable secondary metabolites for the pharmaceutical industry. In this pilot study, we collected 19 soil samples from 14 provinces in China to preliminarily investigate the biodiversity and genetic structure of Streptomyces in soils of China from different dimensions, using recently developed cost-efficient amplicon and whole-genome library preparation methods. Amplicon analysis showed that Actinobacteria were among the most abundant bacteria, with 0.3% of amplicon sequence variants (ASVs) belonging to Streptomyces. Meanwhile, we successfully isolated 136 Streptomyces natural strains and assembled their genomes, including 26 previously unreported species, underscoring the need for further exploration of soil Streptomyces in China. Population genetics analysis revealed that homologous recombination may primarily drive the extensive genetic diversity observed in Streptomyces, as well as a complex population structure. Complementing this, pan-genome analysis shed light on gene diversity within Streptomyces and led to the discovery of rare genes, further emphasizing the vast genetic diversity of this genus. Additionally, multiple metabolic gene clusters were found in these Streptomyces strains, as well as some potentially unique or uncommon ones were found. These findings not only highlight the biological and metabolic diversity of Streptomyces but also provide a technical framework for future studies on the global biodiversity and evolution of this genus. IMPORTANCE Streptomyces, a prominent group of Actinobacteria, holds significant importance in ecosystems and biotechnology due to their diverse array of metabolic products. However, research on the biodiversity of soil Streptomyces across extensive geographical scales in China has been limited, and their genetic diversity has rarely been evaluated using modern population genetics principles. This pilot study successfully addresses these gaps by conducting a preliminary exploration on the biodiversity of Streptomyces in Chinese soils from multiple perspectives, providing valuable insights for a deeper understanding of their biodiversity and a novel technical framework for future large-scale explorations of its diversity.
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Affiliation(s)
- Ziguang Deng
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong Province, China
| | - Wei Yang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Tongtong Lin
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Yaohai Wang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Xiaojing Hua
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Xiaoyu Jiang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Junhao Chen
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Dan Liu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Zhiqiang Ye
- School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Yu Zhang
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Hongan Long
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong Province, China
| | - Jiao Pan
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province, China
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213
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Sawhney SS, Thänert R, Thänert A, Hall-Moore C, Ndao IM, Mahmud B, Warner BB, Tarr PI, Dantas G. Gut microbiome evolution from infancy to 8 years of age. Nat Med 2025:10.1038/s41591-025-03610-0. [PMID: 40175737 DOI: 10.1038/s41591-025-03610-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 02/24/2025] [Indexed: 04/04/2025]
Abstract
The human gut microbiome is most dynamic in early life. Although sweeping changes in taxonomic architecture are well described, it remains unknown how, and to what extent, individual strains colonize and persist and how selective pressures define their genomic architecture. In this study, we combined shotgun sequencing of 1,203 stool samples from 26 mothers and their twins (52 infants), sampled from childbirth to 8 years after birth, with culture-enhanced, deep short-read and long-read stool sequencing from a subset of 10 twins (20 infants) to define transmission, persistence and evolutionary trajectories of gut species from infancy to middle childhood. We constructed 3,995 strain-resolved metagenome-assembled genomes across 399 taxa, and we found that 27.4% persist within individuals. We identified 726 strains shared within families, with Bacteroidales, Oscillospiraceae and Lachnospiraceae, but not Bifidobacteriaceae, vertically transferred. Lastly, we identified weaning as a critical inflection point that accelerates bacterial mutation rates and separates functional profiles of genes accruing mutations.
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Affiliation(s)
- Sanjam S Sawhney
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert Thänert
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Anna Thänert
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Carla Hall-Moore
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Bejan Mahmud
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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214
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Garcia E, Soares F, Rodrigues C, Trovão J, Pothier JF, Camelo A, Santo CE, Dragnev D, Petrova E, Costa J, Bobev S. Expansion of the Host Range of Xanthomonas euroxanthea: First Occurrence in Sunflower in Bulgaria. PLANT DISEASE 2025; 109:810-815. [PMID: 39504143 DOI: 10.1094/pdis-08-24-1691-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2024]
Abstract
Sunflower is a short-season crop of the Asteraceae family and the Helianthus genus and is the fourth most important oilseed crop in the world. During a field campaign, unusual symptoms (necrosis and longitudinal cracking of the petiole) were observed in a sunflower crop grown in the region of Kavarna (Dobrich district, Bulgaria) and strains of the genus Xanthomonas were isolated. Results based on phylogenetic and phylogenomic analyses showed that they clustered with Xanthomonas euroxanthea CPBF 424T species, a pathogenic strain isolated from walnut buds in Portugal and responsible for causing walnut bacterial blight. The sunflower strain showed five out of eight X. euroxanthea-specific markers (XEA4 to XEA8), a pattern also observed in some strains isolated from Solanum lycopersicum, Phaseolus vulgaris, and rainwater sources, reinforcing the emergence of a recent lineage driven by evolutionary adaptations to new plant hosts. This is the first report of X. euroxanthea in sunflower crops in Bulgaria, which represents a potential threat to production, and its distribution should be monitored.
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Affiliation(s)
- Eva Garcia
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra 3030-199, Portugal
| | - Fabiana Soares
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra 3030-199, Portugal
| | - Cristiana Rodrigues
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra 3030-199, Portugal
| | - João Trovão
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra 3030-199, Portugal
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Alexandra Camelo
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- CATAA-Centro de Apoio Tecnológico Agro-Alimentar 6000-459 Castelo Branco, Portugal
| | - Christophe Espírito Santo
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- CATAA-Centro de Apoio Tecnológico Agro-Alimentar 6000-459 Castelo Branco, Portugal
| | - Dian Dragnev
- Department of Phytopathology, Agricultural University, Plovdiv, Bulgaria
| | - Eli Petrova
- Department of Phytopathology, Agricultural University, Plovdiv, Bulgaria
| | - Joana Costa
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra 3030-199, Portugal
| | - Svetoslav Bobev
- Department of Phytopathology, Agricultural University, Plovdiv, Bulgaria
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215
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Roberts WR, Alverson AJ. Three reference genomes for freshwater diatom ecology and evolution. JOURNAL OF PHYCOLOGY 2025; 61:267-274. [PMID: 39930529 PMCID: PMC12044402 DOI: 10.1111/jpy.13545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Revised: 01/10/2025] [Accepted: 01/16/2025] [Indexed: 05/02/2025]
Abstract
Diatoms are an important component of marine and freshwater ecosystems. Although the majority of described diatom species live in freshwater systems, genome sequencing efforts have focused primarily on marine species. Genomic resources for freshwater species have the potential to improve our understanding of diatom ecology and evolution, particularly in the context of major environmental shifts. We used long- and short-read sequencing platforms to assemble reference genomes for three freshwater diatom species, all in the order Thalalassiosirales, which are abundant in the plankton of oceans, lakes, reservoirs, and rivers worldwide. We targeted three species that cover the breadth of phylogenetic diversity in the cyclostephanoid clade of Thalassiosirales: Cyclostephanos tholiformis (JALLPB020000000), Discostella pseudostelligera (JALLBG020000000), and Praestephanos triporus (JALLAZ020000000). The reference genome for D. pseudostelligera was considerably smaller (39 Mb) than those of both P. triporus (73 Mb) and C. tholiformis (177 Mb). Long-read sequencing allowed for the assembly of scaffold-level genomes, including regions rich in repetitive DNA. Compared to short-read assemblies, long-read assemblies increased the contig N50 length as much as 37-fold and reduced the number of contigs by more than 88%. Transcriptome-guided annotation of the protein-coding genes identified between 10,000 and 12,000 genes. This work provides further demonstration of the value of long-read sequencing and provides novel genomic resources for understanding the ecology and evolution of freshwater diatoms.
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Affiliation(s)
- Wade R. Roberts
- Department of Biological SciencesUniversity of ArkansasFayettevilleArkansasUSA
| | - Andrew J. Alverson
- Department of Biological SciencesUniversity of ArkansasFayettevilleArkansasUSA
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216
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Jiang Y, Jiang M, Lu X, Yan M, Shi X, Hu Q, Kan B. Genomic epidemiology and antimicrobial resistance reveal local transmission dynamics of enteric fever in Shenzhen, one of the mega cities in China. J Infect 2025; 90:106469. [PMID: 40058502 DOI: 10.1016/j.jinf.2025.106469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 02/10/2025] [Accepted: 03/04/2025] [Indexed: 03/20/2025]
Abstract
OBJECTIVES Outbreak of enteric fever and the spread of antimicrobial-resistant Salmonella Typhi and S. Paratyphi pose significant public health challenges in low- and middle-income countries. Understanding the transmission dynamics of these pathogens is essential for developing effective control strategies. METHODS We conducted phylogenomic analyses and integrated epidemiological data from 135 S. Typhi and 271 S. Paratyphi A isolates collected in Shenzhen from 2001 to 2017. Phylogenetic and temporal analyses were performed to identify prevalent genotypes and assess transmission patterns. RESULTS Analyses of S. Typhi isolates in Shenzhen revealed high genetic diversity, with genotypes 3.2.1 (37.8%) and 2.1.7 (20%) being most prevalent. Genotype 3.2.1 formed an independent lineage due to mutations in the quinolone resistance-determining region (QRDR). The multidrug-resistant haplotype 58 (genotype 4.3.1) has been present since 2006. S. Paratyphi A isolates were predominantly genotype 2.3.3 (98.5%). Pathogen exchange occurred with at least four other provinces. A cutoff of ≤3 single nucleotide polymorphisms (SNPs) was effective for outbreak investigation, and 22 genomic clusters were found, suggesting undetected outbreaks or transmission events. While 80% of isolates were susceptible to first-line antibiotics, 16.9% of S. Paratyphi A isolates were multidrug-resistant. CONCLUSIONS This study provides insights into the transmission dynamics of enteric fever in Shenzhen, underscoring the need for ongoing genomic surveillance to manage and control outbreaks effectively.
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Affiliation(s)
- Yixiang Jiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China.
| | - Min Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China.
| | - Xin Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Meiying Yan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Xiaolu Shi
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China.
| | - Qinghua Hu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China.
| | - Biao Kan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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217
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Yu K, Huang Z, Liu X, Gao H, Bai X, Sun Z, Wang D. The spread of CTX-M-type extended-spectrum beta-lactamases in China: Epidemiology and evolutionary analyses. J Infect 2025; 90:106457. [PMID: 40043815 DOI: 10.1016/j.jinf.2025.106457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2025] [Revised: 02/23/2025] [Accepted: 02/26/2025] [Indexed: 04/12/2025]
Abstract
CTX-M-type extended-spectrum beta-lactamases (ESBLs) have shown a high level of global transmission, with limited systematic understanding of their epidemic patterns in China. A comprehensive analysis covering 1974-2023 identified 133 (3.2%) blaCTX-Ms-producing strains among 4146 strains from 25 Chinese cities across 82 genera were performed. Integrating with public database strains (n=431), the study comprised 564 blaCTX-Ms-positive isolates sourced from 19 provinces (1986-2022) including 300 (53.2%) clinical and 228 (40.4%) environmental blaCTX-Ms. The most frequent sources of infection were diarrhea (44%), upper respiratory tract infection (22.2%) and urinary tract infection (14%). Phylogenetic studies indicated CTX-M-1 and CTX-M-9 emerged as the predominant subgroups. Lineages exhibited diverse mutation sites without being restricted by geographical conditions. Ka/Ks ratio distribution varied significantly among lineages (P<0.05). Lineages 1 (L1) and L2 were characterized by neutral or purifying selection, whereas L3 was mainly under purifying selection. Adaptive evolution was noted at different loci within each lineage. The influence of geographic distance on phylogeny varied distinctly across different lineages. Notably, for Lineage L3, there was a remarkably strong correlation observed, which implies that human activities exerted a more substantial influence on genetic distances compared to geography. This research provides valuable insights into the epidemiology, genotypic diversity, and evolutionary traits of blaCTX-Ms in China, supporting health risk assessment for early warning systems.
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Affiliation(s)
- Keyi Yu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310005, China
| | - Zhenzhou Huang
- Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Hangzhou, Zhejiang 310021, China
| | - Xiao Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, 102206, China
| | - He Gao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, 102206, China
| | - Xuemei Bai
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, 102206, China
| | - Zhiwen Sun
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, 102206, China
| | - Duochun Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, 102206, China.
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218
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Bargheet A, Noordzij HT, Ponsero AJ, Jian C, Korpela K, Valles-Colomer M, Debelius J, Kurilshikov A, Pettersen VK. Dynamics of gut resistome and mobilome in early life: a meta-analysis. EBioMedicine 2025; 114:105630. [PMID: 40048849 PMCID: PMC11929092 DOI: 10.1016/j.ebiom.2025.105630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 02/13/2025] [Accepted: 02/19/2025] [Indexed: 03/25/2025] Open
Abstract
BACKGROUND The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut. METHODS We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers. FINDINGS We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E. coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults. INTERPRETATION Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow. FUNDING Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Tromsø Research Foundation, Norway.
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Affiliation(s)
- Ahmed Bargheet
- Host-Microbe Interaction Research Group, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway; Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Hanna Theodora Noordzij
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Alise J Ponsero
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Finland
| | - Ching Jian
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Finland
| | - Katri Korpela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Finland
| | - Mireia Valles-Colomer
- Department of Medical and Life Sciences, Pompeu Fabra University, Barcelona, Spain; Department CIBIO, University of Trento, Italy
| | - Justine Debelius
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Veronika Kuchařová Pettersen
- Host-Microbe Interaction Research Group, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway; Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway.
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Dziurzyński M, Nowak ME, Furman M, Okrasińska A, Pawłowska J, Fondi M. Insights into optimization of oleaginous fungi - genome-scale metabolic reconstruction and analysis of Umbelopsis sp. WA50703. Comput Struct Biotechnol J 2025; 27:1431-1439. [PMID: 40242294 PMCID: PMC12002602 DOI: 10.1016/j.csbj.2025.03.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 04/18/2025] Open
Abstract
Oleaginous fungi-known for their high lipid content of up to 80 % of dry mass-are of significant interest for biotechnological applications, particularly in biofuel and fatty acid production. Among these, the genus Umbelopsis, a common soil saprotroph of the Mucoromycota phylum, stands out for its rapid growth, low nutritional requirements, and ability to produce substantial amounts of lipids, especially polyunsaturated fatty acids (PUFAs). Despite previous studies on lipid production in Umbelopsis, metabolic engineering has been underexplored. This study fills that gap by presenting the first comprehensive metabolic model for Umbelopsis sp. WA50703, encompassing 2418 metabolites, 2215 reactions, and 1627 genes (iUmbe1). The model demonstrated a strong predictive accuracy correctly predicting metabolic capabilities in 81.05 % of cases when evaluated against experimental data. The Flux Scanning based on Enforced Objective Flux (FSEOF) algorithm was utilized to identify gene targets for enhancing lipid production. This analysis revealed 33 genes associated with 23 metabolic reactions relevant to lipid biosynthesis. Notably, the reactions catalysed by acetyl-CoA carboxylase and carbonic anhydrase emerged as prime candidates for up-regulation. These findings provide clear guidelines for future metabolic engineering efforts to optimize PUFA production in Umbelopsis strains.
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Affiliation(s)
- Mikołaj Dziurzyński
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, FI 50019, Italy
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Maksymilian E. Nowak
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Maria Furman
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Alicja Okrasińska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Julia Pawłowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, FI 50019, Italy
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220
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Gao W, Wang S, Jiang T, Hu H, Gao R, Zhou M, Wang G. Chromosome-scale and haplotype-resolved genome assembly of Populus trichocarpa. HORTICULTURE RESEARCH 2025; 12:uhaf012. [PMID: 40093378 PMCID: PMC11908830 DOI: 10.1093/hr/uhaf012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 01/05/2025] [Indexed: 03/19/2025]
Abstract
Populus trichocarpa, a pivotal model organism for woody transgenic research, not only garners substantial scientific interest but plays an integral role in forestry economics. Previous genomic assemblies of P. trichocarpa predominantly treated its heterozygous genome as homozygous, thereby neglecting crucial haplotypic diversity. Leveraging the high-fidelity (HiFi) sequencing capabilities of PacBio sequencing and the chromosome conformation capture insights provided by Illumina's Hi-C technique, this study is the first to achieve a near telomere-to-telomere assembly of both paternal and maternal haplotypes in P. trichocarpa. Comparative genomic analysis between these haplotypes has uncovered several allelic variants and pathways critical for trait determination through allele-specific expression. Furthermore, utilizing RNA-seq data from multiple tissues, this investigation has detailed the tissue-specific expression patterns of the leucine-rich repeat gene family, which are essential in mediating plant signal transduction and developmental regulation. Our results not only illuminate the functional genomics landscape of P. trichocarpa but also provide invaluable theoretical underpinnings for the genetic improvement of woody plants and a robust framework for exploring genetic variability and allelic expression disparities in arboreal species.
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Affiliation(s)
- Wentao Gao
- College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Sui Wang
- National Key Laboratory of Smart Farm Technologies and Systems, Northeast Agricultural University, Harbin, Heilongjiang 150038, China
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang 150038, China
| | - Tao Jiang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Heng Hu
- College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Runtian Gao
- College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Murong Zhou
- College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Guohua Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, Heilongjiang 150040, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
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221
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Brangsch H, Marcordes S, Busch A, Weber M, Wolf SA, Semmler T, Höper D, Calvelage S, Linde J, Barth SA. Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs. PLoS One 2025; 20:e0320499. [PMID: 40168336 PMCID: PMC11960956 DOI: 10.1371/journal.pone.0320499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 02/20/2025] [Indexed: 04/03/2025] Open
Abstract
Within a group of three captive lowland tapirs (Tapirus terrestris) suffering from clinically apparent mycobacteriosis, non-tuberculous Mycobacterium avium subsp. hominissuis (MAH) strains were isolated from the animals and the tapir's enclosure. Based on MIRU-VNTR findings, which identified two closely related INMV profiles (124 and 246), a micro-evolutionary event was assumed, and four available MAH strains were submitted to whole genome sequencing (short- and long-read technologies). Surprisingly, the differences based on single nucleotide polymorphisms (SNPs) were exceptionally high between the four strains, i.e., between 841 and 11,166 bases, due to a strong impact of homologous recombination. Thus, an ad hoc core genome multilocus sequence typing (cgMLST) scheme was created and pangenome analysis was conducted for determining the genomic similarity between the strains. The INMV246 isolate obtained from sputum on the enclosure floor and one INMV124 isolate of tapir #2 showed the highest congruence, suggesting that both originated from a shared source. The other two INMV124 isolates were genomically distinct from these strains. Nevertheless, in all four strains two plasmids were detected, which were highly conserved between the strains. The study showed that the genomic variability between MAH strains isolated from the same site within a short period of time can be exceptionally high and the influence of homologous recombination needs to be considered when determining MAH strain relationships, particularly via SNP analyses.
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Affiliation(s)
- Hanka Brangsch
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Sandra Marcordes
- Department of Veterinary Medicine, Cologne Zoo, Cologne, Germany
| | - Anne Busch
- Theoretical Microbial Ecology, Friedrich-Schiller-University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena, Germany
| | - Michael Weber
- Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health (FLI), Institute of Molecular Pathogenesis, National Reference Laboratory for Bovine Tuberculosis, Jena, Germany
| | - Silver A. Wolf
- Robert Koch Institute, Genome Competence Centre (MF1), Berlin, Germany
| | - Torsten Semmler
- Robert Koch Institute, Genome Competence Centre (MF1), Berlin, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health (FLI), Institute of Diagnostic Virology, Greifswald - Isle of Riems, Germany
| | - Sten Calvelage
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health (FLI), Institute of Diagnostic Virology, Greifswald - Isle of Riems, Germany
| | - Jörg Linde
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Stefanie A. Barth
- Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health (FLI), Institute of Molecular Pathogenesis, National Reference Laboratory for Bovine Tuberculosis, Jena, Germany
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222
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Fernández-Palacios P, Vela-Fernández R, Capote FJ, Jurado-Tarifa E, Rodríguez-Iglesias MA, Galán-Sánchez F. Corynebacterium nuruki: A novel pathogen in human catheter-related bacteremia. New Microbes New Infect 2025; 64:101574. [PMID: 40129855 PMCID: PMC11930726 DOI: 10.1016/j.nmni.2025.101574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 02/25/2025] [Accepted: 03/03/2025] [Indexed: 03/26/2025] Open
Abstract
A 72-year-old with lymphoma developed catheter-related bacteremia caused by Corynebacterium nuruki, a microorganism previously unlinked to human infections. Diagnosis included MALDI-TOF and genomic sequencing. Bacteremia was treated with vancomycin and the catheter was replaced. This case introduces C. nuruki as a potential pathogen in immunocompromised patients.
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Affiliation(s)
| | | | | | - Estefanía Jurado-Tarifa
- Instituto de Investigación e Innovación Biomédica de Cádiz (INIBICA), Hospital Universitario Puerta del Mar, Cádiz, Spain
| | - Manuel A. Rodríguez-Iglesias
- Servicio de Microbiología, Hospital Universitario Puerta del Mar, Cádiz, Spain
- Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Cádiz, Spain
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223
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Zhu X, Huang Y, Shi Y, Gao X, Chen D, Liu C, Cao S, Xue X, Li Y. Comparative genomic analysis of food-animal-derived and human-derived Clostridium perfringens isolates from markets in Shandong, China. Front Microbiol 2025; 16:1543511. [PMID: 40236475 PMCID: PMC11996926 DOI: 10.3389/fmicb.2025.1543511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2024] [Accepted: 03/05/2025] [Indexed: 04/17/2025] Open
Abstract
Clostridium perfringens (C. perfringens) is a foodborne pathogen that poses a significant threat to both animal husbandry and public health. In this study, 27 C. perfringens strains were isolated from animal samples and animal-derived food products. Antibiotics resistances among the isolates were phenotypically and genotypically analyzed and Whole genome sequencing (WGS). In combination with the genomes of 141 human-derived C. perfringens strains from public databases, this study conducted comprehensive analyses of antibiotic resistance genes, virulence genes, multilocus sequence typing (MLST), prophage detection, and pan-genome analysis for a total of 168 strains of C. perfringens. Antibiotics resistances among the isolates were phenotypically and genotypically analyzed and found 24 of them (88.9%, 24/27) were identified as multidrug-resistant (MDR). WGS analysis revealed that 13 strains belonged to known sequence types (ST), and the remaining strains represented 10 new STs. By analysis in combination with data of 141 C. perfringens isolates from the database, it was implied that ST221, ST72 and ST370 were present in both animal-derived and human-derived C. perfringens. It is worth noting that 108 out of 168 strains of C. perfringens (64.3%, 108/168) were found to carry prophages, which were found more prevalent in human-derived C. perfringens isolates. Pan-genome and phylogenetic analysis of 168 C. perfringens strains indicated that C. perfringens possesses an open pan-genome with genetic diversity. This study provides genomic insights into C. perfringens from food animals and humans, shedding light on the importance for monitoring the C. perfringens in livestock in China for better public health.
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Affiliation(s)
- Xinyang Zhu
- College of Agriculture and Biology, Liaocheng University, Liaocheng, Shandong, China
| | - Yucui Huang
- College of Agriculture and Biology, Liaocheng University, Liaocheng, Shandong, China
| | - Yuxia Shi
- College of Agriculture and Biology, Liaocheng University, Liaocheng, Shandong, China
| | - Xiaojie Gao
- College of Agriculture and Biology, Liaocheng University, Liaocheng, Shandong, China
| | - Duanduan Chen
- College of Agriculture and Biology, Liaocheng University, Liaocheng, Shandong, China
| | - Cheng Liu
- College of Agriculture and Biology, Liaocheng University, Liaocheng, Shandong, China
| | - Shengliang Cao
- College of Agriculture and Biology, Liaocheng University, Liaocheng, Shandong, China
| | - Xijuan Xue
- Shandong Sinder Technology Co., Ltd., Weifang, Shandong, China
| | - Yubao Li
- School of Pharmaceutical Sciences and Food Engineering, Liaocheng University, Liaocheng, Shandong, China
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224
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Frias-De-Diego A, Jara M, Lanzas C. Influence of Sequencing Technology on Pangenome-Level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens. Open Forum Infect Dis 2025; 12:ofaf183. [PMID: 40212029 PMCID: PMC11983279 DOI: 10.1093/ofid/ofaf183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2025] [Accepted: 03/24/2025] [Indexed: 04/13/2025] Open
Abstract
As sequencing costs decrease, short-read and long-read technologies are indispensable tools for uncovering the genetic drivers behind bacterial pathogen resistance. This study explores the differences between the use of short-read (Illumina) and long-read (Oxford Nanopore Technologies [ONT]) sequencing in detecting antimicrobial resistance (AMR) genes in ESKAPE pathogens (ie, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae). Utilizing a dataset of 1385 whole genome sequences and applying commonly used bioinformatic methods in bacterial genomics, we assessed the differences in genomic completeness, pangenome structure, and AMR gene and point mutation identification. Illumina presented higher genome completeness, while ONT identified a broader pangenome. Hybrid assembly outperformed both Illumina and ONT at identifying key AMR genetic determinants, presented results closer to Illumina's completeness, and revealed ONT-like pangenomic content. Notably, Illumina consistently detected more AMR-related point mutations than its counterparts. This highlights the importance of method selection based on research goals, particularly when using publicly available data ranging a wide timespan. Differences were also observed for specific gene classes and bacterial species, underscoring the need for a nuanced understanding of technology limitations. Overall, this study reveals the strengths and limitations of each approach, advocating for the use of Illumina for common AMR analysis, ONT for studying complex genomes and novel species, and hybrid assembly for a more comprehensive characterization, leveraging the benefits of both technologies.
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Affiliation(s)
- Alba Frias-De-Diego
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Manuel Jara
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Cristina Lanzas
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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225
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Ariute JC, Coelho-Rocha ND, Dantas CWD, de Vasconcelos LAT, Profeta R, de Jesus Sousa T, de Souza Novaes A, Galotti B, Gomes LG, Gimenez EGT, Diniz C, Dias MV, de Jesus LCL, Jaiswal AK, Tiwari S, Carvalho R, Benko-Iseppon AM, Brenig B, Azevedo V, Barh D, Martins FS, Aburjaile F. Probiogenomics of Leuconostoc Mesenteroides Strains F-21 and F-22 Isolated from Human Breast Milk Reveal Beneficial Properties. Probiotics Antimicrob Proteins 2025; 17:500-515. [PMID: 37804433 DOI: 10.1007/s12602-023-10170-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
Abstract
Bacteria of the Leuconostoc genus are Gram-positive bacteria that are commonly found in raw milk and persist in fermented dairy products and plant food. Studies have already explored the probiotic potential of L. mesenteroides, but not from a probiogenomic perspective, which aims to explore the molecular features responsible for their phenotypes. In the present work, probiogenomic approaches were applied in strains F-21 and F-22 of L. mesenteroides isolated from human milk to assess their biosafety at the molecular level and to correlate molecular features with their potential probiotic characteristics. The complete genome of strain F-22 is 1.99 Mb and presents one plasmid, while the draft genome of strain F-21 is 1.89 Mb and presents four plasmids. A high percentage of average nucleotide identity among other genomes of L. mesenteroides (≥ 96%) corroborated the previous taxonomic classification of these isolates. Genomic regions that influence the probiotic properties were identified and annotated. Both strains exhibited wide genome plasticity, cell adhesion ability, proteolytic activity, proinflammatory and immunomodulation capacity through interaction with TLR-NF-κB and TLR-MAPK pathway components, and no antimicrobial resistance, denoting their potential to be candidate probiotics. Further, the strains showed bacteriocin production potential and the presence of acid, thermal, osmotic, and bile salt resistance genes, indicating their ability to survive under gastrointestinal stress. Taken together, our results suggest that L. mesenteroides F-21 and F-22 are promising candidates for probiotics in the food and pharmaceutical industries.
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Affiliation(s)
- Juan Carlos Ariute
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Nina Dias Coelho-Rocha
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Carlos Willian Dias Dantas
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Larissa Amorim Tourinho de Vasconcelos
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Rodrigo Profeta
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Thiago de Jesus Sousa
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Ane de Souza Novaes
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Bruno Galotti
- Laboratory of Biotherapeutic Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Lucas Gabriel Gomes
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Enrico Giovanelli Toccani Gimenez
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Carlos Diniz
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Mariana Vieira Dias
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Luís Cláudio Lima de Jesus
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Arun Kumar Jaiswal
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Sandeep Tiwari
- Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, 40231-300, Brazil
| | - Rodrigo Carvalho
- Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, 40231-300, Brazil
| | - Ana Maria Benko-Iseppon
- Laboratory of Plants Genetics and Biotechnology, Genetics Department, Biosciences Center, Federal University of Pernambuco, Recife, Pernambuco, 50740-600, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, 721172, India
| | - Flaviano S Martins
- Laboratory of Biotherapeutic Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Flavia Aburjaile
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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226
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Chu C, Li D, Gu L, Yang S, Liu C. Evidence for the Existence of Mating Subtypes Within the Schizophyllum commune: Mating Behavior and Genetic Divergence. J Fungi (Basel) 2025; 11:277. [PMID: 40278098 PMCID: PMC12028200 DOI: 10.3390/jof11040277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 03/27/2025] [Accepted: 03/31/2025] [Indexed: 04/26/2025] Open
Abstract
Schizophyllum commune, a Basidiomycota fungus with a tetrapolar mating system, serves as a key model for studying sexual reproduction. In this study, two distinct mating subtypes (I and II) were identified in strain 20R-7-ZF01, isolated from subseafloor sediment, which exhibited eight different mating interaction phenotypes. Intra-subtypes exhibited colony-symmetric tetrapolar interactions (G1), whereas inter-subtype crosses yielded colony-asymmetric phenotypes (G2) and a reduced number of fruiting bodies. Nuclear migration analysis revealed that both subtypes follow the same sexual reproductive process, suggesting functional similarities despite the different reproductive outcomes. Gene silencing of mating-type loci identified the genes bbp2-9 and bbp2-7 within the B locus as key factors in determining mating subtype identity. Additionally, a similar pattern of mating subtype differentiation was observed in five other S. commune strains from both subseafloor and terrestrial environments. These findings highlight the genetic diversity within S. commune, challenge the classical understanding of fungal mating systems, and provide new insights into the genetic evolutionary mechanisms governing fungi with tetrapolar mating systems.
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Affiliation(s)
| | | | | | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; (C.C.); (D.L.); (L.G.)
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; (C.C.); (D.L.); (L.G.)
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227
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Caron T, Crequer E, Le Piver M, Le Prieur S, Brunel S, Snirc A, Cueff G, Roueyre D, Place M, Chassard C, Simon A, de la Vega RCR, Coton M, Coton E, Foulongne-Oriol M, Branca A, Giraud T. Identification of quantitative trait loci (QTLs) for key cheese making phenotypes in the blue-cheese mold Penicillium roqueforti. PLoS Genet 2025; 21:e1011669. [PMID: 40233118 PMCID: PMC12047768 DOI: 10.1371/journal.pgen.1011669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/02/2025] [Accepted: 03/28/2025] [Indexed: 04/17/2025] Open
Abstract
Elucidating the genomic architecture of quantitative traits is essential for our understanding of adaptation and for breeding in domesticated organisms. Penicillium roqueforti is the mold used worldwide for the blue cheese maturation, contributing to flavors through proteolytic and lipolytic activities. The two domesticated cheese populations display very little genetic diversity, but are differentiated and carry opposite mating types. We produced haploid F1 progenies from five crosses, using parents belonging to cheese and non-cheese populations. Analyses of high-quality genome assemblies of the parental strains revealed five large translocations, two having occurred via a circular intermediate, one with footprints of Starship giant mobile elements. Offspring genotyping with genotype-by-sequencing (GBS) revealed several genomic regions with segregation distortion, possibly linked to degeneration in cheese lineages. We found transgressions for several traits relevant for cheese making, with offspring having more extreme trait values than parental strains. We identified quantitative trait loci (QTLs) for colony color, lipolysis, proteolysis, extrolite production, including mycotoxins, but not for growth rates. Some genomic regions appeared rich in QTLs for both lipid and protein metabolism, and other regions for the production of multiple extrolites, indicating that QTLs have pleiotropic effects. Some QTLs corresponded to known biosynthetic gene clusters, e.g., for the production of melanin or extrolites. F1 hybrids constitute valuable strains for cheese producers, with new traits and new allelic combinations, and allowed identifying target genomic regions for traits important in cheese making, paving the way for strain improvement. The findings further contribute to our understanding of the genetic mechanisms underlying rapid adaptation, revealing convergent adaptation targeting major gene regulators.
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Affiliation(s)
- Thibault Caron
- Ecologie Systématique Evolution, IDEEV, Gif-sur-Yvette, France
- Laboratoire Interprofessionnel de Production—SAS L.I.P., Aurillac, France
| | - Ewen Crequer
- Ecologie Systématique Evolution, IDEEV, Gif-sur-Yvette, France
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production—SAS L.I.P., Aurillac, France
| | | | - Sammy Brunel
- Laboratoire Interprofessionnel de Production—SAS L.I.P., Aurillac, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, IDEEV, Gif-sur-Yvette, France
| | - Gwennina Cueff
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production—SAS L.I.P., Aurillac, France
| | - Michel Place
- Laboratoire Interprofessionnel de Production—SAS L.I.P., Aurillac, France
| | | | | | | | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Emmanuel Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | | | - Antoine Branca
- Ecologie Systématique Evolution, IDEEV, Gif-sur-Yvette, France
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, Gif-sur-Yvette, France
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Harrigian F, LeBlanc N, Eriksen RL, Bush E, Salamanca LR, Salgado-Salazar C. Uncovering the Fungus Responsible for Stem and Root Rot of False Indigo: Pathogen Identification, New Disease Description, and Genome Analyses. PLANT DISEASE 2025; 109:921-930. [PMID: 39504142 DOI: 10.1094/pdis-07-24-1396-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2024]
Abstract
Calonectria spp. can cause destructive diseases on forestry crops, legumes like soybean and peanut, and ornamentals. Species of Calonectria affecting ornamental plants are not well characterized or understood, although they have been widely documented as an issue in the ornamental industry. This research focused on the molecular identification, pathogenicity validation, and genome analysis of a Calonectria sp. isolate recovered from ornamental blue false indigo (Baptisia australis) plants showing disease symptoms of crown and root rot in a commercial nursery in Virginia. The fungus on B. australis was identified as C. fujianensis (Nectriaceae, Hypocreales), a member of the C. colhounii species complex, using multilocus sequencing. Pathogenicity tests were fulfilled by inoculating C. fujianensis conidia on B. australis seedlings, confirming a causal relationship between this pathogen and the disease symptoms observed. A 62.7 Mb high-quality hybrid genome assembly generated using Illumina and Nanopore data was obtained, contained in 16 contigs, 4 of which were complete chromosomes. A total of 750 effectors were found in the genome, similar to cutinase and pectinase virulence factors described from other Calonectria species' genomes. Characterization of this novel disease of B. australis advances our understanding of Calonectria as an important but poorly studied group of plant pathogens.
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Affiliation(s)
- Fiona Harrigian
- Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Salinas, CA 93905, U.S.A
| | - Nicholas LeBlanc
- Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Salinas, CA 93905, U.S.A
| | - Renée L Eriksen
- Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Salinas, CA 93905, U.S.A
| | - Elizabeth Bush
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | | | - Catalina Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, U.S.A
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Laufer Halpin A, Mathers AJ, Walsh TR, Zingg W, Okeke IN, McDonald LC, Elkins CA, Harbarth S, Peacock SJ, Srinivasan A, Bell M, Pittet D, Cardo D. A framework towards implementation of sequencing for antimicrobial-resistant and other health-care-associated pathogens. THE LANCET. INFECTIOUS DISEASES 2025; 25:e235-e244. [PMID: 39832513 DOI: 10.1016/s1473-3099(24)00729-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 10/09/2024] [Accepted: 10/22/2024] [Indexed: 01/22/2025]
Abstract
Antimicrobial resistance continues to be a growing threat globally, specifically in health-care settings in which antimicrobial-resistant pathogens cause a substantial proportion of health-care-associated infections (HAIs). Next-generation sequencing (NGS) and the analysis of the data produced therein (ie, bioinformatics) represent an opportunity to enhance our capacity to address these threats. The 3rd Geneva Infection Prevention and Control Think Tank brought together experts to identify gaps, propose solutions, and set priorities for the use of NGS for HAIs and antimicrobial-resistant pathogens. The major deliverable recommendation from this meeting was a proposed framework for implementing the sequencing of HAI pathogens, specifically those harbouring antimicrobial-resistance mechanisms. The key components of the proposed framework relate to wet laboratory quality, sequence data quality, database and tool selection, bioinformatic analyses, data sharing, and NGS data integration, to support public health and actions for infection prevention and control. In this Personal View we detail and discuss the framework in the context of global implementation, specifically in low-income and middle-income countries.
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Affiliation(s)
- Alison Laufer Halpin
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA; US Public Health Service, Rockville, MD, USA.
| | | | - Timothy R Walsh
- Department of Zoology, Ineos Oxford Institute for Antimicrobial Resistance, Oxford, UK
| | - Walter Zingg
- Division of Infectious Diseases and Hospital Hygiene, Universitätsspital Zürich, Zürich, Switzerland
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria
| | - L Clifford McDonald
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christopher A Elkins
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Sharon J Peacock
- Cambridge Biomedical Campus, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Arjun Srinivasan
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael Bell
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Didier Pittet
- Hôpitaux Universitaires de Genève, Geneva, Switzerland
| | - Denise Cardo
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
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230
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Pipponzi S, Primisser S, Antonielli L, Stefani E, Compant S, Sessitsch A, Kostic T. Lettuce fortification through vitamin B 12-producing bacteria - proof of concept study. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2025; 105:3343-3354. [PMID: 39831556 PMCID: PMC11949862 DOI: 10.1002/jsfa.14095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 10/02/2024] [Accepted: 12/09/2024] [Indexed: 01/22/2025]
Abstract
BACKGROUND Vitamin B12 (cobalamin) can be produced de novo only by certain bacteria and archaea. It plays a crucial role in the health of animals and humans, which obtain it only through diet, mainly from animal products. This study aimed to identify endophytic bacterial strains capable of synthesizing vitamin B12 and enriching edible plants with it as a potential solution for vitamin B12 deficiency in vegetarians, vegans, and people with poor diets. RESULTS An in silico genome analysis was performed on 66 bacterial genomes, including the reference strain Pseudomonas denitrificans ATCC 13867, a known vitamin B12 producer. The genomes were analyzed using the Rapid Annotations using Subsystems Technology (RAST) server and the MetaCyc database to verify the presence and completeness of the vitamin B12 metabolic pathway. The ability of the strains to produce vitamin B12 was confirmed with a high-performance liquid chromatography with diode-array detection (HPLC-DAD) analysis of pure culture extracts. Eleven strains produced detectable amounts of vitamin B12 under tested conditions. The best performing candidates were further tested for their efficacy in producing vitamin B12 in lettuce grown under sterile conditions on Murashige and Skoog (MS) medium with or without CoCl2 supplementation. Methylobacterium sp. strain P1-11 produced detectable amounts of vitamin B12 in planta: 1.654 and 2.559 μg per g of dry weight without and with CoCl2 supplementation, respectively. CONCLUSION This is the first time a bacterial endophyte was used to produce vitamin B12 in planta, suggesting that bacterial endophytes could be utilized to enhance the nutraceutical values of plant-based foods. © 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Sara Pipponzi
- Department of Life SciencesUniversity of Modena and Reggio EmiliaReggio EmiliaItaly
- Center for Health & Bioresources, Bioresources UnitAIT Austrian Institute of TechnologyTullnAustria
| | - Stefanie Primisser
- Center for Health & Bioresources, Bioresources UnitAIT Austrian Institute of TechnologyTullnAustria
- Present address:
Institute for Plant HealthLaimburg Research CentreLaimburg 6Auer (Ora)39040South TyrolItaly
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources UnitAIT Austrian Institute of TechnologyTullnAustria
| | - Emilio Stefani
- Department of Life SciencesUniversity of Modena and Reggio EmiliaReggio EmiliaItaly
| | - Stephane Compant
- Center for Health & Bioresources, Bioresources UnitAIT Austrian Institute of TechnologyTullnAustria
| | - Angela Sessitsch
- Center for Health & Bioresources, Bioresources UnitAIT Austrian Institute of TechnologyTullnAustria
| | - Tanja Kostic
- Center for Health & Bioresources, Bioresources UnitAIT Austrian Institute of TechnologyTullnAustria
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Nothdurfter S, Linde J, Sting R, Tomaso H, Heuner K, Meincke M, Brockmann SO, Wagner-Wiening C. Epidemiology of Tularemia among Humans and Animals, Baden-Wuerttemberg, Germany, 2012-2022. Emerg Infect Dis 2025; 31:678-688. [PMID: 40133006 PMCID: PMC11950275 DOI: 10.3201/eid3104.240414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2025] Open
Abstract
Tularemia, a zoonosis caused by Francisella tularensis, is endemic in Baden-Wuerttemberg, Germany. To determine tularemia epidemiology in this region, we characterized the genetic diversity of F. tularensis in human and animal isolates during 2012-2022 by using whole-genome sequencing, combined with human and veterinary surveillance data analysis. Human case numbers varied; most cases occurred in 2021 (n = 34). Arthropod bites were reported most in cases with information on animal exposure (45%, n = 43). Poisson regression confirmed a significant increase in human cases during the study period (p<0.001). No seasonal pattern was identified, but case numbers were lowest in winter. Human surveillance data often lacked exposure details. Positivity rates in animals were 5%-34%, increasing since 2017. Human isolates often clustered with hare-derived strains, although transmission routes often remain unclear. These findings emphasize the importance of combining genome sequencing with detailed epidemiologic tracing to identify infection sources and improve surveillance data.
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Affiliation(s)
| | | | - Reinhard Sting
- ECDC Fellowship Programme, Field Epidemiology Path, European Centre for Disease Prevention and Control, Stockholm, Sweden (S. Nothdurfter); Baden-Wuerttemberg State Health Office, Ministry of Social Affairs, Health and Integration, Stuttgart, Germany (S. Nothdurfter, M. Meincke, S.O. Brockmann, C. Wagner-Wiening); Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany (J. Linde, H. Tomaso); Chemical and Veterinary Analysis Agency Stuttgart, Fellbach, Germany (R. Sting); Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany (K. Heuner)
| | - Herbert Tomaso
- ECDC Fellowship Programme, Field Epidemiology Path, European Centre for Disease Prevention and Control, Stockholm, Sweden (S. Nothdurfter); Baden-Wuerttemberg State Health Office, Ministry of Social Affairs, Health and Integration, Stuttgart, Germany (S. Nothdurfter, M. Meincke, S.O. Brockmann, C. Wagner-Wiening); Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany (J. Linde, H. Tomaso); Chemical and Veterinary Analysis Agency Stuttgart, Fellbach, Germany (R. Sting); Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany (K. Heuner)
| | - Klaus Heuner
- ECDC Fellowship Programme, Field Epidemiology Path, European Centre for Disease Prevention and Control, Stockholm, Sweden (S. Nothdurfter); Baden-Wuerttemberg State Health Office, Ministry of Social Affairs, Health and Integration, Stuttgart, Germany (S. Nothdurfter, M. Meincke, S.O. Brockmann, C. Wagner-Wiening); Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany (J. Linde, H. Tomaso); Chemical and Veterinary Analysis Agency Stuttgart, Fellbach, Germany (R. Sting); Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany (K. Heuner)
| | - Maylin Meincke
- ECDC Fellowship Programme, Field Epidemiology Path, European Centre for Disease Prevention and Control, Stockholm, Sweden (S. Nothdurfter); Baden-Wuerttemberg State Health Office, Ministry of Social Affairs, Health and Integration, Stuttgart, Germany (S. Nothdurfter, M. Meincke, S.O. Brockmann, C. Wagner-Wiening); Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany (J. Linde, H. Tomaso); Chemical and Veterinary Analysis Agency Stuttgart, Fellbach, Germany (R. Sting); Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany (K. Heuner)
| | - Stefan O. Brockmann
- ECDC Fellowship Programme, Field Epidemiology Path, European Centre for Disease Prevention and Control, Stockholm, Sweden (S. Nothdurfter); Baden-Wuerttemberg State Health Office, Ministry of Social Affairs, Health and Integration, Stuttgart, Germany (S. Nothdurfter, M. Meincke, S.O. Brockmann, C. Wagner-Wiening); Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany (J. Linde, H. Tomaso); Chemical and Veterinary Analysis Agency Stuttgart, Fellbach, Germany (R. Sting); Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany (K. Heuner)
| | - Christiane Wagner-Wiening
- ECDC Fellowship Programme, Field Epidemiology Path, European Centre for Disease Prevention and Control, Stockholm, Sweden (S. Nothdurfter); Baden-Wuerttemberg State Health Office, Ministry of Social Affairs, Health and Integration, Stuttgart, Germany (S. Nothdurfter, M. Meincke, S.O. Brockmann, C. Wagner-Wiening); Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany (J. Linde, H. Tomaso); Chemical and Veterinary Analysis Agency Stuttgart, Fellbach, Germany (R. Sting); Highly Pathogenic Microorganisms (ZBS 2), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany (K. Heuner)
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232
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Dirks AC, Methven AS, Miller AN, Orozco-Quime M, Maurice S, Bonito G, Van Wyk J, Ahrendt S, Kuo A, Andreopoulos W, Riley R, Lipzen A, Chovatia M, Savage E, Barry K, Grigoriev IV, Bradshaw AJ, Martin FM, Arnold AE, James TY. Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota). Mol Phylogenet Evol 2025; 205:108286. [PMID: 39788220 DOI: 10.1016/j.ympev.2025.108286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 11/21/2024] [Accepted: 01/05/2025] [Indexed: 01/12/2025]
Abstract
Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.
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Affiliation(s)
- Alden C Dirks
- Department of Ecology and Evolutionary Biology and University of Michigan Herbarium, University of Michigan, Ann Arbor, MI 48109, USA.
| | | | - Andrew N Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
| | - Michelle Orozco-Quime
- Department of Ecology and Evolutionary Biology and University of Michigan Herbarium, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sundy Maurice
- Department of Biosciences, University of Oslo, Blindernveien 31 0316, Oslo, Norway
| | - Gregory Bonito
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Judson Van Wyk
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Steven Ahrendt
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - William Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mansi Chovatia
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alexander J Bradshaw
- Natural History Museum of Utah and School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Champenoux, France
| | - A Elizabeth Arnold
- Department of Ecology and Evolutionary Biology, Bio5 Institute, and Gilbertson Mycological Herbarium, University of Arizona, Tucson, AZ 85719, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology and University of Michigan Herbarium, University of Michigan, Ann Arbor, MI 48109, USA
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Arathi S, Samji A, Eashwarlal K, Gokulkrishnan S, Muthubhavani M, Yasini NP, Uma Maheswari G, Warrier RR. Transcriptome sequencing on different ages of Saraca asoca bark: Insights from tannin biosynthetic pathways and EST-SSR marker design. Fitoterapia 2025; 182:106459. [PMID: 40023231 DOI: 10.1016/j.fitote.2025.106459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 02/21/2025] [Accepted: 02/23/2025] [Indexed: 03/04/2025]
Abstract
The bark of Saraca asoca is extensively used for treating gynecological issues, primarily due to its tannin content. This study focused on transcriptome sequencing of young (BY; 0-6 years), middle-aged (BM; 6-12 years), and old (BO; >12 years) Ashoka barks. The de novo assembly produced 1,37,451 unigenes of 1,31,647,800 bp from BY, 1,16,825 unigenes of 1,15,283,571 bp from BM, and 81,825 unigenes of 68,553,092 bp from BO samples. These transcripts closely matched with Glycine max and Cajanus cajan. Transcriptome analysis identified key genes and enzymes in the tannin biosynthetic pathway, with higher levels of phenylpropanoid and flavonoid pathways observed in middle-aged samples, followed by young and old samples. Pathway enrichment analysis indicated that the Differentially Expressed Genes (DEGs) were predominantly in the biosynthetic pathways of flavonoids, isoflavonoids, anthocyanins, terpenoids, and isoquinoline alkaloids. The study also examined the up-regulated and down-regulated DEGs involved in tannin production across the different sample comparisons, revealing the flavonoid pathway to be the most regulated. Additionally, 9612, 8053, and 4659 simple sequence repeats (SSRs) were identified from BY, BM, and BO transcripts, respectively. Fourteen EST-SSR markers specific to tannins were designed and validated, with one found to be polymorphic. This research represents the first report on transcriptome sequencing and EST-SSR markers from various ages of Saraca asoca bark, providing a foundation for future genetic mapping and conservation efforts of this vulnerable species.
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Affiliation(s)
- S Arathi
- Institute of Forest Genetics and Tree Breeding (IFGTB), Coimbatore, 641 002, India
| | - Aghila Samji
- Institute of Forest Genetics and Tree Breeding (IFGTB), Coimbatore, 641 002, India
| | - Komal Eashwarlal
- Institute of Forest Genetics and Tree Breeding (IFGTB), Coimbatore, 641 002, India
| | - S Gokulkrishnan
- Institute of Forest Genetics and Tree Breeding (IFGTB), Coimbatore, 641 002, India
| | - M Muthubhavani
- Institute of Forest Genetics and Tree Breeding (IFGTB), Coimbatore, 641 002, India
| | - N P Yasini
- Department of Biochemistry, CMS College of Science and Commerce, Coimbatore, India
| | - G Uma Maheswari
- Department of Biotechnology, Jeppiaar Engineering College, Chennai, India
| | - Rekha R Warrier
- Institute of Forest Genetics and Tree Breeding (IFGTB), Coimbatore, 641 002, India.
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234
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Nilsen HK, Olsen AB, Birkbeck TH, Manji F, Colquhoun DJ, Gulla S. Reclassification of Pasteurella skyensis as Phocoenobacter skyensis comb. nov. and description of Phocoenobacter atlanticus sp. nov. isolated from diseased Atlantic salmon ( Salmo salar) and lumpfish ( Cyclopterus lumpus), with subdivision into Phocoenobacter atlanticus subspecies atlanticus subsp. nov. and Phocoenobacter atlanticus subspecies cyclopteri subsp. nov. Int J Syst Evol Microbiol 2025; 75. [PMID: 40202776 DOI: 10.1099/ijsem.0.006729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2025] Open
Abstract
Gram-negative bacteria, similar in 16S rRNA gene sequence to Pasteurella skyensis, have been irregularly cultured from diseased Atlantic salmon (Salmo salar) sea-farmed in Norway since the 1980s and more commonly in later years from diseased lumpfish (Cyclopterus lumpus) farmed in the northeast Atlantic area. Phenotypic and genetic analyses confirmed that the majority of Norwegian isolates in the present study, cultured from both salmon and lumpfish, are closely related to, yet distinct from, P. skyensis and represent a hitherto undescribed species. We further argue, based on genetic similarity levels, that the original placement of P. skyensis within Pasteurella was erroneous and that this species belongs within Phocoenobacter, as Phocoenobacter skyensis comb. nov. Accordingly, we propose the name Phocoenobacter atlanticus sp. nov. for the new species characterized here. Furthermore, this species separates into two genetically and phenotypically distinct lineages, respectively, associated with Atlantic salmon and lumpfish, and for which we propose the names Ph. atlanticus subsp. atlanticus subsp. nov. and Ph. atlanticus subsp. cyclopteri subsp. nov., respectively. The type strain for Ph. atlanticus subsp. atlanticus subsp. nov. is strain NVIB3624T (NCIMB 15512T, CCUG 77520T), and the type strain for Ph. atlanticus subsp. cyclopteri subsp. nov. is strain NVIO9100T (NCIMB 15511T, CCUG 77521T).
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Affiliation(s)
- Hanne K Nilsen
- Section of Aquatic Biosecurity Research, Norwegian Veterinary Institute, Bergen, Norway
| | - Anne Berit Olsen
- Section of Aquatic Biosecurity Research, Norwegian Veterinary Institute, Bergen, Norway
| | - Thomas H Birkbeck
- Division of Infection and Immunity, University of Glasgow, Glasgow, Scotland, UK
| | | | | | - Snorre Gulla
- Fish Health Research Group, Norwegian Veterinary Institute, Ås, Norway
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Iranzadeh A, Alisoltani A, Kiran AM, Breiman RF, Chaguza C, Peno C, Cornick JE, Everett DB, Mulder N. Comparative pangenomics of Streptococcus pneumoniae from Malawi: uncovering genetic variability and pathogenicity. Microb Genom 2025; 11. [PMID: 40232949 DOI: 10.1099/mgen.0.001370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2025] Open
Abstract
Streptococcus pneumoniae is a significant cause of bacterial infections, including pneumonia, meningitis and septicemia, primarily affecting children, the elderly and immunocompromised individuals. This study aimed to elucidate the serotype and lineage distribution and molecular mechanisms underlying pneumococcal invasiveness through a comprehensive pangenomic analysis of 1416 isolates from Malawi. Our analysis comprised 810 isolates from asymptomatic carriers and 606 isolates from patients with bacteraemia or meningitis. We identified 58 serotypes, with serotypes 1, 5 and 12F exhibiting significantly higher prevalence among patients. These serotypes likely exhibit reduced nasopharyngeal colonization and demonstrate rapid dissemination to sterile sites. Notably, these serotypes form a distinct lineage with distinct genomic characteristics, including the absence of V-type ATP synthase. The pangenome analysis revealed two highly conserved surface protein complexes, F-type ATP synthase and SecA1-SecY, which deserve further investigation as potential targets for novel therapeutic interventions.
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Affiliation(s)
- Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Western Cape, South Africa
| | - Arghavan Alisoltani
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Anmol M Kiran
- Malawi-Liverpool-Wellcome Trust, Queen Elizabeth Central Hospital, College of Medicine, Blantyre, Malawi
- Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Chikondi Peno
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Malawi-Liverpool-Wellcome Trust, Queen Elizabeth Central Hospital, College of Medicine, Blantyre, Malawi
- Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jennifer E Cornick
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust, Queen Elizabeth Central Hospital, College of Medicine, Blantyre, Malawi
| | - Dean B Everett
- Department of Public Health and Epidemiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
- Infection Research Unit, Khalifa University, Abu Dhabi, UAE
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Western Cape, South Africa
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Oberti H, Sessa L, Oliveira-Rizzo C, Di Paolo A, Sanchez-Vallet A, Seidl MF, Abreo E. Novel genomic features in entomopathogenic fungus Beauveria bassiana ILB308: accessory genomic regions and putative virulence genes involved in the infection process of soybean pest Piezodorus guildinii. PEST MANAGEMENT SCIENCE 2025; 81:2323-2336. [PMID: 39797536 DOI: 10.1002/ps.8631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 12/12/2024] [Accepted: 12/16/2024] [Indexed: 01/13/2025]
Abstract
BACKGROUND Biological control methods involving entomopathogenic fungi like Beauveria bassiana have been shown to be a valuable approach in integrated pest management as an environmentally friendly alternative to control pests and pathogens. Identifying genetic determinants of pathogenicity in B. bassiana is instrumental for enhancing its virulence against insects like the resistant soybean pest Piezodorus guildinii. This study focused on comparative genomics of different B. bassiana strains and gene expression analyses to identify virulence genes in the hypervirulent strain ILB308, especially in response to infection of P. guildinii and growth on hydrocarbon HC15, a known virulence enhancer. RESULTS Strain ILB308 showed the highest number of virulence-related features, such as candidate virulence proteins, effectors, small secreted proteins and biosynthetic gene clusters. ILB308 also had a high percentage of unique DNA sequences, including six accessory scaffolds. Gene expression analysis at 4 days post inoculation revealed upregulation of known virulence factors, including Tudor domain proteins, LysM motif-containing proteins, subtilisin-like proteases and novel genes encoding secreted effectors and heat-labile enterotoxins. Growth on HC15 led to the upregulation of genes associated with oxidoreductase activity related to cuticular alkane degradation and fermentation metabolism/antioxidant responses in the hemolymph. The low number of known B. bassiana virulence genes points to novel or unknown mechanisms acting on the interaction between P. guildinii and strain ILB308. CONCLUSION The presence of accessory genomic regions and unique virulence genes in ILB308 may contribute to its higher virulence. These genes could be considered as potential targets for enhancing fungal virulence through genetic manipulation. © 2025 Society of Chemical Industry.
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Affiliation(s)
- Héctor Oberti
- Laboratorio de Bioproducción, Bioinsumos, INIA Las Brujas, Canelones, Uruguay
| | - Lucia Sessa
- Laboratorio de Bioproducción, Bioinsumos, INIA Las Brujas, Canelones, Uruguay
| | - Carolina Oliveira-Rizzo
- Plataforma de Microscopía Confocal y Epifluorescencia, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Andrés Di Paolo
- Plataforma de Microscopía Confocal y Epifluorescencia, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Andrea Sanchez-Vallet
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Eduardo Abreo
- Laboratorio de Bioproducción, Bioinsumos, INIA Las Brujas, Canelones, Uruguay
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237
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Mills EG, Hewlett K, Smith AB, Griffith MP, Pless L, Sundermann AJ, Harrison LH, Zackular JP, Van Tyne D. Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium. Nat Microbiol 2025; 10:871-881. [PMID: 40119148 PMCID: PMC11964922 DOI: 10.1038/s41564-025-01958-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 02/14/2025] [Indexed: 03/24/2025]
Abstract
Gastrointestinal colonization by the nosocomial pathogen vancomycin-resistant Enterococcus faecium (VREfm) can lead to bloodstream infections with high mortality rates. Shifts in VREfm lineages found within healthcare settings occur, but reasons underlying these changes are not understood. Here we sequenced 710 VREfm clinical isolates collected between 2017 and 2022 from a large tertiary care centre. Genomic analyses revealed a polyclonal VREfm population, although 46% of isolates formed genetically related clusters, suggesting a high transmission rate. Comparing these data to a global collection of 15,631 publicly available VREfm genomes collected between 2002 and 2022 identified replacement of the sequence type (ST) 17 VREfm lineage by emergent ST80 and ST117 lineages at the local and global level. Comparative genomic and functional analyses revealed that emergent lineages encoded bacteriocin T8, which conferred a competitive advantage over bacteriocin T8-negative strains in vitro and upon colonization of the mouse gut. Bacteriocin T8 carriage was also strongly associated with strain emergence in the global genome collection. These data suggest that bacteriocin T8-mediated competition may have contributed to VREfm lineage replacement.
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Affiliation(s)
- Emma G Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Katharine Hewlett
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alexander B Smith
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marissa P Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lora Pless
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alexander J Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lee H Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joseph P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Microbial Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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238
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Bhanse P, Singh L, Qureshi A. Functional and Genomic Potential of Burkholderia contaminans PB_AQ24 Isolate for Boosting the Growth of Bamboo Seedlings in Heavy Metal Contaminated Soils. Appl Biochem Biotechnol 2025; 197:2437-2456. [PMID: 39754688 DOI: 10.1007/s12010-024-05156-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2024] [Indexed: 01/06/2025]
Abstract
The present study investigated the genomic and functional potential of Burkholderia contaminans PB_AQ24, a bacterial strain isolated from the municipal solid waste dumpsite, for boosting the growth of Dendrocalamus strictus (Male bamboo) seedlings. The isolated strain exhibited high potency for metal solubilization and ACC (1-Aminocyclopropane-1-carboxylate) deaminase activity. Its genome harbored diverse genes responsible for nitrogen and phosphorus utilization (trpABCDES, iaaH, acdS, pstABCS, phoAUD, pqqABCDE, kdpABC, gln, and nirBD) and also an abundance of heavy metal tolerant genes (ftsH, hptX, iscX-fdx-hscAB-iscAUR, mgtA, corA, and copC). Seeds priming experiments carried out in heavy metal contaminated soils (such as waste dumpsite soil (WDS), fly ash dumpsite soil (FAS) and natural garden soil (NGS control)) augmented with Burkholderia contaminans sp. PB_AQ24 showed 85% sustenance of seedlings in WDS and 80% in FAS. The study thus highlighted the potential features in isolated bacterial strain Burkholderia sp. PB_AQ24 (NCBI accession no. JAQOUG000000000), which could boost the growth of bamboo seedlings in heavy metal contaminated soils and may be applied for restoration and rejuvenation of contaminated sites.
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Affiliation(s)
- Poonam Bhanse
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Asifa Qureshi
- CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 440020, Maharashtra, India.
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239
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Biasizzo M, Henigman U, Avberšek J, Jamnikar-Ciglenečki U, Vadnjal S. Clostridioides difficile in raw mechanically separated poultry meat and pasteurized product made from contaminated meat. Anaerobe 2025; 92:102946. [PMID: 40010486 DOI: 10.1016/j.anaerobe.2025.102946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2024] [Revised: 02/07/2025] [Accepted: 02/23/2025] [Indexed: 02/28/2025]
Abstract
OBJECTIVES Clostridioides difficile (C. difficile) is an important foodborne pathogen found in a wide range of products. This study investigated the occurrence of C. difficile in mechanically separated chicken and turkey meat (MSM) and in pasteurized products made from contaminated MSM. METHODS The presence of C. difficile was analysed in 56 MSM samples (32 from turkey and 24 from chicken) and in six pasteurized meat products made from raw meats previously identified as C. difficile-positive. After enrichment, detection was performed by real-time PCR, and culture on selective media for C. difficile. The isolated strains were then characterized by PCR-ribotyping, toxinotyping, and whole-genome sequencing (WGS). RESULTS C. difficile was detected in 16.1 % of MSM samples via real-time PCR, with a 10.7 % isolation rate. One pasteurized product also tested positive. The six isolates obtained displayed diverse PCR-ribotypes, five of which were toxigenic. Notably, the PCR-ribotypes and sequence types in the pasteurized product differed from those identified in the raw meat used for its production. CONCLUSIONS The presence of C. difficile in raw and subsequently pasteurized meat product indicates that the pathogen can survive the pasteurization process and may be present in such products.
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Affiliation(s)
- Majda Biasizzo
- University of Ljubljana, Veterinary Faculty, National Veterinary Institute, Institute of Food Safety, Feed and Environment, Gerbičeva 60, 1000, Ljubljana, Slovenia.
| | - Urška Henigman
- University of Ljubljana, Veterinary Faculty, National Veterinary Institute, Institute of Food Safety, Feed and Environment, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Jana Avberšek
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Urška Jamnikar-Ciglenečki
- University of Ljubljana, Veterinary Faculty, National Veterinary Institute, Institute of Food Safety, Feed and Environment, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Stanka Vadnjal
- University of Ljubljana, Veterinary Faculty, National Veterinary Institute, Institute of Food Safety, Feed and Environment, Gerbičeva 60, 1000, Ljubljana, Slovenia
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240
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Jensen EL, Marchisio C, Ochoa A, Gray R, Parra V, Miller JM, Çilingir FG, Caccone A. Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity. Ecol Evol 2025; 15:e71358. [PMID: 40290375 PMCID: PMC12032190 DOI: 10.1002/ece3.71358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 03/26/2025] [Accepted: 04/15/2025] [Indexed: 04/30/2025] Open
Abstract
The utility and importance of whole-genome sequences are recognized across various fields, including evolution and conservation. However, for some taxa, like extinct species, using methods to generate contiguous genomes that rely on high-quality DNA is impossible. In such cases, an alternative may be to employ synteny-based methods using a genome from a closely related taxon to generate more complete genomes. Here we update the reference genome for the Pinta Island Galapagos giant tortoise (Chelonoidis abingdonii) without conducting additional sequencing through rescaffolding against the most closely related chromosome-level genome assembly, the Aldabra giant tortoise (Aldabrachelys gigantea). This effort resulted in a much more contiguous genome, CheloAbing_2.0, with an N50 that is two orders of magnitude longer and large reductions in L50 and the number of gaps. We then examined the impact of the CheloAbing_2.0 genome on estimates of runs of homozygosity (ROH) using genome resequencing data from 37 individual Galapagos giant tortoises from the 13 extant lineages to test the mechanisms by which a fragmented assembly may over- or underestimate the number and extent of ROH. The use of CheloAbing_2.0 resulted in individual estimates of inbreeding, including ROH proportion (FROH), number (NROH), and cumulative length (SROH), that were statistically different from those derived from the earlier genome assembly. This improved genome will serve as a resource for future efforts focusing on the ecology, evolution, and conservation of this species group. More broadly, our results highlight that synteny-based scaffolding is promising for generating contiguous genomes without needing additional data types.
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Affiliation(s)
- Evelyn L. Jensen
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastleUpon TyneUK
| | - Chiara Marchisio
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastleUpon TyneUK
- Faculty of Health and Life SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - Alexander Ochoa
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
| | - Rachel Gray
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastleUpon TyneUK
| | - Vanessa Parra
- Biology DepartmentUniversity of KentuckyLexingtonKentuckyUSA
| | - Joshua M. Miller
- Department of Biological SciencesMacEwan UniversityEdmontonCanada
| | - F. Gözde Çilingir
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Swiss Federal Institute for Research WSLBirmensdorfSwitzerland
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
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241
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Li X, Wang Z, Zhu M, Wang B, Teng S, Yan J, Wang H, Yuan P, Cao S, Qu X, Wang Z, Zhan K, Choudhury MP, Yang X, Bao Q, He S, Liu L, Zhao P, Jiang J, Xiang H, Fang L, Tang Z, Liao Y, Yi G. Genomic Insights into Post-Domestication Expansion and Selection of Body Size in Ponies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2413023. [PMID: 40009528 PMCID: PMC12021115 DOI: 10.1002/advs.202413023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 01/29/2025] [Indexed: 02/28/2025]
Abstract
Horse domestication revolutionizes human civilization by transforming transportation, agriculture, and warfare patterns. Despite extensive studies on modern domestic horse origins, the intricate demographic history and genetic signatures underlying pony size remain unexplored. Here, a high-quality genome assembly of the Chinese Debao pony is presented, and 452 qualified individuals from 64 horse breeds worldwide are extensively analyzed. The authors' results reveal the conservation of ancient components in East Asian horses and close relationships between Asian horses and Western pony lineages. Genetic analyses suggest an Asian paternal origin for European pony breeds. These pony-sized horses share close genetic affinities, potentially attributed to their early expansion and adaptation to local environments. In addition, promising cis-regulatory elements influencing horse withers height by regulating genes such as RFLNA and FOXO1 are identified. Overall, this study provides insightful perspectives on the dispersal history and genetic determinants underlying body size in ponies, offering broader implications for horse population management and improvement.
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Affiliation(s)
- Xingzheng Li
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Zihao Wang
- Animal Husbandry Research InstituteGuangxi Vocational University of AgricultureNanning530002China
| | - Min Zhu
- Animal Husbandry Research InstituteGuangxi Vocational University of AgricultureNanning530002China
| | - Binhu Wang
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Shaohua Teng
- Animal Husbandry Research InstituteGuangxi Vocational University of AgricultureNanning530002China
| | - Jing Yan
- Animal Husbandry Research InstituteGuangxi Vocational University of AgricultureNanning530002China
| | - Haoyu Wang
- Nanning Capitano Equestrian Club Co., LtdNanning530000China
| | - Pengxiang Yuan
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Shuwei Cao
- Animal Husbandry Research InstituteGuangxi Vocational University of AgricultureNanning530002China
| | - Xiaolu Qu
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Zhen Wang
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Kai Zhan
- Anhui Provincial Key Laboratory of Livestock and Poultry Product SafetyInstitute of Animal Husbandry and Veterinary MedicineAnhui Academy of Agricultural SciencesHefei230031China
| | - Md. Panir Choudhury
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Xintong Yang
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Qi Bao
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Sang He
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Lei Liu
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
| | - Pengju Zhao
- Hainan InstituteZhejiang UniversityYongyou Industry Park, Yazhou Bay Sci‐Tech CitySanya572000China
| | - Jicai Jiang
- Department of Animal ScienceNorth Carolina State UniversityRaleighNC27695USA
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise BreedingSchool of Life Science and EngineeringFoshan UniversityFoshan528225China
| | - Lingzhao Fang
- Center for Quantitative Genetics and GenomicsAarhus UniversityAarhus8000Denmark
| | - Zhonglin Tang
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
- Kunpeng Institute of Modern Agriculture at FoshanAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesFoshan528226China
| | - Yuying Liao
- Guangxi Veterinary Research InstituteNanning530001China
| | - Guoqiang Yi
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‐omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China
- Kunpeng Institute of Modern Agriculture at FoshanAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesFoshan528226China
- Bama Yao Autonomous County Rural Revitalization Research InstituteBama547500China
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242
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Kim IE, Fola AA, Puig E, Maina TK, Hui ST, Ma H, Zuckerman K, Agwati EO, Leonetti A, Crudale R, Luftig MA, Moormann AM, Oduor C, Bailey JA. Comparison of nanopore with illumina whole genome assemblies of the Epstein-Barr virus in Burkitt lymphoma. Sci Rep 2025; 15:10970. [PMID: 40164811 PMCID: PMC11958722 DOI: 10.1038/s41598-025-94737-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 03/17/2025] [Indexed: 04/02/2025] Open
Abstract
Endemic Burkitt lymphoma (eBL) is one of the most prevalent cancer in children in sub-Saharan Africa, and while prior studies have found that Epstein-Barr virus (EBV) type and variation may alter the tumor driver genes necessary for tumor survival, the precise relationship between EBV variation and EBV-associated tumorigenesis remains unclear due to lack of scalable, cost-effective, viral whole-genome sequencing from tumor samples. This study introduces a rapid and cost-effective method of enriching, sequencing, and assembling accurate EBV genomes in BL tumor cell lines through a combination of selective whole genome amplification (sWGA) and subsequent 2-tube multiplex polymerase chain reaction along with long-read sequencing with a portable sequencer. The method was optimized across a range of parameters to yield a high percentage of EBV reads and sufficient coverage across the EBV genome except for large repeat regions. After optimization, we applied our method to sequence 18 cell lines and 3 patient tumors from fine needle biopsies and assembled them with median coverages of 99.62 and 99.68%, respectively. The assemblies showed high concordance (99.61% similarity) to available Illumina-based assemblies. The improved method and assembly pipeline will allow for better understanding of EBV variation in relation to BL and is applicable more broadly for translational research studies, especially useful for laboratories in Africa where eBL is most widespread.
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Affiliation(s)
- Isaac E Kim
- Center for Computational Molecular Biology, Brown University, Box G-E5, Providence, 02912, RI, USA
- Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Abebe A Fola
- Center for Computational Molecular Biology, Brown University, Box G-E5, Providence, 02912, RI, USA
| | - Enrique Puig
- Center for Computational Molecular Biology, Brown University, Box G-E5, Providence, 02912, RI, USA
| | - Titus Kipkemboi Maina
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Sin Ting Hui
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Hongyu Ma
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Kaleb Zuckerman
- Center for Computational Molecular Biology, Brown University, Box G-E5, Providence, 02912, RI, USA
| | - Eddy O Agwati
- Department of Zoology, Maseno University, Maseno, Kenya
- Center for Global Health Research (CGHR), Kenya Medical Research Institute, Kisumu, Kenya
| | - Alec Leonetti
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Rebecca Crudale
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Center for Virology, Duke University School of Medicine, Durham, NC, USA
| | - Ann M Moormann
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Cliff Oduor
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Jeffrey A Bailey
- Center for Computational Molecular Biology, Brown University, Box G-E5, Providence, 02912, RI, USA.
- Warren Alpert Medical School, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
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243
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Chen R, Chen J, Powell OR, Outram MA, Arndell T, Gajendiran K, Wang YL, Lubega J, Xu Y, Ayliffe MA, Blundell C, Figueroa M, Sperschneider J, Vanhercke T, Kanyuka K, Tang D, Zhong G, Gardener C, Yu G, Gourdoupis S, Jaremko Ł, Matny O, Steffenson BJ, Boshoff WHP, Meyer WB, Arold ST, Dodds PN, Wulff BBH. A wheat tandem kinase activates an NLR to trigger immunity. Science 2025; 387:1402-1408. [PMID: 40146821 DOI: 10.1126/science.adp5034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 11/26/2024] [Accepted: 02/14/2025] [Indexed: 03/29/2025]
Abstract
The role of nucleotide-binding leucine-rich repeat (NLR) receptors in plant immunity is well studied, but the function of a class of tandem kinases (TKs) that confer disease resistance in wheat and barley remains unclear. In this study, we show that the SR62 locus is a digenic module encoding the Sr62TK TK and an NLR (Sr62NLR), and we identify the corresponding AvrSr62 effector. AvrSr62 binds to the N-terminal kinase 1 of Sr62TK, triggering displacement of kinase 2, which activates Sr62NLR. Modeling and mutation analysis indicated that this is mediated by overlapping binding sites (i) on kinase 1 for binding AvrSr62 and kinase 2 and (ii) on kinase 2 for binding kinase 1 and Sr62NLR. Understanding this two-component resistance complex may help engineering and breeding plants for durable resistance.
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Affiliation(s)
- Renjie Chen
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jian Chen
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Oliver R Powell
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Megan A Outram
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Taj Arndell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Karthick Gajendiran
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yan L Wang
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jibril Lubega
- National Institute of Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, UK
| | - Yang Xu
- State Key Laboratory of Agricultural and Forestry Biosecurity, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Michael A Ayliffe
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Cheryl Blundell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Thomas Vanhercke
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Kostya Kanyuka
- National Institute of Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, UK
| | - Dingzhong Tang
- State Key Laboratory of Agricultural and Forestry Biosecurity, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guitao Zhong
- State Key Laboratory of Agricultural and Forestry Biosecurity, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Catherine Gardener
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Guotai Yu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Spyridon Gourdoupis
- Bioscience Program, Smart Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
| | - Łukasz Jaremko
- Bioscience Program, Smart Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Wilku B Meyer
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Stefan T Arold
- Bioscience Program, Smart Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
| | - Peter N Dodds
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Brande B H Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Mahmud MN, Momoshed M, Ahamed Talukder MF, Ferdous J, Koly FA, Islam S. Exploring the occurrence of Pseudomonas aeruginosa and comprehensive whole genome analysis of the bcsir_p4_s20 strain from municipal wastewater in Chattogram. World J Microbiol Biotechnol 2025; 41:112. [PMID: 40148700 DOI: 10.1007/s11274-025-04328-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Accepted: 03/17/2025] [Indexed: 03/29/2025]
Abstract
Various studies reported the existence of multidrug-resistant (MDR) Pseudomonas aeruginosa in environmental samples, including hospital wastewater, municipal wastewater, and surface water. In this study, we investigated the impact of untreated municipal wastewater transmitting antibiotic-resistant P. aeruginosa strains in wastewater networks of Chattogram City, Bangladesh, through antibiotic susceptibility profiles and whole-genome sequencing (WGS) of the MDR P. aeruginosa bcsir_p4_s20. Forty-two P. aeruginosa isolates were identified from eight locations using polymerase chain reaction (PCR), targeting the oprI and oprL genes, and antibiotic susceptibility was determined against 11 antibiotics by the disc diffusion method. Resistant isolates were identified at all locations, with the highest resistance frequency displayed towards meropenem, cefepime, and colistin. The WGS of bcsir_p4_s20 was performed using the NextSeq 2000 platform. Several bioinformatics tools, like FastQC, Trimmomatic, SPAdes, and Prokka, were used for quality evaluation, low-quality read and adapter filtration, de novo assembly, and functional annotation. Comprehensive Antibiotic Resistance Database (CARD), AMRFinderPlus, and virulence factor database (VFDB) were employed to determine resistance genes and virulence factors. The strain belongs to the O7 serogroup and sequence type ST357. The analysis identified antibiotic resistance genes (blaPDC-11, sul1, and others) that cause resistance through efflux pump and inactivation mechanisms, and virulent genes responsible for adherence (flagella, type IV pili), enzyme (phospholipase C), iron uptake (pyoverdine), secretion system (exoT, exoU), and toxin (toxA) secretion. Therefore, municipal wastewater is a potential reservoir for MDR P. aeruginosa, and establishing wastewater treatment plants (WWTPs) at the primary source points before discharging it to the wastewater network is suggested to mitigate the risk of outbreaks.
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Affiliation(s)
- Md Nuruddin Mahmud
- Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| | - Momthahena Momoshed
- Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| | | | - Jannatul Ferdous
- Industrial Microbiology Research Division, BCSIR Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, 4220, Bangladesh
| | - Farjana Akter Koly
- Industrial Microbiology Research Division, BCSIR Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, 4220, Bangladesh
| | - Saiful Islam
- Industrial Microbiology Research Division, BCSIR Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, 4220, Bangladesh.
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Davis LJ, Krunić A, Alexander KL, Khin M, Wood JS, Earp C, Rangel-Grimaldo M, Eustáquio AS, Burdette JE, Williamson RT, Oberlies NH, Orjala J. Menominin A and B: Cytotoxic Cyclodepsipeptides from the Freshwater Sponge-Associated Cyanobacterium Nostoc sp. UIC 10607. JOURNAL OF NATURAL PRODUCTS 2025; 88:732-746. [PMID: 39977243 PMCID: PMC11952978 DOI: 10.1021/acs.jnatprod.4c01445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2025]
Abstract
Menominin A (1) and B (2), two cyclodepsipeptides containing a 3,8-dihydroxy-2-methyltetradecanoic acid residue, were isolated from the freshwater sponge-associated cyanobacterium, Nostoc sp. UIC 10607, using bioactivity-guided and spectroscopic approaches. The planar structures of 1 and 2 were established using HRESIMS and one- and two-dimensional NMR experiments. Comparative genomic analysis revealed unique differences in the putative menominin biosynthetic gene cluster compared to that of the closely related cyanobacterial cyclic lipodepsipeptide, hapalosin, assisting in structure elucidation and highlighting the structural diversity of this class of compounds. Configuration assignments were determined using a combination of J-based configuration analysis, chiral HPLC, modified Mosher's ester analysis, and DFT calculations. Menominin A and B demonstrate antiproliferative bioactivity against the high-grade serous ovarian cancer cell line OVCAR3 (IC50 = 3.1 (1) and 2.4 μM (2)). Menominin A and B are the first reported secondary metabolites from a freshwater sponge-associated cyanobacterium, underscoring the potential of freshwater sponges as a microbial culture source in natural product discovery.
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Affiliation(s)
- Lydia J. Davis
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
| | - Aleksej Krunić
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Kelsey L. Alexander
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Manead Khin
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Jared S. Wood
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
| | - Cody Earp
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, North Carolina 27412, United States
| | - Manuel Rangel-Grimaldo
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, North Carolina 27412, United States
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - Joanna E. Burdette
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
| | - R. Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28409, United States
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, North Carolina 27412, United States
| | - Jimmy Orjala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois 60612, United States
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246
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Patra M, Pandey AK, Dubey SK. Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences. World J Microbiol Biotechnol 2025; 41:114. [PMID: 40148599 DOI: 10.1007/s11274-025-04323-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Accepted: 03/13/2025] [Indexed: 03/29/2025]
Abstract
The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.
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Affiliation(s)
- Mrinmoy Patra
- Molecular Ecology Laboratory, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Anand Kumar Pandey
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, 284128, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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247
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Kiraz D, Özcan A. Comparative genome analysis of 15 Streptococcus thermophilus strains isolated from Turkish traditional yogurt. Antonie Van Leeuwenhoek 2025; 118:64. [PMID: 40153053 DOI: 10.1007/s10482-025-02070-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 02/27/2025] [Indexed: 03/30/2025]
Abstract
Streptococcus thermophilus plays a pivotal role in yogurt fermentation, yet strains from traditional fermented products remain largely unexplored compared to their industrial counterparts. This study aimed to characterize the genomic diversity and functional potential of 15 S. thermophilus strains isolated from Turkish traditional yogurts, and to compare them with industrial strains. Through whole-genome sequencing and advanced bioinformatics analyses, we revealed distinct phylogenetic patterns and genetic features that differentiate these traditional strains from industrial isolates. The genomes (1.68-1.86 Mb) exhibited high genetic homogeneity (ANI > 98.69%) while maintaining significant functional diversity. Pan-genome analysis identified 1160 core genes and 5694 accessory genes, highlighting substantial genomic plasticity that enables niche adaptation. Our analysis uncovered several distinctive features: (1) unique phylogenetic clustering patterns based on both housekeeping genes and whole-genome SNPs, suggesting geographical isolation effects; (2) an extensive repertoire of carbohydrate-active enzymes (CAZymes), comprising 111 Glycoside Hydrolases, 227 Glycosyl Transferases, and 44 Carbohydrate Esterases and 13 Carbohydrate-Binding Modules, demonstrating sophisticated carbohydrate metabolism adaptation significantly enriched compared to industrial strains; (3) widespread GABA biosynthesis pathways in 8 strains, including complete gadB gene, indicating potential health-promoting properties; (4) multiple genomic islands containing genes for galactose utilization and stress response, suggesting specific adaptation to traditional fermentation environments; (5) diverse exopolysaccharide biosynthesis and bacteriocin gene clusters; and (6) widespread CRISPR-Cas systems with variable spacer content. Notably, we identified vanY glycopeptide resistance genes across all strains, with two strains additionally harboring vanT. These results reveal the genetic mechanisms behind S. thermophilus adaptation to traditional yogurt environments, offering valuable insights for developing starter cultures and preserving the unique qualities and potential health benefits of traditional dairy products.
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Affiliation(s)
- Deniz Kiraz
- Animal Originated Foodstuffs Department, Central Research Institute of Food and Feed Control, Bursa, Turkey.
| | - Ali Özcan
- Animal Originated Foodstuffs Department, Central Research Institute of Food and Feed Control, Bursa, Turkey
- Food Hygiene and Technology Department, Faculty of Veterinary Medicine, Uludağ University, Bursa, Turkey
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248
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Romyasamit C, Surachat K, Pattaranggoon NC, Suksabay P, Permpoon U, Nam TG, Sornsenee P. Phenotypic and Genomic Insights into Schleiferilactobacillus harbinensis WU01, a Candidate Probiotic with Broad-Spectrum Antimicrobial Activity Against ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter) Pathogens. Foods 2025; 14:1161. [PMID: 40238333 PMCID: PMC11989002 DOI: 10.3390/foods14071161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Revised: 03/21/2025] [Accepted: 03/25/2025] [Indexed: 04/18/2025] Open
Abstract
The increasing prevalence of multidrug-resistant (MDR) pathogens, particularly ESKAPE bacteria, necessitates alternative antimicrobial strategies. Probiotics, particularly lactic acid bacteria, protect against pathogenic infections. This study aimed to characterize Schleiferilactobacillus harbinensis WU01, isolated from fermented palm sap, and evaluate its probiotic potential and antimicrobial activity. Its probiotic characteristics were assessed based on low-pH and bile tolerance, auto-aggregation, hydrophobicity, and adhesion to Caco-2 cells. Antimicrobial activity against ESKAPE pathogens was evaluated using the agar well diffusion assay. Whole-genome sequencing (WGS) and in silico analysis were performed to identify bacteriocin-related genes, virulence factors, and antibiotic-resistance genes. WU01 exhibited a strong tolerance to gastrointestinal conditions, with high survival rates under acidic and bile-salt environments. S. harbinensis WU01 demonstrated significant auto-aggregation, high hydrophobicity, and strong adhesion to Caco-2 cells. Antimicrobial assays revealed inhibitory activity against MDR ESKAPE pathogens, which correlated with the presence of bacteriocin-related genes, including those homologous to Carnocin_CP52. Molecular dynamics (MDs) simulations confirmed the interaction of Carnocin_CP52 with bacterial membranes, suggesting a mechanism for pathogen disruption. WGS confirmed the absence of virulence and antimicrobial-resistance genes, confirming its safety for probiotic applications. These findings suggest that S. harbinensis WU01 possesses probiotic properties and antimicrobial activity against ESKAPE pathogens. The combined results highlight its potential application in functional foods and therapeutic interventions.
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Affiliation(s)
- Chonticha Romyasamit
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; (C.R.); (P.S.)
- Research Center in Tropical Pathobiology, Walailak University, Thasala District, Nakhon Si Thammarat 80160, Thailand
- Center of Excellence in Innovation of Essential Oil and Bioactive Compounds, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand;
| | | | - Pinkanok Suksabay
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; (C.R.); (P.S.)
| | - Uttapol Permpoon
- Department of Pharmacy, Institute of Pharmaceutical Science and Technology, Hanyang University ERICA, Ansan 15588, Republic of Korea; (U.P.); (T.-G.N.)
| | - Tae-Gyu Nam
- Department of Pharmacy, Institute of Pharmaceutical Science and Technology, Hanyang University ERICA, Ansan 15588, Republic of Korea; (U.P.); (T.-G.N.)
| | - Phoomjai Sornsenee
- Department of Family and Preventive Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
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249
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Vinskienė J, Tamošiūnė I, Andriūnaitė E, Gelvonauskienė D, Rugienius R, Hakim MF, Stanys V, Buzaitė O, Baniulis D. Inoculum of Endophytic Bacillus spp. Stimulates Growth of Ex Vitro Acclimatised Apple Plantlets. PLANTS (BASEL, SWITZERLAND) 2025; 14:1045. [PMID: 40219113 PMCID: PMC11990893 DOI: 10.3390/plants14071045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2025] [Revised: 03/24/2025] [Accepted: 03/25/2025] [Indexed: 04/14/2025]
Abstract
In vitro shoot culture and cryopreservation (CP) are techniques essential for the ex situ preservation of genetic resources and the production of plant propagation material of clonally propagated horticultural crops. Changes in plant-associated microbiota diversity and composition induced by in vitro cultivation and CP treatment could have a negative effect on the growth and ex vitro adaptation of the in vitro propagated shoots. Therefore, the aim of the present study was to assess changes in endophytic bacteria diversity in domestic apple tissues induced by in vitro cultivation and CP treatment and to investigate the potential of the bacterial inoculum to improve the rooting and ex vitro acclimatisation of the propagated shoots. Metataxonomic analysis revealed a variation in the endophytic bacteria diversity and taxonomic composition between the field-grown tree dormant bud and the in vitro propagated or CP-treated shoot samples of apple cv. Gala. Whereas Sphingobacteriaceae, Sphingomonadaceae, Pseudomonadaceae, and Beijerinckiaceae families were the most prevalent families in the bud samples, Enterobacteriaceae, Bacillaceae, and Lactobacillaceae were dominant in the in vitro shoots. The bacterial inoculum effect on rooting and ex vitro acclimatisation was assessed using four isolates selected by screening the endophytic isolate collection. Bacillus sp. L3.4, B. toyonensis Nt18, or a combined inoculum resulted in a 21%, 36%, and 59% increase in cumulative root length and a 41%, 46%, and 35% increase in the biomass accumulation of ex vitro acclimatised plantlets, respectively. Root zone microbiota functional diversity analysis implied that growth stimulation was not related to improved nutrient uptake but could involve a pathogen-suppressing effect. The results demonstrate that the application of plant growth-promoting bacteria can potentially improve the performance of the in vitro propagated germplasm.
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Affiliation(s)
- Jurgita Vinskienė
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas Str. 30, 54333 Babtai, Kaunas reg., Lithuania; (J.V.); (I.T.); (E.A.); (D.G.); (R.R.); (M.F.H.); (V.S.)
| | - Inga Tamošiūnė
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas Str. 30, 54333 Babtai, Kaunas reg., Lithuania; (J.V.); (I.T.); (E.A.); (D.G.); (R.R.); (M.F.H.); (V.S.)
| | - Elena Andriūnaitė
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas Str. 30, 54333 Babtai, Kaunas reg., Lithuania; (J.V.); (I.T.); (E.A.); (D.G.); (R.R.); (M.F.H.); (V.S.)
| | - Dalia Gelvonauskienė
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas Str. 30, 54333 Babtai, Kaunas reg., Lithuania; (J.V.); (I.T.); (E.A.); (D.G.); (R.R.); (M.F.H.); (V.S.)
| | - Rytis Rugienius
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas Str. 30, 54333 Babtai, Kaunas reg., Lithuania; (J.V.); (I.T.); (E.A.); (D.G.); (R.R.); (M.F.H.); (V.S.)
| | - Muhammad Fahad Hakim
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas Str. 30, 54333 Babtai, Kaunas reg., Lithuania; (J.V.); (I.T.); (E.A.); (D.G.); (R.R.); (M.F.H.); (V.S.)
| | - Vidmantas Stanys
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas Str. 30, 54333 Babtai, Kaunas reg., Lithuania; (J.V.); (I.T.); (E.A.); (D.G.); (R.R.); (M.F.H.); (V.S.)
| | - Odeta Buzaitė
- Department of Biochemistry, Vytautas Magnus University, Universiteto Str. 10, 53361 Akademija, Kaunas reg., Lithuania;
| | - Danas Baniulis
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas Str. 30, 54333 Babtai, Kaunas reg., Lithuania; (J.V.); (I.T.); (E.A.); (D.G.); (R.R.); (M.F.H.); (V.S.)
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250
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Martín-Díaz A, de Vega C, Martín-Hernanz S, Aparicio A, Albaladejo RG. De novo transcriptome assembly of the plant Helianthemum marifolium for the study of adaptive mechanisms. Sci Data 2025; 12:515. [PMID: 40148317 PMCID: PMC11950303 DOI: 10.1038/s41597-025-04888-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Accepted: 03/24/2025] [Indexed: 03/29/2025] Open
Abstract
The genus Helianthemum, commonly known as rockroses, encompasses 140 species primarily distributed in the Palearctic region, with notable diversification driven by climatic and geological changes. These plants are valuable for studying speciation processes and ecological divergence. The chemical properties of the leaves have also been investigated for containing valuable bioactive compounds with several therapeutic properties. However, the availability of genomic resources for species in this genus are almost entirely lacking. Here, we assembled and annotated the first reference transcriptome of Helianthemum marifolium, a species with wide morphological variability and infraspecific diversity. Illumina paired-end RNA sequences were generated using leaves from 16 individuals, representing the four recognized subspecies, all cultivated in a greenhouse. RNA reads were assembled with Trinity and Oases, and EvidentialGene produced a transcriptome with 122,002 transcripts. The transcriptome showed 59524 hits on the UniProtBK database through BLASTx. This transcriptome will be an invaluable resource for transcriptome-level population studies, conservation genetics of the many endangered species within the genus, and for deepen into the metabolic pathways of leaf-derived compounds.
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Affiliation(s)
- Andrea Martín-Díaz
- Departamento de Biología Vegetal y Ecología. Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
- Departamento de Ecología y Evolución. Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Clara de Vega
- Departamento de Biología Vegetal y Ecología. Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Sara Martín-Hernanz
- Departamento de Biodiversidad, Ecología y Evolución. Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Abelardo Aparicio
- Departamento de Biología Vegetal y Ecología. Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Rafael G Albaladejo
- Departamento de Biología Vegetal y Ecología. Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain.
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