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Chaggar HK, Hudson LK, Orejuela K, Thomas L, Spann M, Garman KN, Dunn JR, Denes TG. Salmonella enterica serovar Braenderup shows clade-specific source associations and a high proportion of molecular epidemiological clustering. Appl Environ Microbiol 2025; 91:e0259424. [PMID: 40116507 PMCID: PMC12016519 DOI: 10.1128/aem.02594-24] [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: 01/23/2025] [Accepted: 01/24/2025] [Indexed: 03/23/2025] Open
Abstract
Salmonella enterica serovar Braenderup (S. enterica ser. Braenderup) is an important clinical serovar in the United States. This serovar was reported by the CDC in 2017 as the fifth most common Salmonella enterica serovar associated with outbreaks in the United States, which have been linked to both fresh produce and food animal products. The goals of this study were to compare the relatedness of human clinical isolates from southeastern USA (Tennessee (n = 106), Kentucky (n = 48), Virginia (n = 252), South Carolina (n = 109), Georgia (n = 159), Alabama (n = 8), Arkansas (n = 26), and Louisiana (n = 91)) and global clinical (n = 5,153) and nonclinical (n = 1,053) isolates obtained from the NCBI. Additionally, we also examined the population structure of S. enterica ser. Braenderup strains (n = 3,131) on EnteroBase and found that all the strains of this serovar are associated with a single cgMLST eBurst group (ceBG 185), confirming that this serovar is monophyletic. We divided the S. enterica ser. Braenderup population into two clades (Clade I and Clade II) and one clade group (Clade Group III). The composition of distinct environmental isolates in the clades differed: Clade I was significantly associated with produce (90.7%; P < 0.0001) and water, soil, and sediment (76.9%; P < 0.0001), and Clade II was significantly associated with poultry environments (62.8%; P < 0.0001). The clade-specific gene associations (e.g., Clade I-associated competence proteins and cytochrome_c_asm protein and Clade II-associated heme-exporter protein and dimethyl sulfoxide [DMSO] reductase-encoding genes) provide potential insights into possible mechanisms driving environmental adaptation and host-pathogen interaction. Phylogenetic analyses identified 218 molecular epidemiological clusters in the current study, which represented a greater proportion of potentially outbreak-related isolates than previously estimated. IMPORTANCE This study provides insights into the genomic diversity of S. enterica ser. Braenderup by revealing distinct clade-specific source attribution patterns and showing that a greater proportion of isolates were associated with epidemiological clusters based on the genomic relatedness than previously estimated. Specifically, we analyzed the diversity of human clinical isolates from southeastern USA and compared them with the global clinical and nonclinical isolates. Our analysis showed different clades of S. enterica ser. Braenderup linked to different environments, providing insights on the potential source of human sporadic infection and outbreaks. These findings can enhance public health surveillance and response strategies targeting S. enterica serovar Braenderup by expanding our understanding of potential transmission pathways and the genomic diversity of clinical and environmental isolates.
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Affiliation(s)
- Harleen K. Chaggar
- Department of Food Science, University of Tennessee, Knoxville, Tennessee, USA
| | - Lauren K. Hudson
- Department of Food Science, University of Tennessee, Knoxville, Tennessee, USA
| | - Kelly Orejuela
- Tennessee Department of Health, Nashville, Tennessee, USA
| | - Linda Thomas
- Division of Laboratory Services, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Maya Spann
- Division of Laboratory Services, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Katie N. Garman
- Division of Laboratory Services, Tennessee Department of Health, Nashville, Tennessee, USA
| | - John R. Dunn
- Tennessee Department of Health, Nashville, Tennessee, USA
| | - Thomas G. Denes
- Department of Food Science, University of Tennessee, Knoxville, Tennessee, USA
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152
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Foysal MJ, Neilan BA, Timms V. The impact of anthropogenic activities on antimicrobial and heavy metal resistance in aquatic environments. Appl Environ Microbiol 2025; 91:e0231724. [PMID: 40071918 PMCID: PMC12016542 DOI: 10.1128/aem.02317-24] [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: 11/19/2024] [Accepted: 02/18/2025] [Indexed: 04/24/2025] Open
Abstract
This study investigated the prevalence and co-occurrence of antimicrobial (AMR) and metal resistance (MR) in aquatic environments with different human impacts. Metagenomes from pristine, rural and urban sites in Australia were analyzed with AMR ++ and customized binning pipelines. AMR was present in all environments, while MR was mainly in rural and urban samples. AMR gene diversity was higher in rural and urban sites, exhibiting resistance to more antibiotic classes (n = 10) than the pristine site (n = 4). Metal and multicompound resistance was more frequent in rural (14%) compared to urban samples (5%). Pristine samples lacked multidrug and multicompound resistance and had lower resistance to aminoglycosides and the MLS group. Multiresistance was evidenced by copper and aminocoumarin resistance in rural samples and aminoglycoside and mercury resistance in Pseudomonas in all environments. These findings highlight the impact of human activities on AMR and MR spread, emphasizing the need for environmental monitoring and management. IMPORTANCE Antimicrobial resistance (AMR) and metal resistance (MR) are critical global health concerns exacerbated by anthropogenic activities. The intricate mechanism underlying the interaction among anthropogenic activities, microbial communities, and resistance remains enigmatic. We developed novel bioinformatic pipelines to unveil this interaction in three aquatic environments. Our findings demonstrate the presence of specific bacterial communities that drive AMR and MR in rural and urban environments. This study underscores the significance of proper agricultural practices, comprehensive monitoring, and management strategies to reduce anthropogenic impacts on environmental resistance.
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Affiliation(s)
- Md Javed Foysal
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
| | - Brett A. Neilan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
| | - Verlaine Timms
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
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153
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Ivanova M, Laage Kragh M, Szarvas J, Tosun ES, Holmud NF, Gmeiner A, Amar C, Guldimann C, Huynh TN, Karpíšková R, Rota C, Gomez D, Aboagye E, Etter A, Centorame P, Torresi M, De Angelis ME, Pomilio F, Okholm AH, Xiao Y, Kleta S, Lüth S, Pietzka A, Kovacevic J, Pagotto F, Rychli K, Zdovc I, Papić B, Heir E, Langsrud S, Møretrø T, Brown P, Kathariou S, Stephan R, Tasara T, Dalgaard P, Njage PMK, Fagerlund A, Aarestrup F, Truelstrup Hansen L, Leekitcharoenphon P. Large-scale phenotypic and genomic analysis of Listeria monocytogenes reveals diversity in the sensitivity to quaternary ammonium compounds but not to peracetic acid. Appl Environ Microbiol 2025; 91:e0182924. [PMID: 40035557 PMCID: PMC12016499 DOI: 10.1128/aem.01829-24] [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: 09/12/2024] [Accepted: 02/05/2025] [Indexed: 03/05/2025] Open
Abstract
Listeria monocytogenes presents a significant concern for the food industry due to its ability to persist in the food processing environment. One of the factors contributing to its persistence is decreased sensitivity to disinfectants. Our objective was to assess the diversity of L. monocytogenes sensitivity to food industry disinfectants by testing the response of 1,671 L. monocytogenes isolates to quaternary ammonium compounds (QACs) and 414 isolates to peracetic acid (PAA) using broth microdilution and growth curve analysis assays, respectively, and to categorize the isolates into sensitive and tolerant. A high phenotype-genotype concordance (95%) regarding tolerance to QACs was obtained by screening the genomes for the presence of QAC tolerance-associated genes bcrABC, emrE, emrC, and qacH. Based on this high concordance, we assessed the QAC genes' dissemination among publicly available L. monocytogenes genomes (n = 39,196). Overall, QAC genes were found in 23% and 28% of the L. monocytogenes collection in this study and in the global data set, respectively. bcrABC and qacH were the most prevalent genes, with bcrABC being the most detected QAC gene in the USA, while qacH dominated in Europe. No significant differences (P > 0.05) in the PAA tolerance were detected among isolates belonging to different lineages, serogroups, clonal complexes, or isolation sources, highlighting limited variation in the L. monocytogenes sensitivity to this disinfectant. The present work represents the largest testing of L. monocytogenes sensitivity to important food industry disinfectants at the phenotypic and genomic level, revealing diversity in the tolerance to QACs while all isolates showed similar sensitivity to PAA. IMPORTANCE Contamination of Listeria monocytogenes within food processing environments is of great concern to the food industry due to challenges in eradicating the isolates once they become established and persistent in the environment. Genetic markers associated with increased tolerance to certain disinfectants have been identified, which alongside other biotic and abiotic factors can favor the persistence of L. monocytogenes in the food production environment. By employing a comprehensive large-scale phenotypic testing and genomic analysis, this study significantly enhances the understanding of the L. monocytogenes tolerance to quaternary ammonium compounds (QACs) and the genetic determinants associated with the increased tolerance. We provide a global overview of the QAC genes prevalence among public L. monocytogenes sequences and their distribution among clonal complexes, isolation sources, and geographical locations. Additionally, our comprehensive screening of the peracetic acid (PAA) sensitivity shows that this disinfectant can be used in the food industry as the lack of variation in sensitivity indicates reliable effect and no apparent possibility for the emergence of tolerance.
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Affiliation(s)
- Mirena Ivanova
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Martin Laage Kragh
- Research Group for Food Microbiology and Hygiene, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Judit Szarvas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Elif Seyda Tosun
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Natacha Friis Holmud
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Alexander Gmeiner
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Corinne Amar
- Public Health England, National Infection Service, London, United Kingdom
| | - Claudia Guldimann
- Chair for Food Safety and Analytics, Ludwig-Maximilians-University Munich, Munich, Germany
| | - TuAnh N. Huynh
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Renáta Karpíšková
- Department of Public Health, Masaryk University, Medical Faculty, Brno, Czech Republic
| | | | | | | | | | - Patrizia Centorame
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G Caporale “Giuseppe Caporale”, Teramo, Italy
| | - Marina Torresi
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G Caporale “Giuseppe Caporale”, Teramo, Italy
| | - Maria Elisabetta De Angelis
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G Caporale “Giuseppe Caporale”, Teramo, Italy
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G Caporale “Giuseppe Caporale”, Teramo, Italy
| | | | - Yinghua Xiao
- Arla Innovation Center, Arla Foods amba, Aarhus N, Denmark
| | - Sylvia Kleta
- German Federal Institute for Risk Assessment (BfR), National Reference Laboratory for Listeria monocytogenes (NRL-Lm), Berlin, Germany
| | - Stefanie Lüth
- German Federal Institute for Risk Assessment (BfR), National Reference Laboratory for Listeria monocytogenes (NRL-Lm), Berlin, Germany
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, National Reference Laboratory for Listeria monocytogenes, Graz, Austria
| | - Jovana Kovacevic
- Food Innovation Center, Oregon State University, Portland, Oregon, USA
| | - Franco Pagotto
- Listeriosis Reference Service, Food Directorate, Bureau of Microbial Hazards, Ottawa, Ontario, Canada
| | - Kathrin Rychli
- Unit for Food Microbiology, Institute for Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Bojan Papić
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Even Heir
- Nofima, The Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Solveig Langsrud
- Nofima, The Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Trond Møretrø
- Nofima, The Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Phillip Brown
- North Carolina State University, Raleigh, North Carolina, USA
| | | | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Paw Dalgaard
- Research Group for Food Microbiology and Hygiene, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Patrick Murigu Kamau Njage
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Frank Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Lisbeth Truelstrup Hansen
- Research Group for Food Microbiology and Hygiene, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
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154
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Kaminsky LM, Burghardt L, Bell TH. Evolving a plant-beneficial bacterium in soil vs. nutrient-rich liquid culture has contrasting effects on in-soil fitness. Appl Environ Microbiol 2025; 91:e0208524. [PMID: 40067020 PMCID: PMC12016532 DOI: 10.1128/aem.02085-24] [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: 10/21/2024] [Accepted: 02/12/2025] [Indexed: 04/24/2025] Open
Abstract
Inoculation of plant-beneficial microbes into agricultural soils can improve crop growth, but such outcomes depend on microbial survival. Here, we assessed how exposure to prior environmental conditions impacts microbial in-soil fitness, particularly focusing on incubation in liquid culture as an unavoidable phase of inoculant production and on pre-incubation in target soils as a potential method to improve performance. We conducted experimental evolution on a phosphorus-solubilizing bacterial species, Priestia megaterium, in (i) soil only, (ii) liquid media only, and (iii) soil followed by liquid media, using population metagenomic sequencing to track mutations over time. Several typical in vitro evolutionary phenomena were observed in liquid media-incubated populations, including clonal interference, genetic hitchhiking, and mutation parallelism between replicate populations, particularly in the sporulation transcription factor spo0A. Liquid media-incubated populations also developed a clear fitness reduction in soil compared to the ancestral isolate. However, soil-incubated populations grew slowly, experienced far fewer generations despite longer absolute time, and accumulated minimal mutational changes. Correspondingly, soil-incubated populations did not display improved survival compared to the ancestral isolate in their target soils, though there did appear to be minor fitness reductions in unfamiliar soil. This work demonstrates that adaptation to liquid media and/or a native soil can impact bacterial fitness in new soil and that bacterial evolution in more complex real-world habitats does not closely resemble bacterial evolution in liquid media. IMPORTANCE Innovative solutions are needed to address emerging challenges in agriculture while reducing its environmental footprint. Management of soil microbiomes could contribute to this effort, as plant growth-promoting microorganisms provide key ecosystem services that support crops. Yet, inoculating beneficial microbes into farm soils yields unreliable results. We require a greater knowledge of the ecology of these taxa to improve their functioning in sustainable agroecosystems. In this report, we demonstrate that exposure to laboratory media and lingering adaptation to another soil can negatively impact the in-soil survival of a phosphorus-solubilizing bacterial species. We go further to highlight the underlying mutations that give rise to these patterns. These insights can be leveraged to improve our understanding of how soil-dwelling beneficial microorganisms adapt to different evolutionary pressures.
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Affiliation(s)
- Laura M. Kaminsky
- Boyce Thompson Institute, Ithaca, New York, USA
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Liana Burghardt
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Terrence H. Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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155
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Gao FZ, Hu LX, Liu YS, Yang HY, He LY, Bai H, Liu F, Jin XW, Ying GG. Unveiling the prevalence of metal resistance genes and their associations with antibiotic resistance genes in heavy metal-contaminated rivers. WATER RESEARCH 2025; 281:123699. [PMID: 40280009 DOI: 10.1016/j.watres.2025.123699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2024] [Revised: 04/15/2025] [Accepted: 04/21/2025] [Indexed: 04/29/2025]
Abstract
Heavy metals can drive antibiotic resistance through co-selection mechanisms. Current knowledge predominantly focuses on relationships between metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) at the river reach scale. It remains unclear the links between MRGs and ARGs at the large river basin scale, as does the role of MRG-ARG colocalization in resistance dissemination. This study employed metagenomics to investigate the prevalence of MRGs in the Xiangjiang River, a historically heavy metal-contaminated river, and their connections with ARGs by combining resistome profiling with colocalization analyses. Results revealed the significant prevalence of MRGs in the river compared to nationwide rivers, but it showed weak correlations with metal concentrations in either water or sediment. The prevalence of MRGs in water was weakly driven by abiotic parameters, but was strongly influenced by microbial composition. The proportion of water MRGs attributable to sewage sources was tightly positively correlated with MRG abundances, suggesting the significant contribution of external waste input. Plasmid-originated MRGs were more abundant in water, while chromosomal MRGs dominated in sediment, indicating medium-specific transfer dynamics. The profile of MRGs were strongly correlated with that of ARGs in both media, encompassing several clinically high-risk ARGs. However, MRG-ARG colocalization events were rarely detected (eight instances in total), consistent with low frequencies in nationwide rivers (3.5 % in sediment; 2.0 % in water), implying their limited roles in resistance dissemination. Overall, the findings enhance our understanding of riverine metal resistome and its associations with antibiotic resistome, while emphasize the rare presence of MRG-ARG colocalization in riverine environments.
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Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Li-Xin Hu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Hai-Yan Yang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Feng Liu
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions, Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Xiao-Wei Jin
- China National Environmental Monitoring Centre, Beijing 100012, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China.
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156
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Chi W, Zhang H, Li X, Zhou Y, Meng Q, He L, Yang Y, Liu S, Shi K. Comparative genomic analysis of 255 Oenococcus oeni isolates from China: unveiling strain diversity and genotype-phenotype associations of acid resistance. Microbiol Spectr 2025:e0326524. [PMID: 40261018 DOI: 10.1128/spectrum.03265-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Accepted: 03/17/2025] [Indexed: 04/24/2025] Open
Abstract
Oenococcus oeni, the only species of lactic acid bacteria capable of fully completing malolactic fermentation under challenging wine conditions, continues to intrigue researchers owing to its remarkable adaptability, particularly in combating acid stress. However, the mechanism underlying its superior adaptation to wine stresses still remains elusive due to the lack of viable genetic manipulation tools for this species. In this study, we conducted genomic sequencing and acid resistance phenotype analysis of 255 O. oeni isolates derived from diverse wine regions across China, aiming to elucidate their strain diversity and genotype-phenotype associations of acid resistance through comparative genomics. A significant correlation between phenotypes and evolutionary relationships was observed. Notably, phylogroup B predominantly consisted of acid-resistant isolates, primarily originating from Shandong and Shaanxi wine regions. Furthermore, we uncovered a noteworthy linkage between prophage genomic islands and acid resistance phenotype. Using genome-wide association studies, we identified key genes correlated with acid resistance, primarily involved in carbohydrates and amino acid metabolism processes. This study offers profound insights into the genetic diversity and genetic basis underlying adaptation mechanisms to acid stress in O. oeni.IMPORTANCEThis study provides valuable insights into the genetic basis of acid resistance in Oenococcus oeni, a key lactic acid bacterium in winemaking. By analyzing 255 isolates from diverse wine regions in China, we identified significant correlations between strain diversity, genomic islands, and acid resistance phenotypes. Our findings reveal that certain prophage-related genomic islands and specific genes are closely linked to acid resistance, offering a deeper understanding of how O. oeni adapts to acidic environments. These discoveries not only advance our knowledge of microbial stress responses but also pave the way for selecting and engineering acid-resistant strains, enhancing malolactic fermentation efficiency and wine quality. This research underscores the importance of genomics in improving winemaking practices and addressing challenges posed by high-acidity wines.
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Affiliation(s)
- Wei Chi
- College of Enology, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling, Shaanxi, China
| | - Hanwen Zhang
- College of Enology, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyi Li
- College of Enology, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling, Shaanxi, China
| | - Yeqin Zhou
- College of Enology, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiang Meng
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Ling He
- College of Enology, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling, Shaanxi, China
| | - Yafan Yang
- College of Enology, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuwen Liu
- College of Enology, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling, Shaanxi, China
| | - Kan Shi
- College of Enology, College of Horticulture, Shaanxi Engineering Research Center for Viti-Viniculture, Viti-Viniculture Engineering Technology Center of State Forestry and Grassland Administration, Heyang Experimental and Demonstrational Stations for Grape, Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling, Shaanxi, China
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157
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Zhang H, Yamamoto E, Markell A, Carrillo C, Locas A. Prevalence of Shiga Toxin-Producing Escherichia coli (STEC) and Risk Characterization Based on Virulence Genes in Retail Raw Ground Meat of Beef, Veal, and Lamb in Canada. J Food Prot 2025; 88:100483. [PMID: 40081812 DOI: 10.1016/j.jfp.2025.100483] [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: 07/15/2024] [Revised: 02/24/2025] [Accepted: 03/08/2025] [Indexed: 03/16/2025]
Abstract
Shiga toxin-producing Escherichia coli (STEC) are potentially pathogenic E. coli that may cause mild to severe gastrointestinal illnesses. STEC-contaminated foods of animal origin have been the most frequently implicated sources of foodborne outbreaks. A multiyear (2016 to 2021) targeted survey was conducted to investigate the prevalence of STEC in retail ground meats (beef, veal, and lamb). Samples were screened for the presence of Shiga toxin genes (stx) to identify presumptive samples, followed by culture and molecular confirmation of isolates to confirm the presence of stx genes and subsequent characterization by whole-genome-sequencing (WGS) for O serogroup and virulence genes (e.g., stx, eae, aggR). A total of 175 STEC strains were isolated from a total of 148 samples where the presence of viable STEC was confirmed out of 2,398 ground meat samples. This represented 1.2% (7/589 positive, 8 unique strains) of the beef samples, 4.7% (58/1,241 positive, 67 unique strains) of the veal samples, and 14.6% (83/568 positive, 100 unique strains) of the lamb samples. The intimin virulence gene, eae, was identified in the STEC strains of veal origin (9/67, 13.4%) only and were classified as belonging to risk level 1 (1/67), level 3 (2/67), and level 4 (6/67) according to the FAO/WHO risk categories. Risk level 2 STEC strains were of beef (2/8, 25.0%), veal (8/67, 11.9%), and lamb (1/100, 1.0%) origin. The majority of the STEC strains, 75.0% (6/8) of the beef, 67.2% (45/67) of the veal, and 94.0% (94/100) of the lamb STEC strains were classified as risk level 5 (lowest level) of the FAO/WHO risk categories. This study's findings indicate that the current food safety control measures implemented for ground meats in Canada are effective at maintaining an acceptable level of possible contamination with STEC strains associated with severe clinical outcomes. Continued application of effective control measures and safe food handling practices by consumers will minimize the potential risk of foodborne infections from raw ground meats.
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Affiliation(s)
- Helen Zhang
- Food Safety Science Directorate, Science Branch, Canadian Food Inspection Agency, 1400 Merivale Road, Ottawa, Ontario K1A 0Y9, Canada.
| | - Etsuko Yamamoto
- Food Safety Science Directorate, Science Branch, Canadian Food Inspection Agency, 1400 Merivale Road, Ottawa, Ontario K1A 0Y9, Canada
| | - Austin Markell
- Food Safety Science Directorate, Science Branch, Canadian Food Inspection Agency, 1400 Merivale Road, Ottawa, Ontario K1A 0Y9, Canada
| | - Catherine Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Bldg 22, CEF 960 Carling Avenue, Ottawa, Ontario K1A 0Y9, Canada
| | - Annie Locas
- Food Safety Science Directorate, Science Branch, Canadian Food Inspection Agency, 1400 Merivale Road, Ottawa, Ontario K1A 0Y9, Canada
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158
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Liu B, Niu X, Zhang C, Zheng S, Gao L, Han M, Feng T, Wu J, Jiang C, Kang S, Xu D, Liu Y. Chromosome-level genome assembly and annotation of Chinese herring (Ilisha elongata). Sci Data 2025; 12:668. [PMID: 40258812 PMCID: PMC12012206 DOI: 10.1038/s41597-025-04790-7] [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: 12/26/2024] [Accepted: 03/07/2025] [Indexed: 04/23/2025] Open
Abstract
The Chinese herring (Ilisha elongata) is a commercially and scientifically significant fish species. In this study, we conducted high-precision whole-genome sequencing using two high-throughput platforms: second-generation MGI and third-generation PacBio. Hi-C technology assisted in assembling the contig sequences onto 24 chromosomes, resulting in a high-quality chromosome-level genome map with excellent continuity and coverage. The completed genome size was approximately 815 Mb, with a contig N50 of 4.82 Mb, scaffold N50 of 32.61 Mb, and a chromosome mounting rate of 95.32%. SNP and InDel purity rates were 0.003% and 0.012%, respectively, and the genome assembly completeness was 96.68%, assessed by BUSCO. Repetitive sequences were annotated via ab initio and homology predictions, identifying 295.7 Mb of repetitive sequences, constituting 35.08% of the genome. A total of 26,381 protein-coding genes were predicted, with 24,596 functionally annotated.
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Affiliation(s)
- Bingjian Liu
- College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China
- National engineering research center for facilitated marine aquaculture, Zhejiang Ocean University, 316022, Zhoushan, China
| | - Xinyi Niu
- College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China
- National engineering research center for facilitated marine aquaculture, Zhejiang Ocean University, 316022, Zhoushan, China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Sixu Zheng
- College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China
- National engineering research center for facilitated marine aquaculture, Zhejiang Ocean University, 316022, Zhoushan, China
| | - Luxiu Gao
- College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China
- National engineering research center for facilitated marine aquaculture, Zhejiang Ocean University, 316022, Zhoushan, China
| | - Mingzhe Han
- College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China
| | - Taobo Feng
- College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China
| | - Jinghua Wu
- College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China
| | - Chaoxuan Jiang
- College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China
| | - Shuaishuo Kang
- College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China
| | - DongDong Xu
- Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, 316021, Zhoushan, China.
| | - Yifan Liu
- College of Marine Science and Technology, Zhejiang Ocean University, 316022, Zhoushan, China.
- National engineering research center for facilitated marine aquaculture, Zhejiang Ocean University, 316022, Zhoushan, China.
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159
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Bozkurt EB, Baysal Ö, Marzec-Grządziel A, Silme RS, Can A, Belen İN, Çapar Ü, Korkut A. Genomic Characterization of Serratia fonticola (EBS19) as a Biocontrol Agent against Botrytis cinerea. Curr Microbiol 2025; 82:252. [PMID: 40252089 DOI: 10.1007/s00284-025-04224-y] [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: 09/25/2024] [Accepted: 04/01/2025] [Indexed: 04/21/2025]
Abstract
Botrytis cinerea (Bc), a plant pathogenic fungus, is the causative agent of gray mold disease, which rapidly develops resistance to fungicides in cultivation areas. This study explores the biocontrol potential of various bacterial isolates collected from the rhizosphere of tomato plants (Solanum lycopersicum). Bacterial isolates were purified and neutralized through phenol vaporization for 2 days. Colonies that inhibited pathogen spore growth were confirmed via antibiosis effect using in vitro bioassays. Bacterial colonies demonstrated up to 84% inhibition of pathogen growth at 7-day post-inoculation (dpi) with a one-layer agar diffusion test and up to 70% inhibition with a double-layer agar diffusion test, compared to control plates. Both bacterial suspension and filtrate significantly suppressed pathogen mycelium growth at 11 and 14 dpi. The isolate used in further studies was identified as Serratia fonticola (EBS19) through whole-genome sequencing. Annotated genome data revealed the presence of genes encoding enzymes crucial for pathogen inhibition. Carbon preference analyses identified specific carbon sources unique to the bacterial strain. These findings are advantageous for developing effective biopreparations that ensure bacterial strain stability in practical applications. In addition, the primary focus was on the interaction between the pathogen's major stress regulator protein (BAG1) and the bacterial glycoside hydrolase. Protein-protein docking analyses elucidated strong interaction between BAG1 and bacterial glycoside hydrolase. In conclusion, this study provides a knowledge for further research using recombinant DNA and gene cloning techniques on the bacterium's mapped genome.
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Affiliation(s)
- Efe Berk Bozkurt
- Molecular Microbiology Unit in Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, 48121, Kötekli-Muğla, Turkey
| | - Ömür Baysal
- Molecular Microbiology Unit in Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, 48121, Kötekli-Muğla, Turkey.
- Molecular Plant and Microbial Biosciences Research Unit (MPMB-RU), University of Worcester, Henwick Grove, Worcester, WR2 6AJ, UK.
| | - Anna Marzec-Grządziel
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation, Puławy, Poland
| | - Ragıp Soner Silme
- Centre for Research and Practice in Biotechnology and Genetic Engineering, Istanbul University, Fatih, 3400, Istanbul, Turkey
| | - Ahmet Can
- Molecular Microbiology Unit in Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, 48121, Kötekli-Muğla, Turkey
| | - İlayda Nur Belen
- Molecular Microbiology Unit in Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, 48121, Kötekli-Muğla, Turkey
| | - Ümran Çapar
- Molecular Microbiology Unit in Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, 48121, Kötekli-Muğla, Turkey
| | - Ahmet Korkut
- Molecular Microbiology Unit in Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, 48121, Kötekli-Muğla, Turkey
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160
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Bini F, Soffritti I, D'Accolti M, Mazziga E, Caballero JD, David S, Argimon S, Aanensen DM, Volta A, Bisi M, Mazzacane S, Caselli E. Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis. BMC Genomics 2025; 26:382. [PMID: 40251489 PMCID: PMC12007294 DOI: 10.1186/s12864-025-11582-1] [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: 12/12/2024] [Accepted: 04/08/2025] [Indexed: 04/20/2025] Open
Abstract
BACKGROUND Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at reducing the presence of pathogens in the hospital environment can simultaneously favor the selection of resistant strains, potentially worsening AMR concerns. In the search for sustainable ways to control bioburden without affecting this aspect, probiotic-based sanitation (PBS) using Bacillus spp. was proposed to achieve stable reduction of pathogens, AMR, and associated HAIs. Although Bacillus probiotics are classified as nonpathogenic, comprehensive data about the potential genetic alterations of these probiotics following prolonged contact with surrounding pathogens are not yet available. This study aimed to assess in depth the genetic content of PBS-Bacillus isolates to evaluate any eventual variations that occurred during their usage. RESULTS WGS analysis was used for the precise identification of PBS-Bacillus species and detailed profiling of their SNPs, resistome, virulome, and mobilome. Analyses were conducted on both the original PBS detergent and 172 environmental isolates from eight hospitals sanitized with PBS over a 30-month period. The two species B. subtilis and B. velezensis were identified in both the original product and the hospital environment, and SNP analysis revealed the presence of two clusters in each species. No virulence/resistance genes or mobile conjugative plasmids were detected in either the original PBS-Bacillus strain or any of the analyzed environmental isolates, confirming their high genetic stability and their low/no tendency to be involved in horizontal gene transfer events. CONCLUSIONS The data obtained by metagenomic analysis revealed the absence of genetic sequences associated with PBS-Bacillus and the lack of alterations in all the environmental isolates analyzed, despite their continuous contact with surrounding pathogens. These results support the safety of the Bacillus species analyzed. Further metagenomic studies aimed at profiling the whole genomes of these and other species of Bacillus, possibly during longer periods and under stress conditions, would be of interest since they may provide further confirmation of their stability and safety.
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Affiliation(s)
- Francesca Bini
- Section of Microbiology, Department of Environmental and Prevention Sciences, and LTTA, University of Ferrara, Ferrara, 44121, Italy
- CIAS Research Center, University of Ferrara, Ferrara, 44122, Italy
| | - Irene Soffritti
- Section of Microbiology, Department of Environmental and Prevention Sciences, and LTTA, University of Ferrara, Ferrara, 44121, Italy
- CIAS Research Center, University of Ferrara, Ferrara, 44122, Italy
| | - Maria D'Accolti
- Section of Microbiology, Department of Environmental and Prevention Sciences, and LTTA, University of Ferrara, Ferrara, 44121, Italy
- CIAS Research Center, University of Ferrara, Ferrara, 44122, Italy
| | - Eleonora Mazziga
- Section of Microbiology, Department of Environmental and Prevention Sciences, and LTTA, University of Ferrara, Ferrara, 44121, Italy
- CIAS Research Center, University of Ferrara, Ferrara, 44122, Italy
| | - Julio Diaz Caballero
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
| | - Silvia Argimon
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
| | - Antonella Volta
- CIAS Research Center, University of Ferrara, Ferrara, 44122, Italy
| | - Matteo Bisi
- CIAS Research Center, University of Ferrara, Ferrara, 44122, Italy
| | - Sante Mazzacane
- CIAS Research Center, University of Ferrara, Ferrara, 44122, Italy
| | - Elisabetta Caselli
- Section of Microbiology, Department of Environmental and Prevention Sciences, and LTTA, University of Ferrara, Ferrara, 44121, Italy.
- CIAS Research Center, University of Ferrara, Ferrara, 44122, Italy.
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161
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de Mattos JS, Keepers K, Innes PA, de Mesquita CPB, Quandt CA, Kane NC, Brandvain Y, Turner K. The first chromosome-scale genome assembly of a microcyclic rust, Puccinia silphii. BMC Genomics 2025; 26:390. [PMID: 40251471 PMCID: PMC12007239 DOI: 10.1186/s12864-025-11593-y] [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] [Received: 09/13/2024] [Accepted: 04/10/2025] [Indexed: 04/20/2025] Open
Abstract
BACKGROUND Rust fungi are destructive pathogens in crop plants, having led to epidemics and damaging crops all over the world. The rust Puccinia silphii (Basidiomycota) infects Silphium integrifolium, which is a member of the most speciose plant family, Asteraceae. RESULTS This study analyzes the first chromosome-scale genome sequence of a rust that infects any dicot, or any species outside of the Poaceae (grasses). We found it to be the smallest genome among the available Pucciniales genome assemblies. Our final assembly was 41.7 Mb in size and consisted of 19 pseudomolecules. The genome had a BUSCO completeness score of 92.1%, with nearly all BUSCO gene losses shared with other Puccinia genomes, and gene losses concentrated in the sulfate assimilation categories. Other gene losses were unique to P. silphii, whose genome contained by far the fewest protein coding genes. A total of 10,399 protein coding genes were predicted, compared to 14,257 in the next smallest genome. Gene losses in P. silphii were concentrated in categories related to meiosis. CONCLUSION This newly assembled genome provides insights into the size limitations of Puccinia genus genomes, as well as important protein gene families that are evolving within the genus including sulphate assimilation genes and DNA replication and its role in the evolution of microcyclic rusts.
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Affiliation(s)
- Jacqueline S de Mattos
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA
- Department of Plant Biology, University of Campinas, Cidade Universitária Zeferino Vaz Barão Geraldo, Campinas, 13083-970, SP, Brazil
| | - Kyle Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA.
| | - Peter A Innes
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA
| | - Clifton P Bueno de Mesquita
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309-0334, USA
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, 1500 Gortner Ave, St Paul, MN, 55108, USA
| | - Kathryn Turner
- Crop Protection Ecology, The Land Institute, 2440 E Water Well Rd, Salina, KS, 67401, USA
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162
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PALOMINO HUARCAYA ROGERA, Castillo-Vilcahuaman C, Martel-Torres SB, Merino Rafael FA, Gutiérrez Moreno SM. Comparative Genomics of Rhamnolipid Synthesis and Monoaromatic Hydrocarbon Tolerance Genes in Environmental Pseudomonas aeruginosa strains. F1000Res 2025; 13:1519. [PMID: 40297566 PMCID: PMC12035672 DOI: 10.12688/f1000research.158761.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/24/2025] [Indexed: 04/30/2025] Open
Abstract
Background Bioremediation faces several compounds to recover oil spilled ecosystem. The BTEX (benzene, toluene, ethylbenzene, and xylene) are toxic hydrocarbons requiring efficient microbial degradation for bioremediation. Pseudomonas aeruginosa can degrade hydrocarbons through emulsification ( rhl genes) and tolerance ( mla genes). However, genomic organization of these systems in environmental P. aeruginosa strains remains unclear. This study aimed to investigate the rhl and mla systems in six strains isolated from hydrocarbon-contaminated sites in Peru. Methods Six Pseudomonas aeruginosa strains were evaluated in this study. Each strain were able to degrade hydrocarbon and tolerate heavy metals. DNA extraction, sequencing, and quality-controlled assembly, functional genome annotation was performed using BAKTA. Comparative analysis included high-quality Pseudomonas genomes from RefSeq, with ANI metrics. A phylogenetic tree was built from core gene alignment, revealed evolutionary connections and was visualized with iTOL. Results The assembled genomes ranged from 5.6 to 6.0 Mbp with ~66% GC content. All the strains were confirmed as P. aeruginosa by ANI; placing them within Clade 1 alongside environmental and clinical strains. Pangenome analysis identified 3,544 core genes and a diverse accessory genome. All strains had rhlABRI genes in a conserved 3'-5' orientation. Most of them contained duplicated rhlB gene, except C1BHIC5 strain. However, rhlG varied in position and orientation, it was often near rhlC, with C1BHIC5 also displaying an exception in rhlG orientation.100% of strains presented mla system, associated with toluene tolerance, with two copies of mlaA, mlaFEDC, and mlaEFD genes arranged with high synteny but variable orientations. In comparison to Pseudomonas putida, where mla genes are positioned between murA and ppcD with an additional toluene tolerance gene ( ttg2D). Conclusions In conclusion, the presence of the rhlABC genes and the BTEX tolerance genes in all of the analyzed strains allowed us to understand the great ability of P. aeruginosa to survive in polluted environments.
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Affiliation(s)
- ROGER A. PALOMINO HUARCAYA
- Laboratorio de Microbiología y Biotecnología Microbiana, Universidad Nacional Mayor de San Marcos Facultad de Ciencias Biologicas, Lima District, Lima Region, +51, Peru
| | - Camila Castillo-Vilcahuaman
- Laboratorio de Genómica Microbiana, Universidad Peruana Cayetano Heredia, Lima District, Lima Region, +51, Peru
| | - Sandro B. Martel-Torres
- Laboratorio de Microbiología y Biotecnología Microbiana, Universidad Nacional Mayor de San Marcos Facultad de Ciencias Biologicas, Lima District, Lima Region, +51, Peru
| | - Fernando A. Merino Rafael
- Laboratorio de Microbiología y Biotecnología Microbiana, Universidad Nacional Mayor de San Marcos Facultad de Ciencias Biologicas, Lima District, Lima Region, +51, Peru
| | - Susana M. Gutiérrez Moreno
- Laboratorio de Microbiología y Biotecnología Microbiana, Universidad Nacional Mayor de San Marcos Facultad de Ciencias Biologicas, Lima District, Lima Region, +51, Peru
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163
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Schell T, Greve C, Podsiadlowski L. Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide. Front Zool 2025; 22:7. [PMID: 40247279 PMCID: PMC12004614 DOI: 10.1186/s12983-025-00561-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 03/23/2025] [Indexed: 04/19/2025] Open
Abstract
Reference genome assemblies are the basis for comprehensive genomic analyses and comparisons. Due to declining sequencing costs and growing computational power, genome projects are now feasible in smaller labs. De novo genome sequencing for non-model or emerging model organisms requires knowledge about genome size and techniques for extracting high molecular weight DNA. Next to quality, the amount of DNA obtained from single individuals is crucial, especially, when dealing with small organisms. While long-read sequencing technologies are the methods of choice for creating high quality genome assemblies, pure short-read assemblies might bear most of the coding parts of a genome but are usually much more fragmented and do not well resolve repeat elements or structural variants. Several genome initiatives produce more and more non-model organism genomes and provide rules for standards in genome sequencing and assembly. However, sometimes the organism of choice is not part of such an initiative or does not meet its standards. Therefore, if the scientific question can be answered with a genome of low contiguity in intergenic parts, missing the high standards of chromosome scale assembly should not prevent publication. This review describes how to set up an animal genome sequencing project in the lab, how to estimate costs and resources, and how to deal with suboptimal conditions. Thus, we aim to suggest optimal strategies for genome sequencing that fulfil the needs according to specific research questions, e.g. "How are species related to each other based on whole genomes?" (phylogenomics), "How do genomes of populations within a species differ?" (population genomics), "Are differences between populations relevant for conservation?" (conservation genomics), "Which selection pressure is acting on certain genes?" (identification of genes under selection), "Did repeats expand or contract recently?" (repeat dynamics).
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Affiliation(s)
- Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Lars Podsiadlowski
- LIB, Museum Koenig Bonn, Centre for Molecular Biodiversity Research (zmb), Adenauerallee 127, 53113, Bonn, Germany.
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164
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Pinto OHB, Biazotti BB, de Souza RSC, Yassitepe JÉDCT, Arruda P, Dante RA, Gerhardt IR. Seasonal bacterial profiles of Vellozia with distinct drought adaptations in the megadiverse campos rupestres. Sci Data 2025; 12:636. [PMID: 40240384 PMCID: PMC12003806 DOI: 10.1038/s41597-025-04984-z] [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: 09/05/2024] [Accepted: 04/10/2025] [Indexed: 04/18/2025] Open
Abstract
Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.
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Affiliation(s)
- Otávio Henrique Bezerra Pinto
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
| | - Bárbara Bort Biazotti
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, 13083-970, Campinas, SP, Brazil
| | - Rafael Soares Correa de Souza
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Symbiomics Microbiome Solutions, Florianópolis, SC, 88050-000, Brazil
| | - Juliana Érika de Carvalho Teixeira Yassitepe
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Embrapa Agricultura Digital, 13083-886, Campinas, SP, Brazil
| | - Paulo Arruda
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, 13083-970, Campinas, SP, Brazil
| | - Ricardo Augusto Dante
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil
- Embrapa Agricultura Digital, 13083-886, Campinas, SP, Brazil
| | - Isabel Rodrigues Gerhardt
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil.
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, SP, Brazil.
- Embrapa Agricultura Digital, 13083-886, Campinas, SP, Brazil.
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Di Pierro F, Sagheddu V, Galletti S, Casaroli A, Labrini E, Soldi S, Cazzaniga M, Bertuccioli A, Matera M, Cavecchia I, Palazzi CM, Tanda ML, Zerbinati N. Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces. Probiotics Antimicrob Proteins 2025:10.1007/s12602-025-10522-5. [PMID: 40238037 DOI: 10.1007/s12602-025-10522-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2025] [Indexed: 04/18/2025]
Abstract
Among the emerging issues in probiotic safety, the possible presence of pks, a gene cluster synthetizing a genotoxin known as colibactin, is one of the most alarming. Indeed, indigenous E. coli strain pks-positive are found in 60% of patients with colorectal cancer, and the most widely used E. coli-based probiotic, known as E. coli Nissle 1917 (DSM 6601), is pks-positive. Starting from 25 potential candidates selected by screening 25 infant stool samples, we have selected an E. coli strain (named 5C, deposited as LMG S-33222) belonging to the phylotype A and having the serovar O173:H1. Having been previously completely sequenced by our group, we have further characterized this strain, demonstrating that it is (i) devoid of the most known potential pathogenic-related genes, (ii) devoid of possible plasmids, (iii) antibiotic-sensitive according to the EFSA panel, (iv) resistant in gastric and enteric juice, (v) significantly producing acetate, (vi) poorly producing histamine, (vii) endowed with a significant in vitro antipathogenic profile, (viii) promoting a significant in vitro immunological response based on IL-10 and IL-12, and (ix) devoid of the pks genes. A comparative genomics versus E. coli Nissle 1917 is also provided. Considering that the other two most commonly used E. coli-based probiotics (E. coli DSM 17252 and E. coli A0 34/86) are respectively pks-positive and alpha-hemolysin-(hly) and cytotoxic necrotizing factor-1-(cnf1) positive, this novel strain (E. coli 5C) is likely the probiotic E. coli strain with the best safety profile available to date for human use.
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Affiliation(s)
- Francesco Di Pierro
- Microbiota International Clinical Society, 10123, Turin, Italy
- Scientific & Research Department, Velleja Research, 20125, Milan, Italy
- Department of Medicine and Technological Innovation, University of Insubria, 21100, Varese, Italy
| | - Valeria Sagheddu
- AAT-Advanced Analytical Technologies, Fiorenzuola d'Arda, 29017, Piacenza, Italy
| | - Serena Galletti
- AAT-Advanced Analytical Technologies, Fiorenzuola d'Arda, 29017, Piacenza, Italy
| | - Alice Casaroli
- AAT-Advanced Analytical Technologies, Fiorenzuola d'Arda, 29017, Piacenza, Italy
| | - Edoardo Labrini
- AAT-Advanced Analytical Technologies, Fiorenzuola d'Arda, 29017, Piacenza, Italy
| | - Sara Soldi
- AAT-Advanced Analytical Technologies, Fiorenzuola d'Arda, 29017, Piacenza, Italy
| | | | - Alexander Bertuccioli
- Microbiota International Clinical Society, 10123, Turin, Italy
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61122, Urbino, Italy
| | - Mariarosaria Matera
- Microbiota International Clinical Society, 10123, Turin, Italy
- Department of Pediatric Emergencies, Misericordia Hospital, 58100, Grosseto, Italy
| | - Ilaria Cavecchia
- Microbiota International Clinical Society, 10123, Turin, Italy
- Microbiomic Department, Koelliker Hospital, 10134, Turin, Italy
| | | | - Maria Laura Tanda
- Endocrine Unit, Department of Medicine and Surgery, University of Insubria, 21100, Varese, Italy
| | - Nicola Zerbinati
- Department of Medicine and Technological Innovation, University of Insubria, 21100, Varese, Italy
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Nebenführ M, Hamadou AB, Aguilar A, Borrell A, Gkafas GA, Janke A. Mediterranean monk seal (Monachus monachus) and leopard seal (Hydrurga leptonyx) de novo genomes to study the demographic history and genetic diversity of southern seals. BMC Biol 2025; 23:102. [PMID: 40241156 PMCID: PMC12004778 DOI: 10.1186/s12915-025-02207-w] [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: 05/03/2024] [Accepted: 04/04/2025] [Indexed: 04/18/2025] Open
Abstract
BACKGROUND The Monachinae, or southern seals, are one of two subfamilies within the Phocidae and are home to iconic pinnipeds such as the leopard seal, a fierce Antarctic top predator, and the Mediterranean monk seal, one of the world's most endangered mammals. These two species are difficult to study and sample, due to their hidden lives in extreme environments or, in case of the monk seal, their critically reduced population sizes; consequently, genetic data from these two species is scarce. However, cost developments and advances in genome sequencing have made it possible to generate continuous genome assemblies from DNA of even stranded individuals, allowing to assemble the first reference genomes of such rarely observed species. RESULTS In this study, we have sequenced the genomes of the leopard seal and the Mediterranean monk seal using PacBio's CCS technology to assemble the very first genomes for these species. Four additional Mediterranean monk seal individuals were sequenced using Illumina short-read technology. These data allowed analysis of their demography and genomic diversity based on whole-genome data, confirming low genetic variability and small numbers of individuals for the Mauritanian population of the Mediterranean monk seal. In contrast, the relatively abundant leopard seal shows a high degree of heterozygosity, comparable in the range of other common carnivores. CONCLUSIONS The first genome assemblies for these seals will lay the groundwork for population-level and other studies to better understand their evolutionary history and biology and to aid conservation efforts.
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Affiliation(s)
- Marcel Nebenführ
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse 9, Frankfurt Am Main, Germany.
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14 - 16, Frankfurt Am Main, Germany.
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Straße 14 - 16, Frankfurt Am Main, Germany.
| | - Alexander Ben Hamadou
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14 - 16, Frankfurt Am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Straße 14 - 16, Frankfurt Am Main, Germany
| | - Alex Aguilar
- Department of Evolutionary Biology, Ecology and Environmental Sciences, and Institute of Biodiversity Research (IRBio), University of Barcelona, Diagonal 643, Barcelona, 08009, Spain
| | - Asunción Borrell
- Department of Evolutionary Biology, Ecology and Environmental Sciences, and Institute of Biodiversity Research (IRBio), University of Barcelona, Diagonal 643, Barcelona, 08009, Spain
| | - Georgios A Gkafas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Axel Janke
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse 9, Frankfurt Am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14 - 16, Frankfurt Am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Straße 14 - 16, Frankfurt Am Main, Germany
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Guo D, Li Y, Lu H, Zhao Y, Kurata N, Wei X, Wang A, Wang Y, Zhan Q, Fan D, Zhou C, Lu Y, Tian Q, Weng Q, Feng Q, Huang T, Zhang L, Gu Z, Wang C, Wang Z, Wang Z, Huang X, Zhao Q, Han B. A pangenome reference of wild and cultivated rice. Nature 2025:10.1038/s41586-025-08883-6. [PMID: 40240605 DOI: 10.1038/s41586-025-08883-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/11/2025] [Indexed: 04/18/2025]
Abstract
Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding1. Here we present a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse varieties of O. sativa. This pangenome contains 3.87 Gb of sequences that are absent from the O. sativa ssp. japonica cv. Nipponbare reference genome. We captured alternate assemblies that include heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes, with 28,907 core genes and 13,728 wild-rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance-gene analogues in wild rice than in cultivars. Our analysis indicates that two cultivated subpopulations, intro-indica and basmati, were generated through gene flows among cultivars in South Asia. We also provide strong evidence to support the theory that the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 differentiated single-nucleotide polymorphisms and 13,853 differentiated presence-absence variations between indica and japonica, which could be traced to the divergence of their respective ancestors and the existence of a larger genetic bottleneck in japonica. This study provides reference resources for enhancing rice breeding, and enriches our understanding of the origins and domestication process of rice.
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Affiliation(s)
- Dongling Guo
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Hengyun Lu
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhao
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Nori Kurata
- Plant Genetics Laboratory and Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Ahong Wang
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yongchun Wang
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qilin Zhan
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Danlin Fan
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Congcong Zhou
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yiqi Lu
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qilin Tian
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qijun Weng
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Huang
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Lei Zhang
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Zhoulin Gu
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ziqun Wang
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Zixuan Wang
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qiang Zhao
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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Shi C, Gu M, Huang Y, You C, Bao S, Xie S, Gong J, Deng G, Wu P, Wu W, Zhu C, Sun X, Zeng J. Integrated genomic and transcriptomic analysis reveals the mechanisms underlying leaf variegation in 'Gonggan' mandarin. BMC PLANT BIOLOGY 2025; 25:472. [PMID: 40229686 PMCID: PMC11998453 DOI: 10.1186/s12870-025-06496-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2025] [Accepted: 04/01/2025] [Indexed: 04/16/2025]
Abstract
BACKGROUND The 'Gonggan' mandarin, an elite local cultivar from Zhaoqing City, Guangdong Province, combines the qualities of mandarin and sweet orange. A leaf-variegated mutant enhances its ornamental and economic value, providing an excellent model for studying chloroplast development and photosynthetic pigment metabolism in citrus. RESULTS We found that, in this variegated mutant, chloroplasts are severely deficient or absent in mesophyll cells. Physiological assessments revealed lower levels of chlorophyll, carotenoids, net photosynthetic rate (Pn), and stomatal conductance (Gs), alongside significantly higher non-photochemical quenching (NPQ) and the non-photochemical quenching coefficient (qN), reflecting increased photoprotective energy dissipation. To uncover the molecular basis of leaf variegation, high-quality genome assemblies and transcriptomes were generated for both the normal and variegated 'Gonggan' mandarin, enabling comparative multi-omics analysis. Key genes involved in chloroplast development, such as TOC159, PDV2, THA8, and SIG5, were downregulated in the variegated leaves. Similarly, structural genes linked to chlorophyll degradation, including CLH2, SGR, NOL, and NYC1, exhibited altered expression. Downregulation of transcription factors GLK, GNC, and GNC-LIKE (GNL), known regulators of chloroplast development and chlorophyll biosynthesis, was also observed. CONCLUSIONS These findings suggest that disrupted expression of critical genes impacts chloroplast development and pigment metabolism, causing the leaf variegation phenotype. Overall, this study lays a foundation for functional genomics research and potential germplasm improvement of 'Gonggan' mandarin, and provides new insights into the mechanisms driving color variation in citrus.
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Affiliation(s)
- Cong Shi
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Science and Technology Research on Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Miaofeng Gu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Yongjing Huang
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Science and Technology Research on Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Congjun You
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Sihan Bao
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Shuangling Xie
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Jinli Gong
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China
| | - Guiming Deng
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Science and Technology Research on Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Pingzhi Wu
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Science and Technology Research on Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wen Wu
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Science and Technology Research on Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Congyi Zhu
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Science and Technology Research on Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Xuepeng Sun
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A&F University, Hangzhou, Zhejiang, 311300, China.
| | - Jiwu Zeng
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Science and Technology Research on Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Carmona-Salido H, López-Solís S, López-Hontangas JL, Amaro C. First Report of a Fatal Septicemia Case Caused by Vibrio metoecus: A Comprehensive Functional and Genomic Study. J Infect Dis 2025; 231:894-901. [PMID: 39405190 DOI: 10.1093/infdis/jiae481] [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: 07/05/2024] [Accepted: 09/26/2024] [Indexed: 04/17/2025] Open
Abstract
BACKGROUND In recent years, we have witnessed an unprecedented increase in the incidence of vibriosis due to global warming. Vibrio metoecus is a recently described Vibrio cholerae-like species that has not been associated with septicemia death in humans. During follow-up of human vibriosis, we received a blood isolate from a patient with secondary septicemia who died a few hours after admission. METHODS Phenotypic and genotypic methods failed to identify the isolate, which could only be identified by average nucleotide identity after genome sequencing. The isolate was subjected to in vitro and ex vivo assays, complemented by comparative genomics focused on the identification of unique genetic traits. Strains and genomes from the same and related species (V. cholerae and Vibrio mimicus) were used for analyses. RESULTS The isolate was the only one able to resist and multiply in human serum. Its genome contained virulence genes shared with V. mimicus and/or V. cholerae, with those associated with sialic acid degradation within pathogenicity island 2 standing out. However, it also presented a unique gene cluster, flanked by a transposase gene, putatively related to surface polysaccharide pseudosialyzation. CONCLUSIONS We document the first case of death caused by septicemia due to V. metoecus and propose that the acquisition of surface pseudosialyzation genes explains the ability of certain isolates of this species to survive in blood. Our discovery underscores the urgent need to monitor and study newly emerging pathogenic species, as climate change may be facilitating their spread and increasing the risk of serious infections in humans.
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Affiliation(s)
- Héctor Carmona-Salido
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
- University Institute for Biotechnology and Biomedicine Research (BIOTECMED), Universitat de València, Valencia, Spain
| | - Sofía López-Solís
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
- University Institute for Biotechnology and Biomedicine Research (BIOTECMED), Universitat de València, Valencia, Spain
| | | | - Carmen Amaro
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
- University Institute for Biotechnology and Biomedicine Research (BIOTECMED), Universitat de València, Valencia, Spain
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170
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Salvà-Serra F, Nimje P, Piñeiro-Iglesias B, Alarcón LA, Cardew S, Inganäs E, Jensie-Markopoulos S, Ohlén M, Sailer HS, Unosson C, Fernández-Juárez V, Pacherres CO, Kühl M, Moore ERB, Marathe NP. Description of Pseudomonas imrae sp. nov., carrying a novel class C β-lactamase gene variant, isolated from gut samples of Atlantic mackerel ( Scomber scombrus). Front Microbiol 2025; 16:1530878. [PMID: 40336828 PMCID: PMC12057487 DOI: 10.3389/fmicb.2025.1530878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Accepted: 03/18/2025] [Indexed: 05/09/2025] Open
Abstract
Three β-lactam resistant bacterial strains isolated from gut samples of wild Atlantic mackerel (Scomber scombrus) collected from the northern North Sea were characterized by polyphasic analyses. The strains were determined to belong to the genus Pseudomonas but could not be assigned to a known species. The nearly-complete 16S rRNA gene sequence showed the highest similarity (99.9%) to four different species, although partial rpoD sequence exhibited relatively low similarities to Pseudomonas proteolytica (93.4%) and other Pseudomonas spp. Genome sequencing and subsequent digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) analysis and core genome analysis confirmed that these strains represent a novel species within the genus Pseudomonas. The three strains demonstrated ANIb values >99.5% with each other, confirming that all three strains (CCUG 74779T = CECT 30571T, CCUG 74780 and CCUG 74781) belong to the same genomospecies. Phylogenomic analysis confirmed that the strains form a distinct genomic clade, representing a novel taxonomic species, for which the name Pseudomonas imrae sp. nov., is proposed, with strain CCUG 74779T (=CECT 30571T) designated as the type strain. We report the complete genome sequence of the type strain of P. imrae sp. nov. and show that it carries a gene encoding a novel variant of a chromosomally-encoded class C β-lactamase, which has been designated as PFL-7.
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Affiliation(s)
- Francisco Salvà-Serra
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Methodology Textiles and Medical Technology, Division Materials and Production, RISE Research Institutes of Sweden, Gothenburg, Sweden
| | | | - Beatriz Piñeiro-Iglesias
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Leonarda Achá Alarcón
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Sofia Cardew
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Elisabeth Inganäs
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Susanne Jensie-Markopoulos
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria Ohlén
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hanna-Sophia Sailer
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christel Unosson
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Víctor Fernández-Juárez
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - Cesar O. Pacherres
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
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Luo Q, Chang M, Lu P, Guo Q, Jiang X, Xiao T, Zhang H, Ma Y, Zhang Y, Yu W, Zhang E, Chen Y, Shen P, Ji J, Ying C, Liu Z, Zhu H, Xiao Y. Genomic epidemiology and phylodynamics of Acinetobacter baumannii bloodstream isolates in China. Nat Commun 2025; 16:3536. [PMID: 40229304 PMCID: PMC11997098 DOI: 10.1038/s41467-025-58772-9] [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: 08/09/2024] [Accepted: 04/01/2025] [Indexed: 04/16/2025] Open
Abstract
In recent decades, Acinetobacter baumannii has become a major global nosocomial pathogen, with bloodstream infections (BSIs) exhibiting mortality rates exceeding 60% and imposing substantial economic burdens. However, limited large-scale genomic epidemiology has hindered understanding of its population dynamics. Here, we analyzed 1506 non-repetitive BSI-causing A. baumannii isolates from 76 Chinese hospitals over a decade (2011-2021). We identified 149 sequence types (STs) and 101 K-locus types (KLs), revealing increased population diversity. International clone (IC) 2 accounted for 81.74% of isolates, with a notable shift in prevalent STs: ST208 increased while ST191 and ST195 declined, aligning with global trends. ST208 exhibited higher virulence, greater antibiotic resistance, enhanced desiccation tolerance, and more complex transmission patterns compared to ST191 and ST195. Its genomic plasticity drives its adaptation and spread. Using the high-resolution Oxford MLST scheme, this study uncovered greater diversity and genetic factors behind ST208's rise. A. baumannii is evolving from a low-virulence, multidrug-resistant pathogen to a more virulent one, highlighting the urgent need to address its growing threat. These findings have critical implications for infection control and public health policies.
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Affiliation(s)
- Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Mengru Chang
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ping Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Qian Guo
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaoqing Jiang
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Tingting Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Haoyu Zhang
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yingying Ma
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Yan Zhang
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wei Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Erjia Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Jinru Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Chaoqun Ying
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Zhiying Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China
| | - Huaiqiu Zhu
- Department of Biomedical Engineering, College of Future Technology, Center for Quantitative Biology, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medical School, College of medicine, Zhejiang University, Hangzhou, China.
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172
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Chakravarty S, Logsdon G, Lonardi S. RAmbler resolves complex repeats in human Chromosomes 8, 19, and X. Genome Res 2025; 35:863-876. [PMID: 40037839 PMCID: PMC12047272 DOI: 10.1101/gr.279308.124] [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: 03/13/2024] [Accepted: 02/06/2025] [Indexed: 03/06/2025]
Abstract
Repetitive regions in eukaryotic genomes often contain important functional or regulatory elements. Despite significant algorithmic and technological advancements in genome sequencing and assembly over the past three decades, modern de novo assemblers still struggle to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from Pacific Biosciences (PacBio) HiFi reads. RAmbler (1) identifies repetitive regions by detecting unusually high coverage regions after mapping HiFi reads to the draft genome assembly, (2) finds single-copy k-mers from the HiFi reads, (i.e., k-mers that are expected to occur only once in the genome), (3) uses the relative location of single-copy k-mers to barcode each HiFi read, (4) clusters HiFi reads based on their shared barcodes, (5) generates contigs by assembling the reads in each cluster, and (6) generates a consensus assembly from the overlap graph of the assembled contigs. Here, we show that RAmbler can reconstruct human centromeres and other complex repeats to a quality comparable to the manually curated Telomere-to-Telomere human genome assembly. Across more than 250 synthetic data sets, RAmbler outperforms hifiasm, LJA, HiCANU, and Verkko across various parameters such as repeat lengths, number of repeats, heterozygosity rates, and depth of sequencing.
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Affiliation(s)
- Sakshar Chakravarty
- Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA
| | - Glennis Logsdon
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA;
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173
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Gutiérrez R, Elizondo-Álvarez T, Ramírez-Cardoce M, Duarte-Martínez F, Cordero-Laurent E, Segura-Retana E, Cascante-Serrano D, Walters-Mais R, Melano RG, Jiménez-Pearson MA. First identification and whole-genome characterization of human-associated Enterobacter roggenkampii and Enterobacter sichuanensis carrying bla IMI-4 carbapenemase in Costa Rica. J Glob Antimicrob Resist 2025; 43:68-75. [PMID: 40239923 DOI: 10.1016/j.jgar.2025.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 04/04/2025] [Accepted: 04/10/2025] [Indexed: 04/18/2025] Open
Abstract
OBJECTIVE All carbapenem-resistant Gram-negative bacterial isolates obtained in the Costa Rican National Network of Bacteriology Laboratories are routinely referred to the National Reference Center for Bacteriology for the national-laboratory for the surveillance and characterization of their carbapenem-related mechanism of resistance. As a result of this healthcare-associated infection surveillance, two bacterial isolates with unknown mechanisms for carbapenem resistance were investigated. METHODS The isolates were subjected to taxonomic identification, antimicrobial susceptibility testing, and whole-genome characterization, using Illumina and Oxford Nanopore technologies, and bioinformatic analyses. RESULTS The isolates were identified as Enterobacter roggenkampii and Enterobacter sichuanensis. Although the isolates presented different antimicrobial resistance profiles, both were resistant to carbapenems, positive for the modified carbapenem inactivation method (mCIM), and showed inhibition of carbapenem resistance with boronic acid. The full characterization of the isolates' genomes, revealed the presence of the rare chromosomal blaIMI-4 gene inserted within 25-kb integrative mobile elements, closely related to EcloIMEX-2. CONCLUSIONS The limited global distribution of the blaIMI-4 variant, along with its identification in two distinct bacterial species in Costa Rica within integrative mobile elements, underscores the critical need for regular antibiotic resistance surveillance using next-generation sequencing technologies. This study demonstrates that this practice allows the timely detection of novel or rare mechanisms of antibiotic resistance.
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Affiliation(s)
- Ricardo Gutiérrez
- Centro Nacional de Referencia de Bacteriología, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Cartago, Costa Rica; One Health Center for Zoonoses and Tropical Infectious Diseases, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts, Saint Kitts and Nevis
| | - Tábata Elizondo-Álvarez
- Centro Nacional de Referencia de Bacteriología, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Cartago, Costa Rica
| | | | - Francisco Duarte-Martínez
- Centro Nacional de Referencia de Inocuidad Microbiológica de Alimentos, Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Cartago, Costa Rica
| | - Estela Cordero-Laurent
- Centro Nacional de Referencia de Inocuidad Microbiológica de Alimentos, Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Cartago, Costa Rica
| | - Elvira Segura-Retana
- Hospital San Juan de Dios, Caja Costarricense de Seguro Social, San José, Costa Rica
| | | | - Romein Walters-Mais
- Hospital Dr. Tony Facio Castro, Caja Costarricense de Seguro Social, Limón, Costa Rica
| | - Roberto G Melano
- Public Health Ontario Laboratory, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - María Antonieta Jiménez-Pearson
- Centro Nacional de Referencia de Bacteriología, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Cartago, Costa Rica.
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174
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Kocer K, Göpel L, Gisch S, Tueffers L, Hauswaldt S, Rupp J, Boutin S, Nurjadi D. Detection of a novel SME-6 Carbapenemase in Serratia ureilytica in Germany. J Antimicrob Chemother 2025:dkaf121. [PMID: 40219834 DOI: 10.1093/jac/dkaf121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Accepted: 03/28/2025] [Indexed: 04/14/2025] Open
Abstract
BACKGROUND Carbapenem resistance in Serratia species is occasionally mediated by the serine carbapenemase Serratia marcescens enzymes (SMEs). During microbiological diagnostics, we identified a carbapenem-resistant Serratia ureilytica isolate in which resistance was not mediated by any known SME variants or other characterized carbapenemases. OBJECTIVES To identify and characterize the underlying resistance mechanism in a carbapenem-resistant Serratia ureilytica isolate that lacks known SME variants or other characterized carbapenemases. METHODS Antimicrobial susceptibility testing (AST) was performed using Vitek, gradient strips, broth microdilution, and disc diffusion methods. WGS was performed to identify the resistance mechanisms. Growth curve analysis and RT-qPCR were performed at 30°C and 37°C. RESULTS WGS identified a novel SME variant, SME-6, which differed from a known variant, SME-2, by two amino acids (G117R and G147E). AST showed carbapenem resistance at 30°C but susceptibility at 37°C. Growth curve analysis showed a shorter lag phase at 30°C compared with 37°C, and RT-qPCR showed a ∼3-fold higher blaSME expression at 30°C. CONCLUSIONS To the best of our knowledge, this study reports the first identification of SME-6 and the first detection of an SME-type carbapenemase in Germany. Resistance was found to be temperature-dependent, with faster growth and higher SME-6 expression at lower temperatures contributing to the phenotype. These findings suggest SME variants may be underdiagnosed using current diagnostic protocols, highlighting the need for adjustments to improve detection of temperature-sensitive resistance mechanisms.
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Affiliation(s)
- Kaan Kocer
- Institute of Medical Microbiology, University Hospital Schleswig-Holstein Campus Lübeck and University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Lisa Göpel
- Institute of Medical Microbiology, University Hospital Schleswig-Holstein Campus Lübeck and University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Sarah Gisch
- Institute of Medical Microbiology, University Hospital Schleswig-Holstein Campus Lübeck and University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Leif Tueffers
- Institute of Medical Microbiology, University Hospital Schleswig-Holstein Campus Lübeck and University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Susanne Hauswaldt
- Institute of Medical Microbiology, University Hospital Schleswig-Holstein Campus Lübeck and University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Jan Rupp
- Institute of Medical Microbiology, University Hospital Schleswig-Holstein Campus Lübeck and University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
- Infectious Disease Clinic, University Hospital Schleswig-Holstein Campus Lübeck and University of Lübeck, Lübeck, Germany
| | - Sébastien Boutin
- Institute of Medical Microbiology, University Hospital Schleswig-Holstein Campus Lübeck and University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
- Airway Research Center North (ARCN), German Center for Lung Research (DZL), Lübeck, Germany
| | - Dennis Nurjadi
- Institute of Medical Microbiology, University Hospital Schleswig-Holstein Campus Lübeck and University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
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175
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He T, Li X, Flores-Vallejo RDC, Radu AM, van Dijl JM, Haslinger K. The endophytic fungus Cosmosporella sp. VM-42 from Vinca minor is a source of bioactive compounds with potent activity against drug-resistant bacteria. CURRENT RESEARCH IN MICROBIAL SCIENCES 2025; 8:100390. [PMID: 40297407 PMCID: PMC12036058 DOI: 10.1016/j.crmicr.2025.100390] [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] [Indexed: 04/30/2025] Open
Abstract
Medicinal plants serve as valuable resources for the isolation of endophytic fungi. Vinca minor is a well-known producer of important vinca alkaloids and emerges as a promising source of endophytic fungi with antibacterial potential and biosynthetic capacity. In this study, we isolated an endophytic fungus from V. minor and identified it as Cosmosporella sp. VM-42. To date, relatively little is known about this fungal genus. The ethyl acetate extract of this isolate selectively inhibited Gram-positive bacteria, such as methicillin-sensitive and methicillin-resistant Staphylococcus aureus (MSSA and MRSA). Therefore, we isolated the most abundant compound from the crude extract and identified it as nectriapyrone with MIC and MBC values ranging from 125 to 62.5 µg/mL against MSSA and MRSA strains. We further sequenced and annotated the 39.07 Mb genome of the isolate, revealing that it encodes 9842 protein-coding genes, including 415 genes for carbohydrate-active enzymes and various biosynthetic gene clusters. Our untargeted metabolomic analysis shows that the fungus produces various secondary metabolites, including cyclodepsipeptides, dimeric naphtho-γ-pyrones, and macrolactones, which are known to have antifungal and antibacterial activities. In addition, we used small-molecule epigenetic modulators to activate the expression of silent biosynthetic gene clusters to broaden the chemical profile of Cosmosporella sp. VM-42. Taken together, we provide a first systematic analysis of Cosmosporella sp. VM-42, and our results show that it is a promising source of compounds with pharmacological potential against drug resistant bacteria.
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Affiliation(s)
- Ting He
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, the Netherlands
| | - Xiao Li
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, the Netherlands
| | - Rosario del Carmen Flores-Vallejo
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9700RB, the Netherlands
| | - Ana-Maria Radu
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9700RB, the Netherlands
| | - Kristina Haslinger
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, the Netherlands
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176
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Chemao-Elfihri MW, Hakmi M, Abbou H, Kartti S, Fahime EE, Belyamani L, Boutayeb S. Staphylococcus hominis as a source of antimicrobial peptides: identification of a new peptide with potential antimicrobial properties using in silico approach. Arch Microbiol 2025; 207:119. [PMID: 40214775 DOI: 10.1007/s00203-025-04323-1] [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: 03/11/2025] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 04/30/2025]
Abstract
The rapid progression of antimicrobial resistance, fueled by the excessive use of antibiotics, has become a major public health concern. Among the pathogens contributing to this crisis, Staphylococcus aureus stands out as a significant therapeutic challenge, especially with the rise of resistant strains like Methicillin-Resistant S. aureus (MRSA). In this context, antimicrobial peptides (AMPs) emerge as a promising alternative, thanks to their unique mechanisms of action. Exploring the genomes of species such as Staphylococcus hominis, known for producing AMPs effective against S. aureus, offers promising opportunities for discovering novel therapeutic agents. In this study, Average Nucleotide Identity (ANI) combined with phylogenetic analysis identified a potential emerging subspecies of Staphylococcus hominis. The core genome analysis led to the identification of a potential antimicrobial peptide. The peptide model simulated with the S. aureus membrane model in molecular dynamics revealed that it interacts primarily with the lipids head groups, leading to an overall rigidification of the bacterial membrane.
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Affiliation(s)
- Mohammed Walid Chemao-Elfihri
- Mohammed VI University of Sciences and Health (UM6SS), Casablanca, 20370, Morocco.
- Mohammed VI Center for Research and Innovation (CM6RI), Rabat, 10100, Morocco.
| | - Mohammed Hakmi
- Mohammed VI University of Sciences and Health (UM6SS), Casablanca, 20370, Morocco
- Mohammed VI Center for Research and Innovation (CM6RI), Rabat, 10100, Morocco
| | - Hanane Abbou
- Mohammed VI University of Sciences and Health (UM6SS), Casablanca, 20370, Morocco
- Mohammed VI Center for Research and Innovation (CM6RI), Rabat, 10100, Morocco
| | - Souad Kartti
- Mohammed VI University of Sciences and Health (UM6SS), Casablanca, 20370, Morocco
- Mohammed VI Center for Research and Innovation (CM6RI), Rabat, 10100, Morocco
| | - Elmostafa El Fahime
- Mohammed VI University of Sciences and Health (UM6SS), Casablanca, 20370, Morocco
- Mohammed VI Center for Research and Innovation (CM6RI), Rabat, 10100, Morocco
| | - Lahcen Belyamani
- Mohammed VI University of Sciences and Health (UM6SS), Casablanca, 20370, Morocco
- Mohammed VI Center for Research and Innovation (CM6RI), Rabat, 10100, Morocco
| | - Saber Boutayeb
- Mohammed VI University of Sciences and Health (UM6SS), Casablanca, 20370, Morocco
- Mohammed VI Center for Research and Innovation (CM6RI), Rabat, 10100, Morocco
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177
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Kim J, Han A, Chu KH. Draft genomes of three bacteria capable of growing on cocamidopropyl betaine or N, N, N-trimethylglycine (betaine): Cupriavidus sp. CuC1, Variovorax sp. VaC1, and Pseudomonas sp. PsB. Microbiol Resour Announc 2025; 14:e0126924. [PMID: 40062870 PMCID: PMC11984117 DOI: 10.1128/mra.01269-24] [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: 11/25/2024] [Accepted: 02/06/2025] [Indexed: 04/11/2025] Open
Abstract
We report three draft genome sequences of Pseudomonas sp. PsB, Cupriavidus sp. CuC1, and Variovorax sp. VaC1. Pseudomonas sp. PsB can grow on N,N,N-trimethylglycine (betaine), but not on cocamidopropyl betaine (CPB), as a sole carbon source. Cupriavidus sp. CuC1 and Variovorax sp. VaC1 can grow only on CPB.
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Affiliation(s)
- Jinha Kim
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
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178
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London LY, Lim CH, Modliszewski JL, Siddiqui NY, Sysoeva TA. Draft genomes of Klebsiella pneumoniae and Streptococcus anginosus strains found in the urine of the same female patient. Microbiol Resour Announc 2025; 14:e0131124. [PMID: 40047509 PMCID: PMC11984145 DOI: 10.1128/mra.01311-24] [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: 12/14/2024] [Accepted: 02/07/2025] [Indexed: 04/11/2025] Open
Abstract
Here, we report the draft genomes of Klebsiella pneumoniae 5008-1 and Streptococcus anginosus 5008-2 strains isolated from a catheterized urine sample obtained from an asymptomatic postmenopausal woman diagnosed with recurrent urinary tract infection and receiving vaginal estrogen cream.
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Affiliation(s)
- Laricca Y. London
- Department of Biological Sciences, Alabama A&M University, Normal, Alabama, USA
| | - Chae Hee Lim
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama, USA
| | - Jennifer L. Modliszewski
- Duke University Center for Genomic and Computational Biology, Department of Bioinformatics and Biostatistics, Duke University, Durham, North Carolina, USA
| | - Nazema Y. Siddiqui
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, Duke University, Durham, North Carolina, USA
| | - Tatyana A. Sysoeva
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama, USA
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179
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Kumar M, Sayavedra L, Baker DJ, Shouche YS, Narbad A. Genome sequence of Eubacterium callanderi AM6, isolated from a Parkinson's disease patient. Microbiol Resour Announc 2025; 14:e0003925. [PMID: 40079595 PMCID: PMC11984119 DOI: 10.1128/mra.00039-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Accepted: 03/02/2025] [Indexed: 03/15/2025] Open
Abstract
Here, we report the genome sequence of Eubacterium callanderi AM6, isolated from a fecal sample obtained from a Parkinson's disease patient. The bacterial genome was sequenced using Illumina technology on a NextSeq 500 platform. The assembled genome of Eubacterium callanderi comprises 4,318,463 base pairs with a G + C content of 47.5%.
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Affiliation(s)
- Madhav Kumar
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Gut Microbiome Division, SKAN Research Trust, Bengaluru, Karnataka, India
| | - Lizbeth Sayavedra
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Dave J. Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Yogesh S. Shouche
- Gut Microbiome Division, SKAN Research Trust, Bengaluru, Karnataka, India
| | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
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180
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Heng YC, Lee JKY, Lim ACH, Kittelmann S. Draft genome sequences of a strain of Clostridium neuense and four Candidatus Clostridium species. Microbiol Resour Announc 2025; 14:e0127424. [PMID: 40111070 PMCID: PMC11984146 DOI: 10.1128/mra.01274-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Accepted: 02/03/2025] [Indexed: 03/22/2025] Open
Abstract
We report the draft genomes of five Clostridium isolates from soil and agricultural by-products, four of which are proposed as Candidatus species. Members of the genus Clostridium are of significant industrial interest, and the availability of their genome sequences facilitates the understanding and exploration of their functional potential.
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Affiliation(s)
- Yu Chyuan Heng
- WIL@NUS Corporate Laboratory, Centre for Translational Medicine, Wilmar International Limited, National University of Singapore, Singapore, Singapore
| | - Jolie Kar Yi Lee
- WIL@NUS Corporate Laboratory, Centre for Translational Medicine, Wilmar International Limited, National University of Singapore, Singapore, Singapore
| | - Amber Ching Han Lim
- WIL@NUS Corporate Laboratory, Centre for Translational Medicine, Wilmar International Limited, National University of Singapore, Singapore, Singapore
| | - Sandra Kittelmann
- WIL@NUS Corporate Laboratory, Centre for Translational Medicine, Wilmar International Limited, National University of Singapore, Singapore, Singapore
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181
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Smith J, Manou M, Milgram J, Hoey S, Warde S, Kirby B, Gordon SV, Kenny K, Kelly PA. Complete genome and transcriptome of Mycobacterium bovis 3488, a clinical isolate with a novel deletion at the RD1 locus. Microbiol Resour Announc 2025; 14:e0083724. [PMID: 40062876 PMCID: PMC11984153 DOI: 10.1128/mra.00837-24] [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: 08/13/2024] [Accepted: 01/09/2025] [Indexed: 04/11/2025] Open
Abstract
In members of the Mycobacterium tuberculosis complex, the RD1 locus encodes a type VII secretion system involved in virulence. Herein, we describe the genome and transcriptomic analysis of Mycobacterium bovis 3488, a clinical isolate from a cat, with a 14.2 kb deletion that encompasses the RD1 locus.
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Affiliation(s)
- Jordy Smith
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Maria Manou
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Joshua Milgram
- Faculty of Agriculture Food & Environment, Koret School of Veterinary Medicine, Hebrew University Jerusalem, Rehovot, Israel
| | - Seamus Hoey
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Susan Warde
- Department of Agriculture, Food and the Marine Laboratories, Celbridge, Kildare, Ireland
| | - Barbara Kirby
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Kevin Kenny
- Department of Agriculture, Food and the Marine Laboratories, Celbridge, Kildare, Ireland
| | - Pamela A. Kelly
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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182
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Passos GS, Pellegrinetti TA, Fiore MF. Metagenome-assembled bacterial genomes from long accurate reads associated with Capilliphycus salinus ALCB114379. Microbiol Resour Announc 2025; 14:e0080724. [PMID: 40079640 PMCID: PMC11984139 DOI: 10.1128/mra.00807-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Accepted: 02/07/2025] [Indexed: 03/15/2025] Open
Abstract
We report the complete genome sequences of five bacteria associated with the marine cyanobacterium Capilliphycus salinus ALCB114379 of the phylum Pseudomonadota. This genetic diversity offers insights into the cyanosphere, shedding light on potential relationships between these microorganisms and their cyanobacterial hosts.
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Affiliation(s)
- Gabriel S. Passos
- University of São Paulo (USP), Center for Nuclear Energy in Agriculture (CENA), Piracicaba, Brazil
| | - Thierry A. Pellegrinetti
- University of São Paulo (USP), Center for Nuclear Energy in Agriculture (CENA), Piracicaba, Brazil
| | - Marli F. Fiore
- University of São Paulo (USP), Center for Nuclear Energy in Agriculture (CENA), Piracicaba, Brazil
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183
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Kim JS, Seo CW, Lim YW. Draft genome sequences of five glacial fungi from Styx Glacier, Antarctica. Microbiol Resour Announc 2025; 14:e0117524. [PMID: 40013813 PMCID: PMC11984203 DOI: 10.1128/mra.01175-24] [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: 10/24/2024] [Accepted: 02/07/2025] [Indexed: 02/28/2025] Open
Abstract
We generated four high-quality draft genomes of fungi isolated from Styx Glacier, Antarctica. The genome announcement of these fungal strains offers insights into their evolution and adaptation to extreme glacial environments, as well as their potential biotechnological applications.
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Affiliation(s)
- Ji Seon Kim
- School of Biological Sciences, Institute of Biodiversity, Seoul National University, Seoul, Republic of Korea
| | - Chang Wan Seo
- School of Biological Sciences, Institute of Biodiversity, Seoul National University, Seoul, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences, Institute of Biodiversity, Seoul National University, Seoul, Republic of Korea
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184
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Lautert-Dutra W, dos Santos FM, Pasinato Napp A, Lovato Melo C. Draft genome sequence of Vreelandella stevensii strain BS235 isolated from hypersaline lakes from Brazilian pantanal. Microbiol Resour Announc 2025; 14:e0074824. [PMID: 40079592 PMCID: PMC11984170 DOI: 10.1128/mra.00748-24] [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: 07/08/2024] [Accepted: 01/16/2025] [Indexed: 03/15/2025] Open
Abstract
Mitigating climate crisis has driven biotechnology research toward capturing and utilizing CO2. Production of biosurfactants by microorganisms' metabolism offers a promising solution. We present the draft genome of Vreelandella stevensii strain BS235 from a hypersaline alkaline lake (Pantanal biome, Brazil). We identified genes related to CO2 metabolism and biosurfactant production.
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Affiliation(s)
- William Lautert-Dutra
- Environmental Monitoring and Biotechnology Laboratory, Institute of Petroleum and Natural Resources (IPR), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Francine Melise dos Santos
- Environmental Monitoring and Biotechnology Laboratory, Institute of Petroleum and Natural Resources (IPR), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Amanda Pasinato Napp
- Environmental Monitoring and Biotechnology Laboratory, Institute of Petroleum and Natural Resources (IPR), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Clarissa Lovato Melo
- Environmental Monitoring and Biotechnology Laboratory, Institute of Petroleum and Natural Resources (IPR), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
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185
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Dasgupta A, Saikia R, Kakoti BB, Handique PJ. Draft genome sequence of benzo[a]pyrene degrading Bacillus altitudinis strain AR19 isolated from Digboi oil refinery (India). Microbiol Resour Announc 2025; 14:e0095724. [PMID: 40079616 PMCID: PMC11984180 DOI: 10.1128/mra.00957-24] [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: 10/26/2024] [Accepted: 02/15/2025] [Indexed: 03/15/2025] Open
Abstract
Bacillus altitudinis AR19, isolated from the Digboi oil refinery (India), has a genome size of 3,630,000 bp with a G+C content of 42.45%. The genome encodes 3,755 protein-coding genes, including those for ring-cleaving dioxygenases and biofilm formation. These genes likely play crucial roles in the bacterium's survival in hydrocarbon-enriched environments.
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Affiliation(s)
- Abhisek Dasgupta
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, India
| | - Ratul Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - Bibhuti B. Kakoti
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, India
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186
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Carascal MB, Gonzales JEM, Tañedo MMJT, Papa DMD, Destura RV, Henson KER. Draft genomes of six methicillin-resistant Staphylococcus aureus in a Philippine tertiary hospital with insights on putative antimicrobial and phage resistance mechanisms. Microbiol Resour Announc 2025; 14:e0009725. [PMID: 39998186 PMCID: PMC11984118 DOI: 10.1128/mra.00097-25] [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: 01/31/2025] [Accepted: 02/05/2025] [Indexed: 02/26/2025] Open
Abstract
The genomes of six methicillin-resistant Staphylococcus aureus (MRSA) revealed CC5(ST5)-SCCmec-IVc-spa-t105-PVL+ (n = 3), CC5(ST6)-SCCmec-IVc-spa-t10002 (n = 1), CC5(ST5)-SCCmec-IVa-spa-t002 (n = 1), and CC8(ST8)-SCCmec-IVa-spa-t008-PVL+ (n = 1) genotypes. All possessed multiple antibiotic resistance genes (putative mecA and blaZ, and dfrG for cotrimoxazole-resistant strains), intact staphylococcal prophages, and putative antiphage systems. The results could aid in MRSA infection management and control.
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Affiliation(s)
- Mark B. Carascal
- Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
| | - Jo-Eliz M. Gonzales
- Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
| | - Ma. Mona Joy T. Tañedo
- Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
- Bacteriophage Ecology, Aquaculture, Therapy, and Systematics Laboratory, Research Center for Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Donna May D. Papa
- Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
- Bacteriophage Ecology, Aquaculture, Therapy, and Systematics Laboratory, Research Center for Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Raul V. Destura
- Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
| | - Karl Evans R. Henson
- Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
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187
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Lantican NB, Barredo GAT, Rosana AR, Siababa ACS, Montecillo AD. Draft genomes of five putative biosurfactant-producing Serratia sp. isolates from Laguna de Bay, Philippines. Microbiol Resour Announc 2025; 14:e0126824. [PMID: 40062877 PMCID: PMC11984192 DOI: 10.1128/mra.01268-24] [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: 11/25/2024] [Accepted: 02/07/2025] [Indexed: 04/11/2025] Open
Abstract
Here, we report on the draft genomes of five putative biosurfactant-producing isolates of Serratia sp. from the East, West, and South bays of Laguna de Bay, Philippines. The contigs ranged from 20 to 21, and the genome lengths ranged from 5,175,553 to 5,214,031 bp.
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Affiliation(s)
- Nacita B. Lantican
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Banos, Los Banos, Laguna, Philippines
| | - Glaezel Angelique T. Barredo
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Banos, Los Banos, Laguna, Philippines
| | - Albert R. Rosana
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Banos, Los Banos, Laguna, Philippines
| | - Ann Clarisse S.V. Siababa
- Genetics and Molecular Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Banos, Los Banos, Laguna, Philippines
| | - Andrew D. Montecillo
- Microbiology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Banos, Los Banos, Laguna, Philippines
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188
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Rodriguez-Grados PM, Arbizu CI, Castillo G, Camel V, Conteras-Liza S. Draft genome sequence of the Serratia liquefaciens strain UNJFSC002, isolated from the soil of a potato field of the Bicentenaria variety. Microbiol Resour Announc 2025; 14:e0049524. [PMID: 39998198 PMCID: PMC11984176 DOI: 10.1128/mra.00495-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 02/04/2025] [Indexed: 02/26/2025] Open
Abstract
In this study, we present the draft genome assembly of the Serratia liquefaciens strain UNJFSC002, isolated from the experimental potato field of the Bicentenaria variety at the Universidad Nacional José Faustino Sánchez Carrión, Lima, Peru.
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Affiliation(s)
- Pedro M. Rodriguez-Grados
- Departamento de Agronomía, Universidad Nacional José Faustino Sanchez Carrión, Lima, Peru
- Centro de Investigación en Germoplasma Vegetal y Mejoramiento Genético de Plantas (CIGEMP), Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Amazonas, Peru
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Amazonas, Peru
| | - Carlos I. Arbizu
- Centro de Investigación en Germoplasma Vegetal y Mejoramiento Genético de Plantas (CIGEMP), Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Amazonas, Peru
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Amazonas, Peru
- Facultad de Ingeniería y Ciencias Agrarias, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Amazonas, Peru
| | - Gianmarco Castillo
- Departamento de Agronomía, Universidad Nacional José Faustino Sanchez Carrión, Lima, Peru
| | - Vladimir Camel
- Escuela Profesional de Ingeniería Ambiental, Universidad Cesar Vallejo, Lima, Peru
| | - Sergio Conteras-Liza
- Departamento de Agronomía, Universidad Nacional José Faustino Sanchez Carrión, Lima, Peru
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189
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Goddard M, Leiva S. Draft genome sequence of a novel species of Radiobacillus (strain PE A8.2) isolated from a red Antarctic seaweed. Microbiol Resour Announc 2025; 14:e0127624. [PMID: 40047494 PMCID: PMC11984126 DOI: 10.1128/mra.01276-24] [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: 12/06/2024] [Accepted: 02/10/2025] [Indexed: 04/11/2025] Open
Abstract
We report the draft genome sequence of Radiobacillus sp. nov. PE A8.2, an endospore-forming bacterium isolated from the surface of the red seaweed Pyropia endiviifolia collected in King George Island, Antarctica. The genome assembly comprised 5,183,530 bp, with a 37.5% G+C content and 5,077 coding sequences.
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Affiliation(s)
- Matías Goddard
- Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
| | - Sergio Leiva
- Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
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190
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Ho D, Gali S, Phua HH, Seabra N, Cutfield WS, O'Sullivan JM, the Gut Bugs Study Group WilsonBrooke C.LeongKarenPortlockTheoAlbertBenPookChrisCreaghChristineSvirskisDarren M.HollandDavidDayFrankieVickersMarkDepczynskiMarysiaEdwardsTaygenFreudlspergerSteffiCatoRoseOkanLilaJayasingheThiliniChiavaroliValentinaSchierdingWilliamConlonCathrynJiangYannan, Pahalagedara ASNW. Complete genome sequence of Escherichia marmotae F12YCO47 isolated from a healthy human fecal sample. Microbiol Resour Announc 2025; 14:e0124124. [PMID: 40130925 PMCID: PMC12017327 DOI: 10.1128/mra.01241-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Accepted: 02/24/2025] [Indexed: 03/26/2025] Open
Abstract
Escherichia marmotae has been found in animals and the environment. Here, we isolated it from a healthy human fecal sample. The 4.91 Mb circular genome (GC content = 50.34%) is associated with three plasmids: pF12YCO47-2 (89.9 kb, 50.2% GC), pF12YCO47-3 (47.9 kb, 44.3% GC), and pF12YCO47-1 (95.4 kb, 47.2% GC).
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Affiliation(s)
- Daniel Ho
- Liggins Institute,
University of Auckland,
Auckland, New Zealand
| | - Sucharita Gali
- Liggins Institute,
University of Auckland,
Auckland, New Zealand
| | - Hui Hui Phua
- Liggins Institute,
University of Auckland,
Auckland, New Zealand
| | - Natalia Seabra
- Liggins Institute,
University of Auckland,
Auckland, New Zealand
| | | | - Justin M. O'Sullivan
- Liggins Institute,
University of Auckland,
Auckland, New Zealand
- Maurice Wilkins Centre
for Molecular Biodiscovery, Auckland,
New Zealand
- MRC Lifecourse
Epidemiology Unit, University of
Southampton,
Southampton, United Kingdom
- Singapore Institute
for Clinical Sciences, Agency for Science, Technology and Research
(A*STAR),
Singapore, Singapore
| | - the Gut Bugs Study GroupWilsonBrooke C.LeongKarenPortlockTheoAlbertBenPookChrisCreaghChristineSvirskisDarren M.HollandDavidDayFrankieVickersMarkDepczynskiMarysiaEdwardsTaygenFreudlspergerSteffiCatoRoseOkanLilaJayasingheThiliniChiavaroliValentinaSchierdingWilliamConlonCathrynJiangYannan
- Liggins Institute,
University of Auckland,
Auckland, New Zealand
- Maurice Wilkins Centre
for Molecular Biodiscovery, Auckland,
New Zealand
- MRC Lifecourse
Epidemiology Unit, University of
Southampton,
Southampton, United Kingdom
- Singapore Institute
for Clinical Sciences, Agency for Science, Technology and Research
(A*STAR),
Singapore, Singapore
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191
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Al-Shiti AY, Faisal RM, Salih TS, Zylstra GJ. Draft genome sequence of the naphthalene-degrading bacterium Rhodococcus pyridinivorans RA1 isolated from an industrial soil sample in Mosul, Iraq. Microbiol Resour Announc 2025; 14:e0061124. [PMID: 40105338 PMCID: PMC11984159 DOI: 10.1128/mra.00611-24] [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: 06/07/2024] [Accepted: 01/04/2025] [Indexed: 03/20/2025] Open
Abstract
Rhodococcus pyridinivorans RA1 was isolated for the ability to grow on naphthalene from an industrial site near Mosul, Iraq. The draft genome is 5,419,924 bp with a GC content of 67.5%.
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Affiliation(s)
| | - Rayan M. Faisal
- Department of Biology, College of Science, University of Mosul, Mosul, Iraq
| | - Talal S. Salih
- Department of Medical Physics, College of Science, University of Mosul, Mosul, Iraq
| | - Gerben J. Zylstra
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
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192
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Moreland RB, Choi BI, Fontes Noronha M, Baker J, Kaindl J, Wolfe AJ. Complete genome sequence of Trueperella bernardiae strain UMB8254, isolated from the bladder of a female with metabolic syndrome and nephrolithiasis. Microbiol Resour Announc 2025; 14:e0126524. [PMID: 40116497 PMCID: PMC11984175 DOI: 10.1128/mra.01265-24] [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: 11/28/2024] [Accepted: 02/13/2025] [Indexed: 03/23/2025] Open
Abstract
Trueperella bernardiae is infrequently isolated, usually in polymicrobial communities, from human hosts with a wide variety of symptoms and diseases. Here, we report a complete genome sequence of Trueperella bernardiae (UMB8254), isolated from the bladder of a human female with metabolic syndrome and nephrolithiasis.
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Affiliation(s)
- Robert B. Moreland
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Brian I. Choi
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Melline Fontes Noronha
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Josh Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Jacob Kaindl
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
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193
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Alam M, Hassan T, Nizami TA, Akter L, Rakib TM. Draft genome sequences of four lactic acid bacteria from fermented chicken meat unveil biosynthetic gene clusters for antimicrobial compounds. Microbiol Resour Announc 2025; 14:e0003825. [PMID: 40062850 PMCID: PMC11984134 DOI: 10.1128/mra.00038-25] [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: 01/17/2025] [Accepted: 02/07/2025] [Indexed: 04/11/2025] Open
Abstract
Lactic acid bacteria play a crucial role in fermented food production and serve as important sources of antimicrobial peptides. This study reports four lactic acid bacteria strains isolated from fermented chicken meat, which harbor biosynthetic gene clusters encoding antimicrobial compounds. These strains are classified within the genera Pediococcus and Lactiplantibacillus.
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Affiliation(s)
- Mahabub Alam
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Tamanna Hassan
- Faculty of Food Science and Technology, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Tanvir Ahmad Nizami
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Lipi Akter
- Transboundary Animal Diseases Research Center, Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Tofazzal Md Rakib
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
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194
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Ma Z, Liu F, Tsui CKM, Cai L. Phylogenomics and adaptive evolution of the Colletotrichum gloeosporioides species complex. Commun Biol 2025; 8:593. [PMID: 40204844 PMCID: PMC11982366 DOI: 10.1038/s42003-025-08024-9] [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: 09/24/2024] [Accepted: 03/31/2025] [Indexed: 04/11/2025] Open
Abstract
The Colletotrichum gloeosporioides species complex (CGSC) is one of the most devastating fungal phytopathogens, and is composed of three main clades: Kahawae, Musae, and Theobromicola. Despite the diversity of CGSC, there is limited understanding on their evolutionary mechanisms. By analysing 49 newly assembled genomes, we found that the expansion of transposable elements, especially long terminal repeat retrotransposons, facilitates the expansion of genome size and genetic variation. In-depth analyses suggested that an intra-chromosomal inversion may have been the driving force behind the divergence of Kahawae clade from its ancestor. Within the Kahawae clade, the narrow-hosted quarantine species C. kahawae has undergone extensive chromosomal rearrangements mediated by repetitive sequences, generating highly dynamic lineage-specific genomic regions compared to the closely related broad-hosted species C. cigarro. The findings of this study highlight the role of chromosomal rearrangements in promoting genetic diversification and host adaptation, and provide new perspectives for understanding the evolution of phytopathogenic fungi.
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Affiliation(s)
- Ziying Ma
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Fang Liu
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Infectious Disease Research Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Lei Cai
- State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China.
- University of Chinese Academy of Sciences, Beijing, PR China.
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195
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Das BK, Kumar V, Roy S, Mohanty D, Dhar S, Pradhan SP. Genome assembly of multidrug-resistant Enterococcus gallinarum IFEGHNEK1 isolated from bighead carp, Hypophthalmichthys nobilis. Microbiol Resour Announc 2025; 14:e0106324. [PMID: 40111077 PMCID: PMC11984158 DOI: 10.1128/mra.01063-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Accepted: 03/01/2025] [Indexed: 03/22/2025] Open
Abstract
Enterococcus gallinarum IFEGHNEK1 is a multidrug-resistant bacterium belonging to the Enterococcaceae family isolated from bighead carp in 2023. We report the complete genome sequence of E. gallinarum (CP169314) containing a 3.15 Mb genome.
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Affiliation(s)
- Basanta Kumar Das
- Aquatic Environmental Biotechnology (AEB) Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Vikash Kumar
- Aquatic Environmental Biotechnology (AEB) Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Suvra Roy
- Aquatic Environmental Biotechnology (AEB) Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Debasmita Mohanty
- Aquatic Environmental Biotechnology (AEB) Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Souvik Dhar
- Aquatic Environmental Biotechnology (AEB) Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Smruti Priyambada Pradhan
- Aquatic Environmental Biotechnology (AEB) Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
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196
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Martínez JRW, Alcalde-Rico M, Jara-Videla E, Reyes J, Carvajal LP, Rincon S, Ríos R, Diaz L, Quesille-Villalobos A, Riquelme-Neira R, Rivas L, Moustafa AM, Hanson B, Undurraga EA, Olivares-Pacheco J, García P, Araos R, Planet PJ, Arias CA, Munita JM. Geographic divergence of methicillin-resistant Staphylococcus aureus ST5-SCC mecI in the aftermath of a major earthquake and tsunami: impact of a plasmid harboring heavy metal resistance genes. mBio 2025; 16:e0366924. [PMID: 40105358 PMCID: PMC11980568 DOI: 10.1128/mbio.03669-24] [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: 12/19/2024] [Accepted: 02/18/2025] [Indexed: 03/20/2025] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health menace. The global spread of MRSA is characterized by successive waves of epidemic clones dominating specific geographical regions. The acquisition of genes encoding resistance to heavy metals (HMRGs) is thought to be a key feature in the geographic divergence of MRSA. However, the cause-effect relationship between the presence of HMRGs and the divergence of MRSA clones remains to be clarified. In this study, we assessed the role that HMRGs may have played in the evolutionary divergence of the MRSA ST5-SCCmecI lineage in Latin America. We conducted a genomic characterization of 113 MRSA clinical isolates from six Latin American healthcare centers, including 53 isolates collected from two cities in Chile (Santiago and Concepción). We found a plasmid (pSCL4752) harboring arsenic, cadmium, and mercury resistance genes in 65% (n = 71) of the ST5-SCCmecI isolates. We also observed a geographic divergence associated with the presence of pSCL4752 in Chilean isolates, with a higher frequency in isolates from Concepción (88%) compared to Santiago (29%). Interestingly, a molecular clock analysis revealed that this divergence occurred in the aftermath of an 8.8 Mw earthquake and tsunami that struck the Concepción area in 2010. Moreover, our results demonstrate that the carriage of pSCL4752 can be beneficial or detrimental for ST5-SCCmecI isolates, depending on the environmental availability of these heavy metals. Our results suggest that the divergence of the ST5-SCCmecI MRSA lineage in Latin America could have been fostered by environmental disasters and influenced by the presence/absence of HMRGs harbored in a plasmid.IMPORTANCEMethicillin-resistant Staphylococcus aureus (MRSA) is a major cause of life-threatening infections worldwide and a growing public health concern. The rise of antibiotic-resistant bacteria, such as MRSA, is often linked to genetic adaptations that enhance their survival. Our research sheds light on how environmental changes, such as those triggered by a natural disaster, can influence the evolution and geographic spread of a highly resistant MRSA lineage in Latin America. We identified a plasmid carrying genes for resistance to arsenic, cadmium, and mercury, which was associated with the geographic divergence of the ST5-SCCmecI MRSA lineage, with striking differences in its prevalence between regions affected by a major earthquake and tsunami. By linking environmental events to pathogen evolution, our study highlights the role of ecological pressures in the spread of MRSA. These findings emphasize the need to integrate environmental monitoring into public health strategies to better understand the global challenge of antimicrobial resistance.
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Affiliation(s)
- Jose R. W. Martínez
- Genomics & Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Manuel Alcalde-Rico
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Grupo de Resistencia a los Antibióticos en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaiso, Chile
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena, CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Estefanía Jara-Videla
- Genomics & Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Lina P. Carvajal
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Sandra Rincon
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Rafael Ríos
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Lorena Diaz
- Genomics & Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Ana Quesille-Villalobos
- Genomics & Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Roberto Riquelme-Neira
- Genomics & Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Santiago, Chile
| | - Lina Rivas
- Genomics & Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Ahmed M. Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Blake Hanson
- Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, Texas, USA
| | - Eduardo A. Undurraga
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Santiago, Chile
- Research Center for Integrated Disaster Risk Management (CIGIDEN), Santiago, Chile
- CIFAR Azrieli Global Scholars Program, CIFAR, Toronto, Canada
| | - Jorge Olivares-Pacheco
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Grupo de Resistencia a los Antibióticos en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaiso, Chile
| | - Patricia García
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Departamento de Enfermedades Infecciosas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rafael Araos
- Genomics & Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Paul J. Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- American Museum of Natural History, New York, New York, USA
| | - César A. Arias
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Jose M. Munita
- Genomics & Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
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197
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Hartley GA, Okhovat M, Hoyt SJ, Fuller E, Pauloski N, Alexandre N, Alexandrov I, Drennan R, Dubocanin D, Gilbert DM, Mao Y, McCann C, Neph S, Ryabov F, Sasaki T, Storer JM, Svendsen D, Troy W, Wells J, Core L, Stergachis A, Carbone L, O'Neill RJ. Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon. CELL GENOMICS 2025; 5:100808. [PMID: 40088887 PMCID: PMC12008813 DOI: 10.1016/j.xgen.2025.100808] [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: 09/16/2024] [Revised: 12/10/2024] [Accepted: 02/12/2025] [Indexed: 03/17/2025]
Abstract
Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here, we characterize fully assembled centromeres in the eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha-satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence that this epigenetic feature is conserved in the absence of satellite arrays. We uncovered a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, we identify duplications and deletions in HLE centromeres that distinguish them from other gibbons. Finally, we observed differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, and thus propose that a combination of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.
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Affiliation(s)
- Gabrielle A Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Savannah J Hoyt
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Emily Fuller
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Nicole Pauloski
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Nicolas Alexandre
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ivan Alexandrov
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ryan Drennan
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA
| | - Yizi Mao
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Christine McCann
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Shane Neph
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Fedor Ryabov
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Takayo Sasaki
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA
| | - Jessica M Storer
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Derek Svendsen
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | | | - Jackson Wells
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA
| | - Leighton Core
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Andrew Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA; Division of Genetics, Oregon National Primate Research Center, Portland, OR, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
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198
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Lian WH, He HH, Wang Y, Zheng ZH, Chen F, Zhou T, Hu CJ, Han JR, Dong L, Li WJ. Rubrolithibacter danxiaensis gen. nov., sp. nov. isolated from red sandy conglomerate in the Danxia Mountain. Antonie Van Leeuwenhoek 2025; 118:66. [PMID: 40195124 DOI: 10.1007/s10482-025-02078-9] [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: 02/07/2025] [Accepted: 03/22/2025] [Indexed: 04/09/2025]
Abstract
A Gram-stain-negative, rod-shaped and non-motile bacterium, designated as strain SYSU DXS3258T, was isolated from red sandy conglomerate sample collected from the Danxia Mountain in Guangdong Province, PR China. The bacterium was found to grow optimally at 28 °C, pH 7.0, and with 0-1% (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain SYSU DXS3258T within the family Sphingobacteriaceae. Strain SYSU DXS3258T showed the highest 16S rRNA gene sequence similarity to Pararcticibacter tournemirensis TF5-37.2-LB10T (95.5%), Paradesertivirga mongoliensis 1-32 T (95.3%) and Desertivirga xinjiangensis 12157 T (95.2%). Digital DNA-DNA hybridization, orthologous average nucleotide identity and average amino acid identity values between strain SYSU DXS3258T and the closest related members within the Sphingobacteriaceae were ≤ 13%, 70.3% and 69.9%, respectively. The genomic DNA G + C content was 38.8%. The major fatty acid was iso-C15:0, C18:0 and C15:0 2-OH. The predominant polar lipids were phosphatidylethanolamine, three glycolipids, one phospholipid and one unidentified polar lipid. The major respiratory quinone was Q-7. Based on phenotypic, phylogenetic, chemotaxonomic and genomic results, we propose that strain SYSU DXS3258T represents a novel species of a novel genus within the family Sphingobacteriaceae, for which the name Rubrolithibacter danxiaensis gen. nov., sp. nov. was proposed. The type strain is SYSU DXS3258T (= MCCC 1K09420T = KCTC 102322 T).
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Affiliation(s)
- Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat‑Sen University, Guangzhou, People's Republic of China
| | - Huan-Huan He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat‑Sen University, Guangzhou, People's Republic of China
| | - Ying Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat‑Sen University, Guangzhou, People's Republic of China
| | - Zhuo-Huan Zheng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat‑Sen University, Guangzhou, People's Republic of China
| | - Fang Chen
- Administrative Commission of Danxiashan National Park, Shaoguan, 512300, People's Republic of China
| | - Ting Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat‑Sen University, Guangzhou, People's Republic of China
| | - Chao-Jian Hu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat‑Sen University, Guangzhou, People's Republic of China
| | - Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat‑Sen University, Guangzhou, People's Republic of China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat‑Sen University, Guangzhou, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat‑Sen University, Guangzhou, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China.
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199
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Connors E, Gallagher KL, Dutta A, Oliver M, Bowman JS. Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot. Polar Biol 2025; 48:62. [PMID: 40206699 PMCID: PMC11976824 DOI: 10.1007/s00300-025-03380-y] [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: 10/15/2024] [Revised: 03/20/2025] [Accepted: 03/21/2025] [Indexed: 04/11/2025]
Abstract
The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon. Supplementary Information The online version contains supplementary material available at 10.1007/s00300-025-03380-y.
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Affiliation(s)
- Elizabeth Connors
- Scripps Institution of Oceanography, UC San Diego, 8622 Kennel Way, La Jolla, CA 92037 USA
- Scripps Polar Center, UC San Diego, La Jolla, CA USA
| | | | - Avishek Dutta
- Department of Geology, University of Georgia, Athens, GA USA
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC USA
| | - Matthew Oliver
- School of Marine Science and Policy, University of Delaware, Newark, DE USA
| | - Jeff S. Bowman
- Scripps Institution of Oceanography, UC San Diego, 8622 Kennel Way, La Jolla, CA 92037 USA
- Scripps Polar Center, UC San Diego, La Jolla, CA USA
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200
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Oliveira ES, Arantes LCRV, Vieira de Lima GB, Alves VV, Gabardo MDP, Brenig B, Azevedo V, Aburjaile FF, Freitas Neto OCD, Ecco R. An outbreak in week-old broiler chicks caused by a highly virulent and multidrug-resistant strain of Salmonella Gallinarum. Avian Pathol 2025:1-7. [PMID: 40091670 DOI: 10.1080/03079457.2025.2480800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
RESEARCH HIGHLIGHTS Salmonella Gallinarum infection in chicks resulted in a mortality rate of 42%.Chicks had unusual lesions such as haemorrhagic enteritis and interstitial pneumonia.Whole genome analysis of the SG isolate revealed exclusive antimicrobial resistance genes.Higher number of exclusive virulence genes were related to severe fowl typhoid in chicks.
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Affiliation(s)
- Eric Santos Oliveira
- Pathology Sector, Department of Veterinary Clinic and Surgery, Veterinary School, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Letícia Cury Rocha Veloso Arantes
- Departament of Preventive Veterinary Medicine, Veterinary School, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Gabryel Bernardo Vieira de Lima
- Departament of Preventive Veterinary Medicine, Veterinary School, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Victória Veiga Alves
- Departament of Preventive Veterinary Medicine, Veterinary School, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | | | - Bertram Brenig
- Institute of Veterinary Medicine, University Göttingen, Göttingen, Germany
| | - Vasco Azevedo
- Genetics, Ecology and Evolution Department, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Flávia Figueira Aburjaile
- Departament of Preventive Veterinary Medicine, Veterinary School, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Oliveiro Caetano de Freitas Neto
- Departament of Preventive Veterinary Medicine, Veterinary School, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Roselene Ecco
- Pathology Sector, Department of Veterinary Clinic and Surgery, Veterinary School, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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