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Berryhill BA, Burke KB, Fontaine J, Brink CE, Harvill MG, Goldberg DA, Konstantinidis KT, Levin BR, Woodworth MH. Enteric Populations of Escherichia coli are Likely to be Resistant to Phages Due to O Antigen Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.08.566299. [PMID: 37986824 PMCID: PMC10659284 DOI: 10.1101/2023.11.08.566299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
There is a surfeit of bioinformatic data showing that bacteriophages abound in the enteric microbiomes of humans. What is the contribution of these viruses in shaping the bacterial strain and species composition of the gut microbiome and how are these phages maintained over time? To address these questions, we performed experiments with Escherichia coli and phages isolated from four fecal microbiota transplantation (FMT) doses as representative samples of non-dysbiotic enteric microbiota and develop and analyze the properties of a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our models predict and experiments confirm that due to production of the O antigen, E. coli in the enteric microbiome are likely to be resistant to infection with co-occurring phages. Furthermore, our modeling suggests that the phages can be maintained in the population due to the high rates of host transition between resistant and sensitive states, which we call leaky resistance. Based on our observations and model predictions, we postulate that the phages found in the human gut are likely to play little role in shaping the composition of E. coli at the strain level in the enteric microbiome in healthy individuals. How general this is for other species of bacteria in the enteric flora is not yet clear, although O antigen expression is common across many taxa.
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Affiliation(s)
- Brandon A. Berryhill
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
- Program in Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Laney Graduate School, Emory University; Atlanta, Georgia, 30322, USA
| | - Kylie B. Burke
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Jake Fontaine
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Catherine E. Brink
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mason G. Harvill
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - David A. Goldberg
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Konstantinos T. Konstantinidis
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bruce R. Levin
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Michael H. Woodworth
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
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202
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Wei H, Chen J, Lu Z, Zhang X, Liu G, Lian B, Chen Y, Zhong F, Yu C, Zhang J. Crape myrtle LiGAoxs displaying activities of gibberellin oxidases respond to branching architecture. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108738. [PMID: 38761544 DOI: 10.1016/j.plaphy.2024.108738] [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: 12/22/2023] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024]
Abstract
In the realm of ornamental horticulture, crape myrtle (Lagerstroemia indica) stands out for its aesthetic appeal, attributed largely to its vibrant flowers and distinctive branching architecture. This study embarked on a comprehensive exploration of the gibberellin oxidase (GAox) gene family in crape myrtle, illuminating its pivotal role in regulating GA levels, a key determinant of plant developmental processes. We identified and characterized 36 LiGAox genes, subdivided into GA2ox, GA3ox, GA20ox, and GAox-like subgroups, through genomic analyses. These genes' evolutionary trajectories were delineated, revealing significant gene expansions attributed to segmental duplication events. Functional analyses highlighted the divergent expression patterns of LiGAox genes across different crape myrtle varieties, associating them with variations in flower color and branching architecture. Enzymatic activity assays on selected LiGA2ox enzymes exhibited pronounced GA2 oxidase activity, suggesting a potential regulatory role in GA biosynthesis. Our findings offered a novel insight into the molecular underpinnings of GA-mediated growth and development in L. indica, providing a foundational framework for future genetic enhancements aimed at optimizing ornamental traits.
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Affiliation(s)
- Hui Wei
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong, 226000, China.
| | - Jinxin Chen
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong, 226000, China.
| | - Zixuan Lu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong, 226000, China.
| | - Xingyue Zhang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong, 226000, China.
| | - Guoyuan Liu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong, 226000, China.
| | - Bolin Lian
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong, 226000, China.
| | - Yanhong Chen
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong, 226000, China.
| | - Fei Zhong
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong, 226000, China.
| | - Chunmei Yu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong, 226000, China.
| | - Jian Zhang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China; Key Lab of Landscape Plant Genetics and Breeding, Nantong, 226000, China.
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203
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Shi K, Feng S, Zhao L, Chen J, Song W, Jia Y, Qu X, Liu Z, Jia W, Du S, Liao M. N-glycosylation on hemagglutinin head reveals inter-branch antigenic variability of avian influenza virus H5-subtypes. Int J Biol Macromol 2024; 273:132901. [PMID: 38848854 DOI: 10.1016/j.ijbiomac.2024.132901] [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: 03/29/2024] [Revised: 05/19/2024] [Accepted: 06/02/2024] [Indexed: 06/09/2024]
Abstract
H5-subtype avian influenza virus (AIV) is globally prevalent and undergoes frequent antigenic drift, necessitating regular updates to vaccines. One of the many influencing elements that cause incompatibility between vaccinations and epidemic strains is the dynamic alteration of glycosylation sites. However, the biological significance of N-glycosylation in the viral evolution and antigenic changes is unclear. Here, we performed a systematic analysis of glycosylation sites on the HA1 subunit of H5N1, providing insights into the changes of primary glycosylation sites, including 140 N, 156 N, and 170 N within the antigenic epitopes of HA1 protein. Multiple recombinant viruses were then generated based on HA genes of historical vaccine strains and deactivated for immunizing SPF chickens. Inactivated recombinant strains showed relatively closer antigenicity compared to which has identical N-glycosylation patterns. The N-glycosylation modification discrepancy highlights the inter-branch antigenic diversity of H5-subtype viruses in avian influenza and serves as a vital foundation for improving vaccination tactics.
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Affiliation(s)
- Keyi Shi
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Saixiang Feng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Li Zhao
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Junhong Chen
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wei Song
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yusheng Jia
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyun Qu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhicheng Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Weixin Jia
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
| | - Shouwen Du
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Wuhan 430030, China.
| | - Ming Liao
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Zhongkai University of Agricultural and Engineering, Guangzhou 510550, China.
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204
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Okoh EB, Payne M, Lan R, Riegler M, Chapman TA, Bogema DR. A Multilocus Sequence Typing Scheme for Rapid Identification of Xanthomonas citri Based on Whole-Genome Sequencing Data. PHYTOPATHOLOGY 2024; 114:1480-1489. [PMID: 38669587 DOI: 10.1094/phyto-12-23-0490-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Xanthomonas citri is a plant-pathogenic bacterium associated with a diverse range of host plant species. It has undergone substantial reclassification and currently consists of 14 different subspecies or pathovars that are responsible for a wide range of plant diseases. Whole-genome sequencing (WGS) provides a cutting-edge advantage over other diagnostic techniques in epidemiological and evolutionary studies of X. citri because it has a higher discriminatory power and is replicable across laboratories. WGS also allows for the improvement of multilocus sequence typing (MLST) schemes. In this study, we used genome sequences of Xanthomonas isolates from the NCBI RefSeq database to develop a seven-gene MLST scheme that yielded 19 sequence types (STs) that correlated with phylogenetic clades of X. citri subspecies or pathovars. Using this MLST scheme, we examined 2,911 Xanthomonas species assemblies from NCBI GenBank and identified 15 novel STs from 37 isolates that were misclassified in NCBI. In total, we identified 545 X. citri assemblies from GenBank with 95% average nucleotide identity to the X. citri type strain, and all were classified as one of the 34 STs. All MLST classifications correlated with a phylogenetic position inferred from alignments using 92 conserved genes. We observed several instances where strains from different pathovars formed closely related monophyletic clades and shared the same ST, indicating that further investigation of the validity of these pathovars is required. Our MLST scheme described here is a robust tool for rapid classification of X. citri pathovars using WGS and a powerful method for further comprehensive taxonomic revision of X. citri pathovars.
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Affiliation(s)
- Efenaide B Okoh
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW, Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Toni A Chapman
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
| | - Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia
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205
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Williams SE, Varliero G, Lurgi M, Stach JEM, Race PR, Curnow P. Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 39073401 DOI: 10.1099/mic.0.001478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.
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Affiliation(s)
- Sam E Williams
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs., Lyngby, Denmark
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Miguel Lurgi
- Department of Biosciences, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul R Race
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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206
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Dekhil N, Mardassi H. Delineating the evolutionary pathway to multidrug-resistant outbreaks of a Mycobacterium tuberculosis L4.1.2.1/Haarlem sublineage. Int J Infect Dis 2024; 144:107077. [PMID: 38697608 DOI: 10.1016/j.ijid.2024.107077] [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: 02/20/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024] Open
Abstract
OBJECTIVES We sought to capture the evolutionary itinerary of the Mycobacterium tuberculosis L4.1.2.1/Haarlem sublineage in northern Tunisia, where it caused a major multidrug-resistant (MDR) tuberculosis outbreak in a context strictly negative for HIV infection. METHODS We combined whole genome sequencing and Bayesian approaches using a representative collection of drug-susceptible and drug-resistant L4.1.2.1/Haarlem clinical strains (n = 121) recovered from the outbreak region over 16 years. RESULTS In the absence of drug resistance, the L4.1.2.1/Haarlem sublineage showed a propensity for rapid transmission as witnessed by the high clustering (44.6%) and recent transmission rates (25%), as well as the reduced mean distance between genome pairs. The entire pool of L4.1.2.1/Haarlem MDR strains was found to be linked to either the aforementioned major outbreak (68 individuals, 2001-2016) or to a minor, newly uncovered outbreak (six cases, 2001-2011). Strikingly, the two outbreaks descended independently from a common ancestor that can be dated back to 1886. CONCLUSIONS Our data point to the intrinsic propensity for rapid transmission of the M. tuberculosis L4.1.2.1/Haarlem sublineage in northern Tunisia, linking the overall MDR tuberculosis epidemic to a single ancestor. These findings bring out the important role of the bacillus' genetic background in the emergence of successful MDR M. tuberculosis clones.
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Affiliation(s)
- Naira Dekhil
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Helmi Mardassi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.
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207
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Rivero de Aguilar J, Barroso O, Bonaccorso E, Cadena H, Hussing L, Jorquera J, Martinez J, Martínez‐de la Puente J, Marzal A, León Miranda F, Merino S, Matta NE, Ramenofsky M, Rozzi R, Valeris‐Chacín CE, Vásquez RA, Vianna JA, Wingfield JC. Associations among MHC genes, latitude, and avian malaria infections in the rufous-collared sparrow ( Zonotrichia capensis). Ecol Evol 2024; 14:e11634. [PMID: 39026957 PMCID: PMC11255377 DOI: 10.1002/ece3.11634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
The major histocompatibility complex (MHC) is a genetic region in jawed vertebrates that contains key genes involved in the immune response. Associations between the MHC and avian malaria infections in wild birds have been observed and mainly explored in the Northern Hemisphere, while a general lack of information remains in the Southern Hemisphere. Here, we investigated the associations between the MHC genes and infections with Plasmodium and Haemoproteus blood parasites along a latitudinal gradient in South America. We sampled 93 rufous-collared sparrows (Zonotrichia capensis) individuals from four countries, Colombia, Ecuador, Peru, and Chile, and estimated MHC-I and MHC-II allele diversity. We detected between 1-4 (MHC-I) and 1-6 (MHC-II) amino acidic alleles per individual, with signs of positive selection. We obtained generalized additive mixed models to explore the associations between MHC-I and MHC-II diversity and latitude. We also explored the relationship between infection status and latitude/biome. We found a non-linear association between the MHC-II amino acidic allele diversity and latitude. Individuals from north Chile presented a lower MHC genetic diversity than those from other locations. We also found an association between deserts and xeric shrublands and a lower prevalence of Haemoproteus parasites. Our results support a lower MHC genetic in arid or semi-arid habitats in the region with the lower prevalence of Haemoproteus parasites.
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Affiliation(s)
- Juan Rivero de Aguilar
- Centro Subantártico Cabo de Hornos (CHIC)Universidad de MagallanesPuerto WilliamsChile
- Departamento de Ciencias Ecológicas, Facultad de CienciasUniversidad de ChileSantiagoChile
- Instituto de Ecología y Biodiversidad, Facultad de CienciasUniversidad de ChileSantiagoChile
| | - Omar Barroso
- Centro Subantártico Cabo de Hornos (CHIC)Universidad de MagallanesPuerto WilliamsChile
| | - Elisa Bonaccorso
- Laboratorio de Biología Evolutiva, and Instituto Biósfera, Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de QuitoQuitoEcuador
- Centro de la Biodiversidad y Cambio ClimáticoUniversidad Tecnológica IndoaméricaQuitoEcuador
| | - Hector Cadena
- Centro de la Biodiversidad y Cambio ClimáticoUniversidad Tecnológica IndoaméricaQuitoEcuador
| | - Lucas Hussing
- Departamento de Ciencias Ecológicas, Facultad de CienciasUniversidad de ChileSantiagoChile
| | - Josefina Jorquera
- Departamento de Ecología, Instituto Para el Desarrollo Sustentable, Facultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Javier Martinez
- Departamento de Biomedicina y Biotecnología (Area de Parasitología)Universidad de Alcalá de HenaresMadridSpain
| | - Josué Martínez‐de la Puente
- Departamento de ParasitologíaUniversidad de GranadaGranadaSpain
- Ciber de Epidemiología y Salud Pública (CIBERESP)MadridSpain
| | - Alfonso Marzal
- Departamento de Anatomía, Biología Celular y Zoología, Facultad de BiologíaUniversidad de ExtremaduraBadajozSpain
- Grupo de Investigaciones en Fauna SilvestreUniversidad Nacional de San MartínTarapotoPeru
| | - Fabiola León Miranda
- Departamento de Ecología, Instituto Para el Desarrollo Sustentable, Facultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Santiago Merino
- Departamento de Ecología EvolutivaMuseo Nacional de Ciencias Naturales CSICMadridSpain
| | - Nubia E. Matta
- Departamento de Biología, Facultad de CienciasUniversidad Nacional de ColombiaBogotáColombia
| | - Marilyn Ramenofsky
- Department of Neurobiology, Physiology and BehaviorUniversity of CaliforniaDavisCaliforniaUSA
| | - Ricardo Rozzi
- Centro Subantártico Cabo de Hornos (CHIC)Universidad de MagallanesPuerto WilliamsChile
| | - Carlos E. Valeris‐Chacín
- Centro Subantártico Cabo de Hornos (CHIC)Universidad de MagallanesPuerto WilliamsChile
- Departamento de Ciencias Ecológicas, Facultad de CienciasUniversidad de ChileSantiagoChile
| | - Rodrigo A. Vásquez
- Centro Subantártico Cabo de Hornos (CHIC)Universidad de MagallanesPuerto WilliamsChile
- Departamento de Ciencias Ecológicas, Facultad de CienciasUniversidad de ChileSantiagoChile
- Instituto de Ecología y Biodiversidad, Facultad de CienciasUniversidad de ChileSantiagoChile
| | - Juliana A. Vianna
- Departamento de Ecología, Instituto Para el Desarrollo Sustentable, Facultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
- Millennium Institute Center for Genome Regulation (CRG)Millennium Institute of Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Millennium Nucleus of Patagonian Limit of Life (LiLi)SantiagoChile
| | - John C. Wingfield
- Department of Neurobiology, Physiology and BehaviorUniversity of CaliforniaDavisCaliforniaUSA
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Wang Q, Liu H, Yao Y, Chen H, Yang Z, Xie H, Cui R, Liu H, Li C, Gong W, Yu Y, Hua X, Li S. Emergence of novel hypervirulent Acinetobacter baumannii strain and herpes simplex type 1 virus in a case of community-acquired pneumonia in China. J Infect Public Health 2024; 17:102456. [PMID: 38820896 DOI: 10.1016/j.jiph.2024.05.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/24/2024] [Accepted: 05/16/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND A. baumannii is an important and common clinical pathogen, especially in the intensive care unit (ICU). This study aimed to characterize one hypervirulent A. baumannii strain in a patient with community-acquired pneumonia and herpes simplex type 1 virus infection. METHODS Minimum inhibitory concentrations (MICs) were determined using the Kirby-Bauer (K-B) and broth microdilution methods. Galleria mellonella infection model experiment was conducted. Whole-genome sequencing (WGS) was performed using the Illumina and Nanopore platforms. The resistance and virulence determinants were identified using the ABRicate program with ResFinder and the VFDB database. The capsular polysaccharide locus (K locus) and lipooligosaccharide outer core locus (OC locus) were identified using Kleborate with Kaptive. Phylogenetic analyses were conducted using the BacWGSTdb server. RESULTS A. baumannii XH2146 strain belongs to ST10Pas and ST447Oxf. The strain was resistant to cefazolin, ciprofloxacin, and trimethoprim/sulfamethoxazole (TMP-SMX). Bautype and Kaptive analyses showed that XH2146 contains OCL2 and KL49. WGS analysis revealed that the strain harbored blaADC-76, blaOXA-68, ant(3'')-IIa, tet(B), and sul2. Notably, tet(B) and sul2, both were located within a 114,700-bp plasmid (designated pXH2146-1). Virulence assay revealed A. baumannii XH2146 possessed higher virulence than A. baumannii AB5075 at 12 h. Comparative genomic analysis showed that A. baumannii ST447 strains were mainly isolated from the USA and exhibited a relatively close genetic relationship. Importantly, 11 strains were observed to carry blaOXA-58; blaOXA-23 was identified in 11 isolates and three ST447 A. baumannii strains harbored blaNDM-1. CONCLUSIONS Early detection of community-acquired hypervirulent Acinetobacter baumannii strains is recommended to prevent their extensive spread in hospitals.
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Affiliation(s)
- Qiujing Wang
- Department of Infectious Diseases, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, Zhejiang, China
| | - Haiyang Liu
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, 158 Shangtang Road, Hangzhou, Zhejiang 310014, China
| | - Yue Yao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hangfei Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhejuan Yang
- Department of Infectious Diseases, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, Zhejiang, China
| | - Haibo Xie
- Intensive care unit (ICU), Zhoushan Women and Children Hospital, China
| | - Rongna Cui
- Intensive care unit (ICU), Zhoushan Women and Children Hospital, China
| | - Huasheng Liu
- Department of Infectious Diseases, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, Zhejiang, China
| | - Chuner Li
- Microbiological laboratory, Zhoushan Hospital, Wenzhou Medical University, China
| | - Weiping Gong
- Department of dermatology, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, Zhejiang, China
| | - Yunsong Yu
- Center for General Practice Medicine, Department of Infectious Diseases, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Shibo Li
- Department of Infectious Diseases, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, Zhejiang, China.
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209
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Sreya PK, Hari Naga Papa Rao A, Suresh G, Sasikala C, Venkata Ramana C. Genomic and functional insights of a mucin foraging Rhodopirellula halodulae sp. nov. Syst Appl Microbiol 2024; 47:126523. [PMID: 38897058 DOI: 10.1016/j.syapm.2024.126523] [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: 02/10/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Nine novel strains were obtained from various algal and seagrass samples. The analysis of the 16S rRNA gene-based phylogenetic tree revealed monophyletic placement of all novel strains within the Rhodopirellula genus. The type strain was identified as JC737T, which shared 99.1 % 16S rRNA gene sequence identity with Rhodopirellula baltica SH1T, while strain JC740 was designated as an additional strain. The genome sizes of strains JC737T and JC740 were 6.6 and 6.7 Mb, respectively, and the G + C content was 56.2 %. The strains cladded distinctly in the phylogenomic tree, and the ANI and dDDH values of the strain JC737T were 75.8-76.1 % and 20.8-21.3 %, respectively, in comparison to other Rhodopirellula members. The strain demonstrated a versatile degradation capability, exhibiting a diverse array of complex polysaccharides, including mucin which had not been previously identified within the members of the phylum Planctomycetota. The phylogenomic, pan-genomic, morphological, physiological, and genomic characterization of the strain lead to the proposal to describe the strain as Rhodopirellula halodulae sp. nov.
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Affiliation(s)
- P K Sreya
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Atham Hari Naga Papa Rao
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Gandham Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | | | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India.
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210
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Lin J, Bjørk PK, Kolte MV, Poulsen E, Dedic E, Drace T, Andersen SU, Nadzieja M, Liu H, Castillo-Michel H, Escudero V, González-Guerrero M, Boesen T, Pedersen JS, Stougaard J, Andersen KR, Reid D. Zinc mediates control of nitrogen fixation via transcription factor filamentation. Nature 2024; 631:164-169. [PMID: 38926580 PMCID: PMC11222152 DOI: 10.1038/s41586-024-07607-6] [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: 06/22/2023] [Accepted: 05/24/2024] [Indexed: 06/28/2024]
Abstract
Plants adapt to fluctuating environmental conditions by adjusting their metabolism and gene expression to maintain fitness1. In legumes, nitrogen homeostasis is maintained by balancing nitrogen acquired from soil resources with nitrogen fixation by symbiotic bacteria in root nodules2-8. Here we show that zinc, an essential plant micronutrient, acts as an intracellular second messenger that connects environmental changes to transcription factor control of metabolic activity in root nodules. We identify a transcriptional regulator, FIXATION UNDER NITRATE (FUN), which acts as a sensor, with zinc controlling the transition between an inactive filamentous megastructure and an active transcriptional regulator. Lower zinc concentrations in the nodule, which we show occur in response to higher levels of soil nitrate, dissociates the filament and activates FUN. FUN then directly targets multiple pathways to initiate breakdown of the nodule. The zinc-dependent filamentation mechanism thus establishes a concentration readout to adapt nodule function to the environmental nitrogen conditions. In a wider perspective, these results have implications for understanding the roles of metal ions in integration of environmental signals with plant development and optimizing delivery of fixed nitrogen in legume crops.
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Affiliation(s)
- Jieshun Lin
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Peter K Bjørk
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Marie V Kolte
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Emil Poulsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Emil Dedic
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Taner Drace
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Huijun Liu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Viviana Escudero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas. Universidad Politécnica de Madrid, Madrid, Spain
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Dugald Reid
- La Trobe Institute for Sustainable Agriculture and Food (LISAF), La Trobe University, Melbourne, Victoria, Australia.
- Department of Animal, Plant and Soil Sciences, School of Agriculture Bioscience and Environment, La Trobe University, Melbourne, Victoria, Australia.
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211
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Lopes AR, Low M, Martín-Hernández R, de Miranda JR, Pinto MA. Varroa destructor shapes the unique viral landscapes of the honey bee populations of the Azores archipelago. PLoS Pathog 2024; 20:e1012337. [PMID: 38959190 PMCID: PMC11221739 DOI: 10.1371/journal.ppat.1012337] [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: 03/15/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
The worldwide dispersal of the ectoparasitic mite Varroa destructor from its Asian origins has fundamentally transformed the relationship of the honey bee (Apis mellifera) with several of its viruses, via changes in transmission and/or host immunosuppression. The extent to which honey bee-virus relationships change after Varroa invasion is poorly understood for most viruses, in part because there are few places in the world with several geographically close but completely isolated honey bee populations that either have, or have not, been exposed long-term to Varroa, allowing for separate ecological, epidemiological, and adaptive relationships to develop between honey bees and their viruses, in relation to the mite's presence or absence. The Azores is one such place, as it contains islands with and without the mite. Here, we combined qPCR with meta-amplicon deep sequencing to uncover the relationship between Varroa presence, and the prevalence, load, diversity, and phylogeographic structure of eight honey bee viruses screened across the archipelago. Four viruses were not detected on any island (ABPV-Acute bee paralysis virus, KBV-Kashmir bee virus, IAPV-Israeli acute bee paralysis virus, BeeMLV-Bee macula-like virus); one (SBV-Sacbrood virus) was detected only on mite-infested islands; one (CBPV-Chronic bee paralysis virus) occurred on some islands, and two (BQCV-Black queen cell virus, LSV-Lake Sinai virus,) were present on every single island. This multi-virus screening builds upon a parallel survey of Deformed wing virus (DWV) strains that uncovered a remarkably heterogeneous viral landscape featuring Varroa-infested islands dominated by DWV-A and -B, Varroa-free islands naïve to DWV, and a refuge of the rare DWV-C dominating the easternmost Varroa-free islands. While all four detected viruses investigated here were affected by Varroa for one or two parameters (usually prevalence and/or the Richness component of ASV diversity), the strongest effect was observed for the multi-strain LSV. Varroa unambiguously led to elevated prevalence, load, and diversity (Richness and Shannon Index) of LSV, with these results largely shaped by LSV-2, a major LSV strain. Unprecedented insights into the mite-virus relationship were further gained from implementing a phylogeographic approach. In addition to enabling the identification of a novel LSV strain that dominated the unique viral landscape of the easternmost islands, this approach, in combination with the recovered diversity patterns, strongly suggests that Varroa is driving the evolutionary change of LSV in the Azores. This study greatly advances the current understanding of the effect of Varroa on the epidemiology and adaptive evolution of these less-studied viruses, whose relationship with Varroa has thus far been poorly defined.
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Affiliation(s)
- Ana R. Lopes
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, Porto, Portugal
| | - Matthew Low
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Raquel Martín-Hernández
- Centro de Investigación Apícola y Agroambiental (CIAPA), IRIAF, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Marchamalo, Spain
| | | | - M. Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal
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212
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Wiegand T, Hoffmann FT, Walker MWG, Tang S, Richard E, Le HC, Meers C, Sternberg SH. TnpB homologues exapted from transposons are RNA-guided transcription factors. Nature 2024; 631:439-448. [PMID: 38926585 DOI: 10.1038/s41586-024-07598-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
Transposon-encoded tnpB and iscB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination1-4. These widespread gene families were repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas12 (refs. 5,6). We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas adaptive immunity. Here, using phylogenetics, structural predictions, comparative genomics and functional assays, we uncover multiple independent genesis events of programmable transcription factors, which we name TnpB-like nuclease-dead repressors (TldRs). These proteins use naturally occurring guide RNAs to specifically target conserved promoter regions of the genome, leading to potent gene repression in a mechanism akin to CRISPR interference technologies invented by humans7. Focusing on a TldR clade found broadly in Enterobacteriaceae, we discover that bacteriophages exploit the combined action of TldR and an adjacently encoded phage gene to alter the expression and composition of the host flagellar assembly, a transformation with the potential to impact motility8, phage susceptibility9, and host immunity10. Collectively, this work showcases the diverse molecular innovations that were enabled through repeated exaptation of transposon-encoded genes, and reveals the evolutionary trajectory of diverse RNA-guided transcription factors.
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Affiliation(s)
- Tanner Wiegand
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Florian T Hoffmann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Matt W G Walker
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Egill Richard
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Hoang C Le
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Chance Meers
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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213
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Roman I, Fedorenko V, Gromyko O. Phylogenomic analyses of the genus Actinoplanes: description of four novel genera. Int J Syst Evol Microbiol 2024; 74. [PMID: 39046446 DOI: 10.1099/ijsem.0.006464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
The genus Actinoplanes comprises 57 species (in February 2024) that are important components of ecosystems and are widely used in biotechnology, especially pharmaceuticals. Phylogenetic analysis of the family Micromonosporaceae (based on the 16S rRNA gene sequence) allowed us to group members of different genera into separate clades; however, the genus Actinoplanes was divided into three separate clades. Such phylogenetic heterogeneity could be due to the limitations of 16S rRNA gene analysis. In response to this heterogeneity, genomic phylogeny was performed. Phylogenomic reconstruction based on 324 single-copy orthologous genes allowed us to divide the genus Actinoplanes first into four clades and then, based on average nucleotide identity analysis, into five clades. Finally, chemotaxonomic analysis of each clade confirmed each clade's distinctiveness and the necessity to reclassify the genus Actinoplanes. The obtained data allowed us to divide the genus Actinoplanes into five genera: Actinoplanes, Paractinoplanes, Winogradskya, Symbioplanes and Amorphoplanes.
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Affiliation(s)
- Ivan Roman
- Department of Genetics and Biotechnology, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Oleksandr Gromyko
- Department of Genetics and Biotechnology, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
- Microbial Culture Collection of Antibiotic Producers, Faculty of Biology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
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214
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Buiatte ABG, Souza SSR, Costa LRM, Peres PABM, de Melo RT, Sommerfeld S, Fonseca BB, Zac Soligno NI, Ikhimiukor OO, Armendaris PM, Andam CP, Rossi DA. Five centuries of genome evolution and multi-host adaptation of Campylobacter jejuni in Brazil. Microb Genom 2024; 10. [PMID: 39028633 DOI: 10.1099/mgen.0.001274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024] Open
Abstract
Consumption of raw, undercooked or contaminated animal food products is a frequent cause of Campylobacter jejuni infection. Brazil is the world's third largest producer and a major exporter of chicken meat, yet population-level genomic investigations of C. jejuni in the country remain scarce. Analysis of 221 C. jejuni genomes from Brazil shows that the overall core and accessory genomic features of C. jejuni are influenced by the identity of the human or animal source. Of the 60 sequence types detected, ST353 is the most prevalent and consists of samples from chicken and human sources. Notably, we identified the presence of diverse bla genes from the OXA-61 and OXA-184 families that confer beta-lactam resistance as well as the operon cmeABCR related to multidrug efflux pump, which contributes to resistance against tetracyclines, macrolides and quinolones. Based on limited data, we estimated the most recent common ancestor of ST353 to the late 1500s, coinciding with the time the Portuguese first arrived in Brazil and introduced domesticated chickens into the country. We identified at least two instances of ancestral chicken-to-human infections in ST353. The evolution of C. jejuni in Brazil was driven by the confluence of clinically relevant genetic elements, multi-host adaptation and clonal population growth that coincided with major socio-economic changes in poultry farming.
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Affiliation(s)
- Ana Beatriz Garcez Buiatte
- Molecular Epidemiology Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Stephanie S R Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | | | | | - Roberta Torres de Melo
- Molecular Epidemiology Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Simone Sommerfeld
- Infectious Disease Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | | | - Nicole I Zac Soligno
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Odion O Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Paulo Marcel Armendaris
- Federal Agriculture Defense Laboratory/RS - LFDA/RS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Daise Aparecida Rossi
- Molecular Epidemiology Laboratory, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
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215
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Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S. Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet 2024; 71:103029. [PMID: 38518712 DOI: 10.1016/j.fsigen.2024.103029] [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: 07/29/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Affiliation(s)
- Haoliang Fan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Kai Feng
- Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China.
| | - Liuxi Hong
- Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China.
| | - Qiancheng Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou 510663, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China.
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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216
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Jia M, Zhu S, Xue MY, Chen H, Xu J, Song M, Tang Y, Liu X, Tao Y, Zhang T, Liu JX, Wang Y, Sun HZ. Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome. Nat Microbiol 2024; 9:1884-1898. [PMID: 38866938 DOI: 10.1038/s41564-024-01723-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem.
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Affiliation(s)
- Minghui Jia
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Senlin Zhu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Ming-Yuan Xue
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Xianghu Laboratory, Hangzhou, China
| | - Hongyi Chen
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Jinghong Xu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Mengdi Song
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- M20 Genomics, Hangzhou, China
| | - Yifan Tang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Xiaohan Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Ye Tao
- Shanghai Biozeron Biotechnology Company, Shanghai, China
| | - Tianyu Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- M20 Genomics, Hangzhou, China
| | - Jian-Xin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Yongcheng Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Hui-Zeng Sun
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China.
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China.
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217
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Michel M, Skourtanioti E, Pierini F, Guevara EK, Mötsch A, Kocher A, Barquera R, Bianco RA, Carlhoff S, Coppola Bove L, Freilich S, Giffin K, Hermes T, Hiß A, Knolle F, Nelson EA, Neumann GU, Papac L, Penske S, Rohrlach AB, Salem N, Semerau L, Villalba-Mouco V, Abadie I, Aldenderfer M, Beckett JF, Brown M, Campus FGR, Chenghwa T, Cruz Berrocal M, Damašek L, Duffett Carlson KS, Durand R, Ernée M, Fântăneanu C, Frenzel H, García Atiénzar G, Guillén S, Hsieh E, Karwowski M, Kelvin D, Kelvin N, Khokhlov A, Kinaston RL, Korolev A, Krettek KL, Küßner M, Lai L, Look C, Majander K, Mandl K, Mazzarello V, McCormick M, de Miguel Ibáñez P, Murphy R, Németh RE, Nordqvist K, Novotny F, Obenaus M, Olmo-Enciso L, Onkamo P, Orschiedt J, Patrushev V, Peltola S, Romero A, Rubino S, Sajantila A, Salazar-García DC, Serrano E, Shaydullaev S, Sias E, Šlaus M, Stančo L, Swanston T, Teschler-Nicola M, Valentin F, Van de Vijver K, Varney TL, Vigil-Escalera Guirado A, Waters CK, Weiss-Krejci E, Winter E, Lamnidis TC, Prüfer K, Nägele K, Spyrou M, Schiffels S, Stockhammer PW, Haak W, Posth C, Warinner C, Bos KI, Herbig A, Krause J. Ancient Plasmodium genomes shed light on the history of human malaria. Nature 2024; 631:125-133. [PMID: 38867050 PMCID: PMC11222158 DOI: 10.1038/s41586-024-07546-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 05/09/2024] [Indexed: 06/14/2024]
Abstract
Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia BCE, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.
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MESH Headings
- Female
- Humans
- Male
- Altitude
- Americas/epidemiology
- Asia/epidemiology
- Biological Evolution
- Disease Resistance/genetics
- DNA, Ancient/analysis
- Europe/epidemiology
- Genome, Mitochondrial/genetics
- Genome, Protozoan/genetics
- History, Ancient
- Malaria/parasitology
- Malaria/history
- Malaria/transmission
- Malaria/epidemiology
- Malaria, Falciparum/epidemiology
- Malaria, Falciparum/history
- Malaria, Falciparum/parasitology
- Malaria, Falciparum/transmission
- Malaria, Vivax/epidemiology
- Malaria, Vivax/history
- Malaria, Vivax/parasitology
- Malaria, Vivax/transmission
- Plasmodium/genetics
- Plasmodium/classification
- Plasmodium falciparum/genetics
- Plasmodium falciparum/isolation & purification
- Plasmodium malariae/genetics
- Plasmodium malariae/isolation & purification
- Plasmodium vivax/genetics
- Plasmodium vivax/isolation & purification
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Affiliation(s)
- Megan Michel
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, .
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
| | - Federica Pierini
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Angela Mötsch
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
| | - Arthur Kocher
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Raffaela A Bianco
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
| | - Selina Carlhoff
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lorenza Coppola Bove
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- Department of Legal Medicine, Toxicology and Physical Anthropology, University of Granada, Granada, Spain
| | - Suzanne Freilich
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Taylor Hermes
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Arkansas, Fayetteville, AR, USA
| | - Alina Hiß
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Florian Knolle
- Department of Medical Engineering and Biotechnology, University of Applied Sciences Jena, Jena, Germany
| | - Elizabeth A Nelson
- Microbial Palaeogenomics Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, Australia
- Adelaide Data Science Centre, University of Adelaide, Adelaide, Australia
| | - Nada Salem
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
| | - Lena Semerau
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón, IUCA-Aragosaurus, Universitity of Zaragoza, Zaragoza, Spain
| | - Isabelle Abadie
- Inrap - Institut national de recherches archéologiques préventives, Paris, France
- Centre Michel de Boüard, Centre de recherches archéologiques et historiques anciennes et médiévales, Université de Caen Normandie, Caen, France
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, Merced, CA, USA
| | | | - Matthew Brown
- Sociology and Anthropology Department, Farmingdale State College, Farmingdale, NY, USA
| | - Franco G R Campus
- Department of History, Human Sciences, and Education, University of Sassari, Sassari, Italy
| | - Tsang Chenghwa
- Institute of Anthropology, National Tsing Hua University, Hsinchu, Taiwan
| | - María Cruz Berrocal
- Institute of Heritage Sciences (INCIPIT), Spanish National Research Council (CSIC), Santiago de Compostela, Spain
| | - Ladislav Damašek
- Institute of Classical Archaeology, Faculty of Arts, Charles University, Prague, Czech Republic
| | | | - Raphaël Durand
- Service d'archéologie préventive Bourges plus, Bourges, France
- UMR 5199 PACEA, Université de Bordeaux, Pessac Cedex, France
| | - Michal Ernée
- Department of Prehistoric Archaeology, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Hannah Frenzel
- Anatomy Institute, University of Leipzig, Leipzig, Germany
| | - Gabriel García Atiénzar
- Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Universidad de Alicante, San Vicente del Raspeig (Alicante), Spain
| | | | - Ellen Hsieh
- Institute of Anthropology, National Tsing Hua University, Hsinchu, Taiwan
| | - Maciej Karwowski
- Institut für Urgeschichte und Historische Archäologie, University of Vienna, Vienna, Austria
| | - David Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Nikki Kelvin
- Division of Ancient Pathogens, BioForge Canada Limited, Halifax, Nove Scotia, Canada
| | - Alexander Khokhlov
- Samara State University of Social Sciences and Education, Samara, Russia
| | - Rebecca L Kinaston
- BioArch South, Waitati, New Zealand
- Griffith Centre for Social and Cultural Studies, Griffith University, Nathan, Queensland, Australia
| | - Arkadii Korolev
- Samara State University of Social Sciences and Education, Samara, Russia
| | - Kim-Louise Krettek
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, Weimar, Germany
| | - Luca Lai
- Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Cory Look
- Sociology and Anthropology Department, Farmingdale State College, Farmingdale, NY, USA
| | - Kerttu Majander
- Department of Environmental Science, Integrative Prehistory and Archaeological Science, University of Basel, Basel, Switzerland
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Michael McCormick
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- Initiative for the Science of the Human Past at Harvard, Department of History, Harvard University, Cambridge, MA, USA
| | - Patxuka de Miguel Ibáñez
- Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Universidad de Alicante, San Vicente del Raspeig (Alicante), Spain
- Servicio de Obstetricia, Hospital Virgen de los Lirios-Fisabio, Alcoi, Spain
- Sección de Antropología, Sociedad de Ciencias Aranzadi, Donostia - San Sebastián, Spain
| | - Reg Murphy
- University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Kerkko Nordqvist
- Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
| | - Friederike Novotny
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Martin Obenaus
- Silva Nortica Archäologische Dienstleistungen, Thunau am Kamp, Austria
| | - Lauro Olmo-Enciso
- Department of History, University of Alcalá, Alcalá de Henares, Spain
| | - Päivi Onkamo
- Department of Biology, University of Turku, Turku, Finland
| | - Jörg Orschiedt
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt, Halle, Germany
- Institut für Prähistorische Archäologie, Freie Universität Berlin, Berlin, Germany
| | - Valerii Patrushev
- Centre of Archaeological and Ethnographical Investigation, Mari State University, Yoshkar-Ola, Russia
| | - Sanni Peltola
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alejandro Romero
- Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico, Universidad de Alicante, San Vicente del Raspeig (Alicante), Spain
- Departamento de Biotecnología, Universidad de Alicante, San Vicente del Raspeig, Spain
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, Valencia, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Elena Serrano
- Instituto Internacional de Investigaciones Prehistóricas, Universidad de Cantabria, Santander, Spain
- TAR Arqueología, Madrid, Spain
| | | | - Emanuela Sias
- Centro Studi sulla Civiltà del Mare, Stintino, Italy
| | - Mario Šlaus
- Anthropological Center, Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Ladislav Stančo
- Institute of Classical Archaeology, Faculty of Arts, Charles University, Prague, Czech Republic
| | - Treena Swanston
- Department of Anthropology, Economics and Political Science, MacEwan University, Edmonton, Alberta, Canada
| | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | | | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Center for Archaeological Sciences, University of Leuven, Leuven, Belgium
- Dienst Archeologie - Stad Mechelen, Mechelen, Belgium
| | - Tamara L Varney
- Department of Anthropology, Lakehead University, Thunder Bay, Ontario, Canada
| | | | - Christopher K Waters
- Heritage Department, National Parks of Antigua and Barbuda, St. Paul's Parish, Antigua and Barbuda
| | - Estella Weiss-Krejci
- Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria
- Institut für Ur- und Frühgeschichte, Heidelberg University, Heidelberg, Germany
- Department of Social and Cultural Anthropology, University of Vienna, Vienna, Austria
| | - Eduard Winter
- Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Thiseas C Lamnidis
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Maria Spyrou
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, .
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218
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Chen Y, Luo S, Hu Y, Mao B, Wang X, Lu Z, Shan Q, Zhang J, Wang S, Feng G, Wang C, Liang C, Tang N, Niu R, Wang J, Han J, Yang N, Wang H, Zhou Q, Li W. All-RNA-mediated targeted gene integration in mammalian cells with rationally engineered R2 retrotransposons. Cell 2024:S0092-8674(24)00694-9. [PMID: 38981481 DOI: 10.1016/j.cell.2024.06.020] [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: 11/15/2023] [Revised: 04/17/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
All-RNA-mediated targeted gene integration methods, rendering reduced immunogenicity, effective deliverability with non-viral vehicles, and a low risk of random mutagenesis, are urgently needed for next-generation gene addition technologies. Naturally occurring R2 retrotransposons hold promise in this context due to their site-specific integration profile. Here, we systematically analyzed the biodiversity of R2 elements and screened several R2 orthologs capable of full-length gene insertion in mammalian cells. Robust R2 system gene integration efficiency was attained using combined donor RNA and protein engineering. Importantly, the all-RNA-delivered engineered R2 system showed effective integration activity, with efficiency over 60% in mouse embryos. Unbiased high-throughput sequencing demonstrated that the engineered R2 system exhibited high on-target integration specificity (99%). In conclusion, our study provides engineered R2 tools for applications based on hit-and-run targeted DNA integration and insights for further optimization of retrotransposon systems.
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Affiliation(s)
- Yangcan Chen
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Shengqiu Luo
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanping Hu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Bangwei Mao
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinge Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zongbao Lu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingtong Shan
- Northeast Agricultural University, Harbin 150030, China
| | - Jin Zhang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siqi Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Guihai Feng
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chenxin Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chen Liang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Tang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Rui Niu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaqiang Wang
- Northeast Agricultural University, Harbin 150030, China
| | - Jiabao Han
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Yang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoyi Wang
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Qi Zhou
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Wei Li
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Bejing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
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219
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Birkholz N, Kamata K, Feussner M, Wilkinson ME, Cuba Samaniego C, Migur A, Kimanius D, Ceelen M, Went SC, Usher B, Blower TR, Brown CM, Beisel CL, Weinberg Z, Fagerlund RD, Jackson SA, Fineran PC. Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein. Nature 2024; 631:670-677. [PMID: 38987591 DOI: 10.1038/s41586-024-07644-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/31/2024] [Indexed: 07/12/2024]
Abstract
In all organisms, regulation of gene expression must be adjusted to meet cellular requirements and frequently involves helix-turn-helix (HTH) domain proteins1. For instance, in the arms race between bacteria and bacteriophages, rapid expression of phage anti-CRISPR (acr) genes upon infection enables evasion from CRISPR-Cas defence; transcription is then repressed by an HTH-domain-containing anti-CRISPR-associated (Aca) protein, probably to reduce fitness costs from excessive expression2-5. However, how a single HTH regulator adjusts anti-CRISPR production to cope with increasing phage genome copies and accumulating acr mRNA is unknown. Here we show that the HTH domain of the regulator Aca2, in addition to repressing Acr synthesis transcriptionally through DNA binding, inhibits translation of mRNAs by binding conserved RNA stem-loops and blocking ribosome access. The cryo-electron microscopy structure of the approximately 40 kDa Aca2-RNA complex demonstrates how the versatile HTH domain specifically discriminates RNA from DNA binding sites. These combined regulatory modes are widespread in the Aca2 family and facilitate CRISPR-Cas inhibition in the face of rapid phage DNA replication without toxic acr overexpression. Given the ubiquity of HTH-domain-containing proteins, it is anticipated that many more of them elicit regulatory control by dual DNA and RNA binding.
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Affiliation(s)
- Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Kotaro Kamata
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
| | - Maximilian Feussner
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Max E Wilkinson
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Angela Migur
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | | | - Marijn Ceelen
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute for Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Sam C Went
- Department of Biosciences, Durham University, Durham, UK
| | - Ben Usher
- Department of Biosciences, Durham University, Durham, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Durham, UK
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.
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Li C, Chen X, Jia Z, Zhai L, Zhang B, Grüters U, Ma S, Qian J, Liu X, Zhang J, Müller C. Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities. Nat Ecol Evol 2024; 8:1270-1284. [PMID: 38849504 DOI: 10.1038/s41559-024-02437-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/13/2024] [Indexed: 06/09/2024]
Abstract
Microbial inoculation involves transplanting microorganisms from their natural habitat to new plants or soils to improve plant performance, and it is being increasingly used in agriculture and ecological restoration. However, microbial inoculants can invade and alter the composition of native microbial communities; thus, a comprehensive analysis is urgently needed to understand the overall impact of microbial inoculants on the biomass, diversity, structure and network complexity of native communities. Here we provide a meta-analysis of 335 studies revealing a positive effect of microbial inoculants on soil microbial biomass. This positive effect was weakened by environmental stress and enhanced by the use of fertilizers and native inoculants. Although microbial inoculants did not alter microbial diversity, they induced major changes in the structure and bacterial composition of soil microbial communities, reducing the complexity of bacterial networks and increasing network stability. Finally, higher initial levels of soil nutrients amplified the positive impact of microbial inoculants on fungal biomass, actinobacterial biomass, microbial biomass carbon and microbial biomass nitrogen. Together, our results highlight the positive effects of microbial inoculants on soil microbial biomass, emphasizing the benefits of native inoculants and the important regulatory roles of soil nutrient levels and environmental stress.
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Affiliation(s)
- Chong Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
| | - Xinli Chen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Lu Zhai
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK, USA
| | - Bo Zhang
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Uwe Grüters
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
| | - Shilin Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Jing Qian
- Yangzhou China Grand Canal Museum, Yangzhou, China
| | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China.
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China.
| | - Christoph Müller
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Liebig Centre for Agroecology and Climate Impact Research, Justus-Liebig University, Giessen, Germany
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221
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Sangal V, Marrs ECL, Nelson A, Perry JD. Phylogenomic analyses of multidrug resistant Corynebacterium striatum strains isolated from patients in a tertiary care hospital in the UK. Eur J Clin Microbiol Infect Dis 2024; 43:1495-1501. [PMID: 38801486 PMCID: PMC11271431 DOI: 10.1007/s10096-024-04857-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024]
Abstract
Corynebacterium striatum is an emerging nosocomial pathogen. This is the first report showing the presence of three distinct multidrug resistant lineages of C. striatum among patients in a UK hospital. The presence of ErmX, Tet(W), Bla and AmpC proteins, and mutations in gyrA gene are associated with the resistance to clindamycin, doxycycline, penicillin and moxifloxacin, respectively. These strains are equipped with several corynebacterial virulence genes including two SpaDEF-type and a novel pilus gene cluster, which needs further molecular characterisation. This study highlights a need of developing an active surveillance strategy for routine monitoring and preventing potential cross-transmission among susceptible patients.
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Affiliation(s)
- Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
| | - Emma C L Marrs
- Microbiology Research Department, Freeman Hospital, Newcastle upon Tyne, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - John D Perry
- Microbiology Research Department, Freeman Hospital, Newcastle upon Tyne, UK
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222
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Machado E, Vasconcellos S, Gomes L, Catanho M, Ramos J, de Carvalho L, Goldenberg T, Redner P, Caldas P, Campos C, Dalcolmo M, Lourenço MC, Lasunskaia E, Mussi V, Spinassé L, Vinhas S, Rigouts L, Cogneau S, de Rijk P, Utpatel C, Kaustova J, van der Laan T, de Neeling H, Rastogi N, Levina K, Kütt M, Mokrousov I, Zhuravlev V, Makhado N, Žolnir-Dovč M, Jankovic V, de Waard J, Sisco MC, van Soolingen D, Niemann S, de Jong BC, Meehan CJ, Suffys P. Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species. Microb Genom 2024; 10. [PMID: 39016539 DOI: 10.1099/mgen.0.001266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024] Open
Abstract
Species belonging to the Mycobacterium kansasii complex (MKC) are frequently isolated from humans and the environment and can cause serious diseases. The most common MKC infections are caused by the species M. kansasii (sensu stricto), leading to tuberculosis-like disease. However, a broad spectrum of virulence, antimicrobial resistance and pathogenicity of these non-tuberculous mycobacteria (NTM) are observed across the MKC. Many genomic aspects of the MKC that relate to these broad phenotypes are not well elucidated. Here, we performed genomic analyses from a collection of 665 MKC strains, isolated from environmental, animal and human sources. We inferred the MKC pangenome, mobilome, resistome, virulome and defence systems and show that the MKC species harbours unique and shared genomic signatures. High frequency of presence of prophages and different types of defence systems were observed. We found that the M. kansasii species splits into four lineages, of which three are lowly represented and mainly in Brazil, while one lineage is dominant and globally spread. Moreover, we show that four sub-lineages of this most distributed M. kansasii lineage emerged during the twentieth century. Further analysis of the M. kansasii genomes revealed almost 300 regions of difference contributing to genomic diversity, as well as fixed mutations that may explain the M. kansasii's increased virulence and drug resistance.
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Affiliation(s)
- Edson Machado
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Sidra Vasconcellos
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Lia Gomes
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Marcos Catanho
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Jesus Ramos
- Laboratório de Referência Nacional para Tuberculose, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Luciana de Carvalho
- Laboratório de Referência Nacional para Tuberculose, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Telma Goldenberg
- Laboratório de Referência Nacional para Tuberculose, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Paulo Redner
- Laboratório de Referência Nacional para Tuberculose, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Paulo Caldas
- Laboratório de Referência Nacional para Tuberculose, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Carlos Campos
- Laboratório de Referência Nacional para Tuberculose, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Margareth Dalcolmo
- Serviço de Pesquisa Clínica, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Maria Cristina Lourenço
- Laboratório de Bacteriologia e Bioensaios, Instituto Nacional de Infectologia, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Elena Lasunskaia
- Laboratório de Biologia do Reconhecer, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Vinicius Mussi
- Laboratório de Biologia do Reconhecer, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Lizania Spinassé
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, ES, Brazil
| | - Solange Vinhas
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, ES, Brazil
| | - Leen Rigouts
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sari Cogneau
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pim de Rijk
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christian Utpatel
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Jarmila Kaustova
- Department of Diagnostic Mycobacterioses, Regional Institute of Public Health, Ostrava, Czech Republic
| | - Tridia van der Laan
- National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Han de Neeling
- National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Nalin Rastogi
- TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe, Guadeloupe, France
| | - Klavdia Levina
- Mycobacteriology Section of Microbiology Laboratory, North Estonia Medical Centre, Tallinn, Estonia
| | - Marge Kütt
- Mycobacteriology Section of Microbiology Laboratory, North Estonia Medical Centre, Tallinn, Estonia
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Ndivhu Makhado
- Department of Microbiological Pathology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
- National Health Laboratory Service, Dr George Mukhari Tertiary Laboratory, Medical Microbiology, Pretoria, South Africa
- Global Institute of Health, University of Antwerp, Antwerp, Belgium
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Manca Žolnir-Dovč
- National Reference Laboratory for Mycobacteria, University Clinic of Respiratory and Allergic Diseases, Golnik, Slovenia
| | - Vera Jankovic
- Mycobacteria Reference Laboratory, Croatian National Institute of Public Health, Zagreb, Croatia
| | - Jacobus de Waard
- Tuberculosis Department. Servicio Autónomo Instituto de Biomedicina Dr. Jacinto Convit, Universidad Central de Venezuela, Caracas, Venezuela
- One Health Research Group, Universidad de Las Américas, Quito, Ecuador
| | - Maria Carolina Sisco
- Tuberculosis Department. Servicio Autónomo Instituto de Biomedicina Dr. Jacinto Convit, Universidad Central de Venezuela, Caracas, Venezuela
| | - Dick van Soolingen
- National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Stefan Niemann
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Bouke C de Jong
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J Meehan
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Philip Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
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Kobayashi H, Tanizawa Y, Sakamoto M, Ohkuma M, Tohno M. Lacrimispora brassicae sp. nov. isolated from fermented cabbage, and proposal of Clostridium indicum Gundawar et al. 2019 and Clostridium methoxybenzovorans Mechichi et al. 1999 as heterotypic synonyms of Lacrimispora amygdalina (Parshina et al. 2003) Haas and Blanchard 2020 and Lacrimispora indolis (McClung and McCoy 1957) Haas and Blanchard 2020, respectively. Int J Syst Evol Microbiol 2024; 74. [PMID: 39016536 DOI: 10.1099/ijsem.0.006456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024] Open
Abstract
A Gram-stain-negative, endospore-forming, rod-shaped, indole-producing bacterial strain, designated YZC6T, was isolated from fermented cabbage. Strain YZC6T grew at 10-37 °C, pH 5.5-8.5, and with up to 2 % (w/v) NaCl. The major cellular fatty acids were C16 : 0 and C18 : 1 cis 11 dimethyl acetal. Phylogenetic analysis of the 16S rRNA gene revealed that strain YZC6T belonged to the genus Lacrimispora and was closely related to Lacrimispora aerotolerans DSM 5434T (98.3 % sequence similarity), Lacrimispora saccharolytica WM1T (98.1 %), and Lacrimispora algidixylanolytica SPL73T (98.1 %). The average nucleotide identity based on blast (below 87.8 %) and digital DNA-DNA hybridization (below 36.1 %) values between the novel isolate and its corresponding relatives showed that strain YZC6T could be readily distinguished from its closely related species. Based on genotypic, phenotypic, and chemotaxonomic data, a novel Lacrimispora species, Lacrimispora brassicae sp. nov., was proposed, with YZC6T as the type strain (=MAFF 212518T=JCM 32810T=DSM 112100T). This study also proposed Clostridium indicum Gundawar et al. 2019 as a later heterotypic synonym of Lacrimispora amygdalina (Parshina et al. 2003) Haas and Blanchard 2020 and Clostridium methoxybenzovorans Mechichi et al. 1999 as a later heterotypic synonym of Lacrimispora indolis (McClung and McCpy 1957) Haas and Blanchard 2020.
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Affiliation(s)
- Hisami Kobayashi
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Tohno
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
- Innovative Animal Production System, University of Tsukuba, 305-8571 Tsukuba, Japan
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224
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Shan F, Li L, Bi Y, Wang W, Amu G, Li M, Zhou H, Yao R. Exotic medicinal plants from the Silk Road promote the diversification of traditional Chinese medicines. Pharmacol Res 2024; 205:107243. [PMID: 38815881 DOI: 10.1016/j.phrs.2024.107243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/16/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND As a political, economic, and cultural exchange channel between ancient China and countries in Asia, Europe, and Africa, the Silk Road has promoted political, trade, and cultural exchanges between China and foreign countries in Chinese history and also promoted the development of traditional Chinese medicine. METHODS This article summarizes the introduction of medicinal materials from the Han to Qing Dynasties, spanning approximately 2000 years. RESULTS A total of 235 types of medicinal plant materials were imported. An analysis of 178 medicinal herbs of known origin, belonging to 72 families revealed their effectiveness in treating 20 diseases. The maximum number of medicinal herbs used to treat gastrointestinal and digestive disorders (GAS) was 122. The applications and origin of exotic medicinal materials, including draconis sanguis and olibanum have changed during the development of the Silk Road. Imported medicinal materials are affected by five factors, including local demand, adaptability, cultural exchange, scarcity, and medical theory. Five modes for introducing medicinal materials include the onshore Silk Road, the maritime Silk Road, diplomatic envoys and gifts, overseas Chinese, cultural exchange, and medical integration. The application of exotic medicinal materials expands the resources and application fields of traditional Chinese medicine, enriching the theory of traditional Chinese medicine. CONCLUSION Traditional Chinese medicinal compounds introduced to China through the ancient Silk Road not only promoted their integration into foreign medicine but also had long-lasting impacts to date and over a wide range, thereby considerably affecting the pharmaceutical and general healthcare industries.
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Affiliation(s)
- Feibiao Shan
- Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot 010010, China; Inner Mongolia Medical University, Hohhot 010059, China
| | - Ling Li
- Inner Mongolia Medical University, Hohhot 010059, China
| | - Yaqiong Bi
- Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot 010010, China
| | - Wenle Wang
- Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot 010010, China
| | - Guleng Amu
- Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot 010010, China
| | - Minhui Li
- Inner Mongolia Traditional Chinese & Mongolian Medical Research Institute, Hohhot 010010, China; Inner Mongolia Medical University, Hohhot 010059, China.
| | - Hua Zhou
- State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510006, China; Chinese Medicine Guangdong Laboratory (Hengqin Laboratory), Guangdong-Macao ln-Depth Cooperation Zone in Hengqin, 519000, China.
| | - Ruyu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
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225
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Leoni Swart A, Laventie BJ, Sütterlin R, Junne T, Lauer L, Manfredi P, Jakonia S, Yu X, Karagkiozi E, Okujava R, Jenal U. Pseudomonas aeruginosa breaches respiratory epithelia through goblet cell invasion in a microtissue model. Nat Microbiol 2024; 9:1725-1737. [PMID: 38858595 DOI: 10.1038/s41564-024-01718-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 04/29/2024] [Indexed: 06/12/2024]
Abstract
Pseudomonas aeruginosa, a leading cause of severe hospital-acquired pneumonia, causes infections with up to 50% mortality rates in mechanically ventilated patients. Despite some knowledge of virulence factors involved, it remains unclear how P. aeruginosa disseminates on mucosal surfaces and invades the tissue barrier. Using infection of human respiratory epithelium organoids, here we observed that P. aeruginosa colonization of apical surfaces is promoted by cyclic di-GMP-dependent asymmetric division. Infection with mutant strains revealed that Type 6 Secretion System activities promote preferential invasion of goblet cells. Type 3 Secretion System activity by intracellular bacteria induced goblet cell death and expulsion, leading to epithelial rupture which increased bacterial translocation and dissemination to the basolateral epithelium. These findings show that under physiological conditions, P. aeruginosa uses coordinated activity of a specific combination of virulence factors and behaviours to invade goblet cells and breach the epithelial barrier from within, revealing mechanistic insight into lung infection dynamics.
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Affiliation(s)
| | | | | | - Tina Junne
- Biozentrum, University of Basel, Basel, Switzerland
| | - Luisa Lauer
- Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Xiao Yu
- Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology (CMI2O), Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Evdoxia Karagkiozi
- Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology (CMI2O), Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Rusudan Okujava
- Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology (CMI2O), Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland.
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226
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Ugwuanyi IR, Steele A, Glamoclija M. Microbial Ecology of an Arctic Travertine Geothermal Spring: Implications for Biosignature Preservation and Astrobiology. ASTROBIOLOGY 2024; 24:734-753. [PMID: 38985714 DOI: 10.1089/ast.2023.0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Jotun springs in Svalbard, Norway, is a rare warm environment in the Arctic that actively forms travertine. In this study, we assessed the microbial ecology of Jotun's active (aquatic) spring and dry spring transects. We evaluated the microbial preservation potential and mode, as well as the astrobiological relevance of the travertines to marginal carbonates mapped at Jezero Crater on Mars (the Mars 2020 landing site). Our results revealed that microbial communities exhibited spatial dynamics controlled by temperature, fluid availability, and geochemistry. Amorphous carbonates and silica precipitated within biofilm and on the surface of filamentous microorganisms. The water discharged at the source is warm, with near neutral pH, and undersaturated in silica. Hence, silicification possibly occurred through cooling, dehydration, and partially by a microbial presence or activities that promote silica precipitation. CO2 degassing and possible microbial contributions induced calcite precipitation and travertine formation. Jotun revealed that warm systems that are not very productive in carbonate formation may still produce significant carbonate buildups and provide settings favorable for fossilization through silicification and calcification. Our findings suggest that the potential for amorphous silica precipitation may be essential for Jezero Crater's marginal carbonates because it significantly increases the preservation potential of putative martian organisms.
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Affiliation(s)
- Ifeoma R Ugwuanyi
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, USA
| | - Andrew Steele
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, District of Columbia, USA
| | - Mihaela Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, USA
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Medina A, Vega Y, Medina J, López RN, Vayas P, Soria J, Velásquez‐Yambay C, Sánchez‐Gavilanes L, Bastidas‐Caldes C, Calero‐Cáceres W. Characterization of antimicrobial resistance profiles in Escherichia coli isolated from captive mammals in Ecuador. Vet Med Sci 2024; 10:e1546. [PMID: 39016692 PMCID: PMC11253296 DOI: 10.1002/vms3.1546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/20/2024] [Accepted: 06/28/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND This study focuses on the AMR profiles in E. coli isolated from captive mammals at EcoZoo San Martín, Baños de Agua Santa, Ecuador, highlighting the role of wildlife as reservoirs of resistant bacteria. AIMS The aim of this research is to investigate the antimicrobial resistance profiles of E. coli strains isolated from various species of captive mammals, emphasizing the potential zoonotic risks and the necessity for integrated AMR management strategies. MATERIALS & METHODS A total of 189 fecal samples were collected from 70 mammals across 27 species. These samples were screened for E. coli, resulting in 90 identified strains. The resistance profiles of these strains to 16 antibiotics, including 10 β-lactams and 6 non-β-lactams, were determined using the disk diffusion method. Additionally, the presence of Extended-Spectrum Beta-Lactamase (ESBL) genes and other resistance genes was analyzed using PCR. RESULTS Significant resistance was observed, with 52.22% of isolates resistant to ampicillin, 42.22% to ceftriaxone and cefuroxime, and 27.78% identified as ESBL-producing E. coli. Multiresistance (resistance to more than three antibiotic groups) was found in 35.56% of isolates. Carnivorous and omnivorous animals, particularly those with prior antibiotic treatments, were more likely to harbor resistant strains. DISCUSSION These findings underscore the role of captive mammals as indicators of environmental AMR. The high prevalence of resistant E. coli in these animals suggests that zoos could be significant reservoirs for the spread of antibiotic-resistant bacteria. The results align with other studies showing that diet and antibiotic treatment history influence resistance profiles. CONCLUSION The study highlights the need for an integrated approach involving veterinary care, habitat management, and public awareness to prevent captive wildlife from becoming reservoirs of antibiotic-resistant bacteria. Improved waste management practices and responsible antibiotic use are crucial to mitigate the risks of AMR in zoo environments and reduce zoonotic threats.
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Affiliation(s)
- Anabell Medina
- UTA RAM One HealthDepartment of Food and Biotechnology Science and EngineeringUniversidad Técnica de AmbatoAmbatoEcuador
| | - Yadira Vega
- Department of Animal WelfareEco Zoológico San MartínBañosEcuador
| | - Jennifer Medina
- UTA RAM One HealthDepartment of Food and Biotechnology Science and EngineeringUniversidad Técnica de AmbatoAmbatoEcuador
| | - Rosa N. López
- UTA RAM One HealthDepartment of Food and Biotechnology Science and EngineeringUniversidad Técnica de AmbatoAmbatoEcuador
| | - Patricio Vayas
- UTA RAM One HealthDepartment of Food and Biotechnology Science and EngineeringUniversidad Técnica de AmbatoAmbatoEcuador
| | - Joyce Soria
- UTA RAM One HealthDepartment of Food and Biotechnology Science and EngineeringUniversidad Técnica de AmbatoAmbatoEcuador
| | - Cristian Velásquez‐Yambay
- UTA RAM One HealthDepartment of Food and Biotechnology Science and EngineeringUniversidad Técnica de AmbatoAmbatoEcuador
| | - Lissette Sánchez‐Gavilanes
- UTA RAM One HealthDepartment of Food and Biotechnology Science and EngineeringUniversidad Técnica de AmbatoAmbatoEcuador
| | - Carlos Bastidas‐Caldes
- One Health Research Group, BiotecnologíaFacultad de Ingeniería y Ciencias Aplicadas (FICA)Universidad de las Américas (UDLA)QuitoEcuador
| | - William Calero‐Cáceres
- UTA RAM One HealthDepartment of Food and Biotechnology Science and EngineeringUniversidad Técnica de AmbatoAmbatoEcuador
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228
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Dunowska M, More GD, Biggs PJ, Cave NJ. Genomic analysis of canine pneumoviruses and canine respiratory coronavirus from New Zealand. N Z Vet J 2024; 72:191-200. [PMID: 38650102 DOI: 10.1080/00480169.2024.2339845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
AIMS To isolate canine respiratory coronavirus (CRCoV) and canine pneumovirus (CnPnV) in cell culture and to compare partial genomic sequences of CRCoV and CnPnV from New Zealand with those from other countries. METHODS Oropharyngeal swab samples from dogs affected by canine infectious respiratory disease syndrome that were positive for CnPnV (n = 15) or CRCoV (n = 1) by virus-specific reverse transcriptase quantitative PCR (RT-qPCR) in a previous study comprised the starting material. Virus isolation was performed in HRT-18 cells for CRCoV and RAW 264.7 and Vero cells for CnPnV. The entire sequence of CnPnV G protein (1,266 nucleotides) and most (8,063/9,707 nucleotides) of the 3' region of CRCoV that codes for 10 structural and accessory proteins were amplified and sequenced. The sequences were analysed and compared with other sequences available in GenBank using standard molecular tools including phylogenetic analysis. RESULTS Virus isolation was unsuccessful for both CRCoV and CnPnV. Pneumovirus G protein was amplified from 3/15 (20%) samples that were positive for CnPnV RNA by RT-qPCR. Two of these (NZ-048 and NZ-049) were 100% identical to each other, and 90.9% identical to the third one (NZ-007). Based on phylogenetic analysis of the G protein gene, CnPnV NZ-048 and NZ-049 clustered with sequences from the USA, Thailand and Italy in group A, and CnPnV NZ-007 clustered with sequences from the USA in group B. The characteristics of the predicted genes (length, position) and their putative protein products (size, predicted structure, presence of N- and O-glycosylation sites) of the New Zealand CRCoV sequence were consistent with those reported previously, except for the region located between open reading frame (ORF)3 (coding for S protein) and ORF6 (coding for E protein). The New Zealand virus was predicted to encode 5.9 kDa, 27 kDa and 12.7 kDa proteins, which differed from the putative coding capacity of this region reported for CRCoV from other countries. CONCLUSIONS This report represents the first characterisation of partial genomic sequences of CRCoV and CnPnV from New Zealand. Our results suggest that the population of CnPnV circulating in New Zealand is not homogeneous, and that the viruses from two clades described overseas are also present here. Limited conclusions can be made based on only one CRCoV sequence, but the putative differences in the coding capacity of New Zealand CRCoV support the previously reported variability of this region. The reasons for such variability and its biological implications need to be further elucidated.
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Affiliation(s)
- M Dunowska
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - G D More
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - P J Biggs
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - N J Cave
- Tāwharau Ora - School of Veterinary Science, Massey University, Palmerston North, New Zealand
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229
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Liu X, Wang D, Qi X, Gu Y, Huang X, Liang P. Propionate outperforms conventional acetate as electron donors for highly-sensitive electrochemical active biofilm sensors in water biotoxicity early-warning. ENVIRONMENTAL RESEARCH 2024; 252:119127. [PMID: 38750998 DOI: 10.1016/j.envres.2024.119127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
Abstract
With the ability to generate in situ real-time electric signals, electrochemically active biofilm (EAB) sensors have attracted wide attention as a promising water biotoxicity early-warning device. Organic matters serving as the electron donors potentially affect the electric signal's output and the sensitivity of the EAB sensor. To explore the influence of organic matters on EAB sensor's performance, this study tested six different organic matters during the sensor's inoculation. Besides the acetate, a conventional and widely used organic matter, propionate and lactate were also found capable of starting up the sensor. Moreover, the propionate-fed (PF) sensor delivered the highest sensitivity, which are respectively 1.4 times and 2.8 times of acetate-fed (AF) sensor and lactate-fed (LF) sensor. Further analysis revealed that EAB of PF sensor had more vulnerable intracellular metabolism than the others, which manifested as the most severe energy metabolic suppression and reactive oxygen species attack. Regarding the microbial function, a two-component system that was deemed as an environment awareness system was found in the EAB of PF, which also contributed to its high sensitivity. Finally, PF sensor was tested in real water environment to deliver early-warning signals.
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Affiliation(s)
- Xinning Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Donglin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiang Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Yuyi Gu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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230
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Huang J, Li T, Zhu Y, Li Q, Kuo CJ, Guo X, Wei B, Ni P, Dong K. Molecular Characterization and Potential Host-switching of Swine Farm associated Clostridioides difficile ST11. Vet Microbiol 2024; 294:110129. [PMID: 38810364 DOI: 10.1016/j.vetmic.2024.110129] [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: 08/05/2023] [Revised: 05/19/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
OBJECTIVE To conduct molecular prevalence and genetic polymorphism analysis of 24 Swine Farm associated C. difficile ST11 strains, in addition to other representative sequenced ST strains. METHODS The collected C. difficile strains underwent whole genome sequencing and bioinformatic analysis using the illumina NovaSeq platform, SPAdes, Prokka, MOB-suite, and FastTree. Virulence and antibiotic resistance genes were identified through NCBI Pathogen Database. Cytotoxicity tests were conducted on HT-29 cells and Vero cells to verify the function of toxin A and toxin B. RESULTS The most prevalent resistance genes in ST11 were found to be against β-lactamases, aminoglycosides, and tetracycline. A C. difficile isolate (strain 27) with tcdA deletion and high antibiotic resistance genes was far apart from other swine farm associated ST11 isolates in the phylogenetic branch. The remarkable genetic similarity between animal and human C. difficile strains suggests potential transmission of ST11 strains between animals and humans. The plasmid replicon sequences repUS43 were identified in all ST11 strains except one variant (strain 27), and 91.67% (22/24) of these were assessed by MOB-typer as having mobilizable plasmids. CONCLUSION Swine farm associated C. difficile ST11 carried fewer virulence genes than ST11 strains collected from NCBI database. It is critical to monitor the evolution of C. difficile strains to understand their changing characteristics, host-switching, and develop effective control and prevention strategies.
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Affiliation(s)
- Jiewen Huang
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tinghua Li
- Department of Laboratory Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongzhang Zhu
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Xiaokui Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Beiwen Wei
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Peihua Ni
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Ke Dong
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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231
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Fernandez JE, Egli A, Overesch G, Perreten V. Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution. Nat Commun 2024; 15:5526. [PMID: 38951499 PMCID: PMC11217367 DOI: 10.1038/s41467-024-49644-9] [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: 02/13/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
An international collection of Staphylococcus aureus of clonal complex (CC) 398 from diverse hosts spanning all continents and a 30 year-period is studied based on whole-genome sequencing (WGS) data. The collection consists of publicly available genomic data from 2994 strains and 134 recently sequenced Swiss methicillin-resistant S. aureus (MRSA) CC398 strains. A time-calibrated phylogeny reveals the presence of distinct phylogroups present in Asia, North and South America and Europe. European MRSA diverged from methicillin-susceptible S. aureus (MSSA) at the beginning of the 1950s. Two major European phylogroups (EP4 and EP5), which diverged approximately 1974, are the main drivers of MRSA CC398 spread in Europe. Within EP5, an emergent MRSA lineage spreading among the European horse population (EP5-Leq) diverged approximately 1996 from the pig lineage (EP5-Lpg), and also contains human-related strains. EP5-Leq is characterized by staphylococcal cassette chromosome mec (SCCmec) IVa and spa type t011 (CC398-IVa-t011), and EP5-Lpg by CC398-SCCmecVc-t011. The lineage-specific antibiotic resistance and virulence gene patterns are mostly mediated by the acquisition of mobile genetic elements like SCCmec, S. aureus Genomic Islands (SaGIs), prophages and transposons. Different combinations of virulence factors are present on S. aureus pathogenicity islands (SaPIs), and novel antimicrobial resistance gene containing elements are associated with certain lineages expanding in Europe. This WGS-based analysis reveals the actual evolutionary trajectory and epidemiological trend of the international MRSA CC398 population considering host, temporal, geographical and molecular factors. It provides a baseline for global WGS-based One-Health studies of adaptive evolution of MRSA CC398 as well as for local outbreak investigations.
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Affiliation(s)
- Javier Eduardo Fernandez
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Gudrun Overesch
- Center for Zoonoses, Animal Bacterial Diseases and Antimicrobial Resistance, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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232
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Irwin NAT, Richards TA. Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes. Nat Microbiol 2024; 9:1713-1724. [PMID: 38806669 PMCID: PMC11222145 DOI: 10.1038/s41564-024-01707-9] [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: 07/28/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
Nucleosomes are DNA-protein complexes composed of histone proteins that form the basis of eukaryotic chromatin. The nucleosome was a key innovation during eukaryotic evolution, but its origin from histone homologues in Archaea remains unclear. Viral histone repeats, consisting of multiple histone paralogues within a single protein, may reflect an intermediate state. Here we examine the diversity of histones encoded by Nucleocytoviricota viruses. We identified 258 histones from 168 viral metagenomes with variable domain configurations including histone singlets, doublets, triplets and quadruplets, the latter comprising the four core histones arranged in series. Viral histone repeats branch phylogenetically between Archaea and eukaryotes and display intermediate functions in Escherichia coli, self-assembling into eukaryotic-like nucleosomes that stack into archaeal-like oligomers capable of impacting genomic activity and condensing DNA. Histone linkage also facilitates nucleosome formation, promoting eukaryotic histone assembly in E. coli. These data support the hypothesis that viral histone repeats originated in stem-eukaryotes and that nucleosome evolution proceeded through histone repeat intermediates.
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Affiliation(s)
- Nicholas A T Irwin
- Merton College, University of Oxford, Oxford, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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Ma Y, López‐Pujol J, Yan D, Zhou Z, Deng Z, Niu J. Complete chloroplast genomes of the hemiparasitic genus Cymbaria: Insights into comparative analysis, development of molecular markers, and phylogenetic relationships. Ecol Evol 2024; 14:e11677. [PMID: 38962021 PMCID: PMC11221886 DOI: 10.1002/ece3.11677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 05/18/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
The hemiparasitic tribe Cymbarieae (Orobanchaceae) plays a crucial role in elucidating the initial stage of the transition from autotrophism to heterotrophism. However, the complete chloroplast genome of the type genus Cymbaria has yet to be reported. In addition, the traditional Mongolian medicine Cymbaria daurica is frequently subjected to adulteration or substitution because of the minor morphological differences with Cymbaria mongolica. In this study, the complete chloroplast genomes of the two Cymbaria species were assembled and annotated, and those of other published 52 Orobanchaceae species were retrieved for comparative analyses. We found that the Cymbaria chloroplast genomes are characterized by pseudogenization or loss of stress-relevant genes (ndh) and a unique rbcL-matK inversion. Unlike the high variability observed in holoparasites, Cymbaria and other hemiparasites exhibit high similarity to autotrophs in genome size, guanine-cytosine (GC) content, and intact genes. Notably, four pairs of specific DNA barcodes were developed and validated to distinguish the medicinal herb from its adulterants. Phylogenetic analyses revealed that the genus Cymbaria and the Schwalbea-Siphonostegia clade are grouped into the tribe Cymbarieae, which forms a sister clade to the remaining Orobanchaceae parasitic lineages. Moreover, the diversification of monophyletic Cymbaria occurred during the late Miocene (6.72 Mya) in the Mongol-Chinese steppe region. Our findings provide valuable genetic resources for studying the phylogeny of Orobanchaceae and plant parasitism, and genetic tools to validate the authenticity of the traditional Mongolian medicine "Xinba.".
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Affiliation(s)
- Yang Ma
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Jordi López‐Pujol
- Botanic Institute of Barcelona (IBB)CSIC‐CMCNBBarcelonaSpain
- Escuela de Ciencias AmbientalesUniversidad Espíritu Santo (UEES)SamborondónEcuador
| | - Dongqing Yan
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Zhen Zhou
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Zekun Deng
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Jianming Niu
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian PlateauHohhotChina
- Inner Mongolia Key Laboratory of Grassland Ecology and the Candidate State Key Laboratory of Ministry of Science and TechnologyHohhotChina
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234
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Wang Z, Zhang W, Zhou Y, Zhang Q, Kulkarni KP, Melmaiee K, Tian Y, Dong M, Gao Z, Su Y, Yu H, Xu G, Li Y, He H, Liu Q, Sun H. Genetic and epigenetic signatures for improved breeding of cultivated blueberry. HORTICULTURE RESEARCH 2024; 11:uhae138. [PMID: 38988623 PMCID: PMC11233858 DOI: 10.1093/hr/uhae138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/05/2024] [Indexed: 07/12/2024]
Abstract
Blueberry belongs to the Vaccinium genus and is a highly popular fruit crop with significant economic importance. It was not until the early twentieth century that they began to be domesticated through extensive interspecific hybridization. Here, we collected 220 Vaccinium accessions from various geographical locations, including 154 from the United States, 14 from China, eight from Australia, and 29 from Europe and other countries, comprising 164 Vaccinium corymbosum, 15 Vaccinium ashei, 10 lowbush blueberries, seven half-high blueberries, and others. We present the whole-genome variation map of 220 accessions and reconstructed the hundred-year molecular history of interspecific hybridization of blueberry. We focused on the two major blueberry subgroups, the northern highbush blueberry (NHB) and southern highbush blueberry (SHB) and identified candidate genes that contribute to their distinct traits in climate adaptability and fruit quality. Our analysis unveiled the role of gene introgression from Vaccinium darrowii and V. ashei into SHB in driving the differentiation between SHB and NHB, potentially facilitating SHB's adaptation to subtropical environments. Assisted by genome-wide association studies, our analysis suggested VcTBL44 as a pivotal gene regulator governing fruit firmness in SHB. Additionally, we conducted whole-genome bisulfite sequencing on nine NHB and 12 SHB cultivars, and characterized regions that are differentially methylated between the two subgroups. In particular, we discovered that the β-alanine metabolic pathway genes were enriched for DNA methylation changes. Our study provides high-quality genetic and epigenetic variation maps for blueberry, which offer valuable insights and resources for future blueberry breeding.
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Affiliation(s)
- Zejia Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Wanchen Zhang
- Jilin Provincial Laboratory of Crop Germplasm Resources, College of Horticulture, Jilin Agricultural University, No. 2888 Xincheng Street, Economic Development District, Changchun 130118, China
| | - Yangyan Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Qiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Krishnanand P Kulkarni
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA
| | - Kalpalatha Melmaiee
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA
| | - Youwen Tian
- Jilin Provincial Laboratory of Crop Germplasm Resources, College of Horticulture, Jilin Agricultural University, No. 2888 Xincheng Street, Economic Development District, Changchun 130118, China
| | - Mei Dong
- Jilin Provincial Laboratory of Crop Germplasm Resources, College of Horticulture, Jilin Agricultural University, No. 2888 Xincheng Street, Economic Development District, Changchun 130118, China
| | - Zhaoxu Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Yanning Su
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Hong Yu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Guohui Xu
- College of Life and Health, Dalian University, Dalian 116622, China
| | - Yadong Li
- Jilin Provincial Laboratory of Crop Germplasm Resources, College of Horticulture, Jilin Agricultural University, No. 2888 Xincheng Street, Economic Development District, Changchun 130118, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Haiyue Sun
- Jilin Provincial Laboratory of Crop Germplasm Resources, College of Horticulture, Jilin Agricultural University, No. 2888 Xincheng Street, Economic Development District, Changchun 130118, China
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Tütüncü HE, Durmuş N, Sürmeli Y. Unraveling the potential of uninvestigated thermoalkaliphilic lipases by molecular docking and molecular dynamic simulation: an in silico characterization study. 3 Biotech 2024; 14:179. [PMID: 38882640 PMCID: PMC11176153 DOI: 10.1007/s13205-024-04023-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/29/2024] [Indexed: 06/18/2024] Open
Abstract
Thermoalkaliphilic lipase enzymes are mostly favored for use in the detergent industry. While there has been considerable research on Geobacillus lipases, a significant portion of these enzymes remains unexplored or undocumented in the scientific literature. This work performed in silico phylogeny, sequence alignment, structural and enzyme-substrate interaction analyses of the five thermoalkaliphilic lipases belonging to different Geobacillus species (Geobacillus stearothermophilus lipase = GsLip, Geobacillus sp. B4113_201601 lipase = Gb4Lip, Geobacillus kaustophilus HTA426 lipase = GkLip, Geobacillus sp. SP22 lipase = GspLip, Geobacillus sp. NTU 03 lipase = GntLip). For this purpose, unreviewed enzyme sequences of five Geobacillus thermoalkaliphilic lipases were analyzed at sequence and phylogeny levels. 3D homology enzyme models were built, validated, and investigated by different bioinformatics tools. The ligand interactions screening using seven para-nitrophenyl (pNP) esters and enzyme-ligand interactions were analyzed on Gb4Lip:pNP-C12 and BTL2:pNP-C12 by MD simulation. Biophysicochemical characteristic analysis showed that Gb4Lip had a theoretical T m value of above 65 ºC, and a higher aliphatic index indicating greater thermal stability. Sequence alignment showed a hydrophilic threonine in the α6 helix of Gb4Lip, indicating high enzymatic activity. A normalized temperature factor B (B'-factor) analysis showed that the lid domains of five lipases significantly possessed lower B'-factor values, compared to G. thermocatenulatus lipase 2 (BTL2), indicating that they had higher rigidity. Molecular docking results indicated that the five lipases had the highest binding affinity toward pNP-C12. The RMSF investigation revealed that the thermostability of Gb4Lip is influenced by specific molecular elements: D202-S203 within the αB region of the lid domain, and E274-Q275 within the b3 strand, as well as W278 in the b3-b4 loop, and H282 in the b4 strand of the Ca2+-binding region. MD simulation analysis showed that catalytic residue S114 and at least one oxyanion hole residue (F17 and/or Q114) in Gb4Lip frequently formed hydrogen bonds with the pNP-C12 ligand at 343 K and 348 K throughout the simulation process, indicating that Gb4Lip might catalyze relatively long-chain ligand pNP-C12 with high performance. In conclusion, Gb4Lip might be a more suitable candidate as the detergent additive. In addition, this investigation can offer valuable perspectives on Family I.5 lipases such as Gb4Lip for future exploration in the field of protein engineering. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04023-5.
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Affiliation(s)
- Havva Esra Tütüncü
- Department of Nutrition and Dietetics, Malatya Turgut Özal University, 44210 Malatya, Turkey
| | - Naciye Durmuş
- Department of Molecular Biology and Genetics, İstanbul Technical University, 34485 Istanbul, Turkey
| | - Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, 59030 Tekirdağ, Turkey
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Dost I, Abdel-Glil M, Persson S, Conza KL, Oleastro M, Alves F, Maurischat S, Scholtzek A, Mazuet C, Diancourt L, Tenson T, Schmoock G, Neubauer H, Schwarz S, Seyboldt C. Genomic study of European Clostridioides difficile ribotype 002/sequence type 8. Microb Genom 2024; 10. [PMID: 39051872 DOI: 10.1099/mgen.0.001270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024] Open
Abstract
Clostridioides difficile has significant clinical importance as a leading cause of healthcare-associated infections, with symptoms ranging from mild diarrhoea to severe colitis, and possible life-threatening complications. C. difficile ribotype (RT) 002, mainly associated with MLST sequence type (ST) 8, is one of the most common RTs found in humans. This study aimed at investigating the genetic characteristics of 537 C. difficile genomes of ST8/RT002. To this end, we sequenced 298 C. difficile strains representing a new European genome collection, with strains from Germany, Denmark, France and Portugal. These sequences were analysed against a global dataset consisting of 1,437 ST8 genomes available through Enterobase. Our results showed close genetic relatedness among the studied ST8 genomes, a diverse array of antimicrobial resistance (AMR) genes and the presence of multiple mobile elements. Notably, the pangenome analysis revealed an open genomic structure. ST8 shows relatively low overall variation. Thus, clonal isolates were found across different One Health sectors (humans, animals, environment and food), time periods, and geographical locations, suggesting the lineage's stability and a universal environmental source. Importantly, this stability did not hinder the acquisition of AMR genes, emphasizing the adaptability of this bacterium to different selective pressures. Although only 2.4 % (41/1,735) of the studied genomes originated from non-human sources, such as animals, food, or the environment, we identified 9 cross-sectoral core genome multilocus sequence typing (cgMLST) clusters. Our study highlights the importance of ST8 as a prominent lineage of C. difficile with critical implications in the context of One Health. In addition, these findings strongly support the need for continued surveillance and investigation of non-human samples to gain a more comprehensive understanding of the epidemiology of C. difficile.
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Affiliation(s)
- Ines Dost
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
- Present address: Landesuntersuchungsamt Rheinland-Pfalz, Koblenz, Germany
| | - Mostafa Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Søren Persson
- Statens Serum Institut, Dept. Bacteria, Parasites and Fungi, Unit of Foodborne Infections, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Karen Loaiza Conza
- Statens Serum Institut, Dept. Bacteria, Parasites and Fungi, Unit of Foodborne Infections, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Mónica Oleastro
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - Frederico Alves
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
- Chief Scientific Office, European Food Safety Authority (EFSA), Parma, Italy
| | - Sven Maurischat
- German Federal Institute for Risk Assessment, Department Biological Safety, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Anissa Scholtzek
- German Federal Institute for Risk Assessment, Department Biological Safety, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Christelle Mazuet
- Institut Pasteur, Université Paris Cité, Centre National de Référence Bactéries anaérobies et Botulisme, F-75015 Paris, France
| | - Laure Diancourt
- Institut Pasteur, Université Paris Cité, Centre National de Référence Bactéries anaérobies et Botulisme, F-75015 Paris, France
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Gernot Schmoock
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
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237
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Wang Q, Lei X, Wang Y, Di P, Meng X, Peng W, Rong J, Wang Y. Genome-wide identification of the LEA gene family in Panax ginseng: Evidence for the role of PgLEA2-50 in plant abiotic stress response. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108742. [PMID: 38772166 DOI: 10.1016/j.plaphy.2024.108742] [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: 01/21/2024] [Revised: 04/21/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024]
Abstract
Ginseng frequently encounters environmental stress during its growth and development. Late Embryogenesis Abundant (LEA) proteins play a crucial role in combating adversity stress, particularly against abiotic challenges In this study, 107 LEA genes from ginseng, spanning eight subfamilies, were identified, demonstrating significant evolutionary conservation, with the LEA2 subfamily being most prominent. Gene duplication events, primarily segmental duplications, have played a major role in the expansion of the LEA gene family, which has undergone strong purifying selection. PgLEAs were unevenly distributed across 22 chromosomes, with each subfamily featuring unique structural domains and conserved motifs. PgLEAs were expressed in various tissues, exhibiting distinct variations in abundance and tissue specificity. Numerous regulatory cis-elements, related to abiotic stress and hormones, were identified in the promoter region. Additionally, PgLEAs were regulated by a diverse array of abiotic stress-related transcription factors. A total of 35 PgLEAs were differentially expressed following treatments with ABA, GA, and IAA. Twenty-three PgLEAs showed significant but varied responses to drought, extreme temperatures, and salinity stress. The transformation of tobacco with the key gene PgLEA2-50 enhanced osmoregulation and antioxidant levels in transgenic lines, improving their resistance to abiotic stress. This study offers insights into functional gene analysis, focusing on LEA proteins, and establishes a foundational framework for research on ginseng's resilience to abiotic stress.
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Affiliation(s)
- Qi Wang
- Jilin Agricultural University, Changchun, Jilin, China
| | - Xiujuan Lei
- Jilin Agricultural University, Changchun, Jilin, China
| | - Yihan Wang
- Jilin Agricultural University, Changchun, Jilin, China
| | - Peng Di
- Jilin Agricultural University, Changchun, Jilin, China
| | - Xiangru Meng
- Jilin Agricultural University, Changchun, Jilin, China
| | - Wenyue Peng
- Jilin Agricultural University, Changchun, Jilin, China
| | - Junbo Rong
- Jilin Agricultural University, Changchun, Jilin, China
| | - Yingping Wang
- Jilin Agricultural University, Changchun, Jilin, China.
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238
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Zong X, Lou Y, Xia M, Zhao K, Chen J, Huang J, Yang S, Wang L. Recombination and repeat-induced point mutation landscapes reveal trade-offs between the sexual and asexual cycles of Magnaporthe oryzae. J Genet Genomics 2024; 51:723-734. [PMID: 38490361 DOI: 10.1016/j.jgg.2024.03.003] [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: 01/30/2024] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
The fungal disease caused by Magnaporthe oryzae is one of the most devastating diseases that endanger many crops worldwide. Evidence shows that sexual reproduction can be advantageous for fungal diseases as hybridization facilitates host-jumping. However, the pervasive clonal lineages of M. oryzae observed in natural fields contradict this expectation. A better understanding of the roles of recombination and the fungi-specific repeat-induced point mutation (RIP) in shaping its evolutionary trajectory is essential to bridge this knowledge gap. Here we systematically investigate the RIP and recombination landscapes in M. oryzae using a whole genome sequencing data from 252 population samples and 92 cross progenies. Our data reveal that the RIP can robustly capture the population history of M. oryzae, and we provide accurate estimations of the recombination and RIP rates across different M. oryzae clades. Significantly, our results highlight a parent-of-origin bias in both recombination and RIP rates, tightly associating with their sexual potential and variations of effector proteins. This bias suggests a critical trade-off between generating novel allelic combinations in the sexual cycle to facilitate host-jumping and stimulating transposon-associated diversification of effectors in the asexual cycle to facilitate host coevolution. These findings provide unique insights into understanding the evolution of blast fungus.
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Affiliation(s)
- Xifang Zong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Yaxin Lou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Mengshuang Xia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Kunyang Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Jingxuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Ju Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210000, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210000, China.
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China.
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239
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Narang G, Jakhan J, Tamang S, Yadav K, Singh V. Characterization of drug resistance genes in Indian Plasmodium falciparum and Plasmodium vivax field isolates. Acta Trop 2024; 255:107218. [PMID: 38636585 DOI: 10.1016/j.actatropica.2024.107218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
One of the major challenges for malaria control and elimination is the spread and emergence of antimalarial drug resistance. Mutations in Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) field isolates for five drug resistance genes viz. crt, mdr1, dhps, dhfr and kelch known to confer resistance to choloroquine (CQ), sulfadoxine-pyrimethamine (SP) and artemisinin (ART) and its derivatives were analyzed. A total of 342 symptomatic isolates of P. falciparum (Pf) and P. vivax (Pv) from 1993 to 2014 were retrieved from malaria parasite repository at National Institute of Malaria Research (NIMR). Sample DNA was extracted from dried blood spots and various targeted single nucleotide polymorphisms (SNPs) associated with antimalarial drug resistance were analysed for these isolates. 72S (67.7%) and 76T (83.8%) mutations along with SVMNT haplotype (67.7%) predominated the study population for Pfcrt. The most prevalent SNPs were 108N (73.2%) and 437G (24.8%) and the most prevalent haplotypes were ACNRNI (51.9%) and SAKAA (74.5%) in Pfdhfr and Pfdhps respectively. Only two mutations in Pfmdr1, 86Y (26.31%) and 184F (56.26%), were seen frequently in our study population. No mutations associated with Pfk13 were observed. For Pv, all the studied isolates showed two Pvdhps mutations, 383G and 553G, and two Pfdhfr mutations, 58R and 117N. Similarly, three mutations, viz. 958M, 908L and 1076L were found in Pvmdr1. No variations were observed in Pvcrt-o and Pvk12 genes. Overall, our study demonstrates an increase in mutations associated with SP resistance in both Pf and Pv, however, no single nucleotide polymorphisms (SNPs) associated with ART resistance have been observed for either species. Various SNPs associated with CQ resistance were seen in Pf; whereas only Pvmdr1 associated resistant SNPs were observed in Pv. Therefore, molecular characterization of drug resistance genes is essential for timely monitoring and prevention of malaria by identifying the circulating drug resistant parasites in the country.
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Affiliation(s)
- Geetika Narang
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Jahnvi Jakhan
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Suman Tamang
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Karmveer Yadav
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077, India
| | - Vineeta Singh
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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240
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Zhao X, Qin J, Chen G, Yang C, Wei J, Li W, Jia W. Whole-genome sequencing, multilocus sequence typing, and resistance mechanism of the carbapenem-resistant Pseudomonas aeruginosa in China. Microb Pathog 2024; 192:106720. [PMID: 38815778 DOI: 10.1016/j.micpath.2024.106720] [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: 03/12/2024] [Revised: 05/14/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Pseudomonas aeruginosa is a significant pathogen responsible for severe multisite infections with high morbidity and mortality rates. This study analyzed carbapenem-resistant Pseudomonas aeruginosa (CRPA) at a tertiary hospital in Shandong, China, using whole-genome sequencing (WGS). The objective was to explore the mechanisms and molecular characteristics of carbapenem resistance. A retrospective analysis of 91 isolates from January 2022 to March 2023 was performed, which included strain identification and antimicrobial susceptibility testing. WGS was utilized to determine the genome sequences of these CRPA strains, and the species were precisely identified using average nucleotide identification (ANI), with further analysis on multilocus sequence typing and strain relatedness. Some strains were found to carry the ampD and oprD genes, while only a few harbored carbapenemase genes or related genes. Notably, all strains possessed the mexA, mexE, and mexX genes. The major lineage identified was ST244, followed by ST235. The study revealed a diverse array of carbapenem resistance mechanisms among hospital isolates, differing from previous studies in mainland China. It highlighted that carbapenem resistance is not due to a single mechanism but rather a combination of enzyme-mediated resistance, AmpC overexpression, OprD dysfunction, and efflux pump overexpression. This research provides valuable insights into the evolutionary mechanisms and molecular features of CRPA resistance in this region, aiding in the national prevention and control of CRPA, and offering references for targeting and developing new drugs.
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Affiliation(s)
- Xue Zhao
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Jiangnan Qin
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Guang Chen
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Chao Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jie Wei
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Wanxiang Li
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China
| | - Wei Jia
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong Province, China.
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241
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Wu TJ, Lin CC, Ma LT, Yang CK, Ho CL, Wang SY, Chu FH. Functional identification of specialized diterpene synthases from Chamaecyparis obtusa and C. obtusa var. formosana to illustrate the putative evolution of diterpene synthases in Cupressaceae. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 344:112080. [PMID: 38582272 DOI: 10.1016/j.plantsci.2024.112080] [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: 01/09/2024] [Revised: 03/12/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Chamaecyparis obtusa and C. obtusa var. formosana of the Cupressaceae family are well known for their fragrance and excellent physical properties. To investigate the biosynthesis of unique diterpenoid compounds, diterpene synthase genes for specialized metabolite synthesis were cloned from C. obtusa and C. obtusa var. formosana. Using an Escherichia coli co-expression system, eight diterpene synthases (diTPSs) were characterized. CoCPS and CovfCPS are class II monofunctional (+)-copalyl diphosphate synthases [(+)-CPSs]. Class I monofunctional CoLS and CovfLS convert (+)-copalyl diphosphate [(+)-CPP] to levopimaradiene, CoBRS, CovfBRS1, and CovfBRS3 convert (+)-CPP to (-)-beyerene, and CovfSDS converts (+)-CPP to (-)-sandaracopimaradiene. These enzymes are all monofunctional diterpene syntheses in Cupressaceae family of gymnosperm, and differ from those in Pinaceae. The discovery of the enzyme responsible for the biosynthesis of tetracyclic diterpene (-)-beyerene was characterized for the first time. Diterpene synthases with different catalytic functions exist in closely related species within the Cupressaceae family, indicating that this group of monofunctional diterpene synthases is particularly prone to the evolution of new functions and development of species-specific specialized diterpenoid constituents.
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Affiliation(s)
- Tsai-Jung Wu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Chi-Chun Lin
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Li-Ting Ma
- Academy of Circular Economy, National Chung-Hsing University, Taichung, Taiwan
| | - Chih-Kai Yang
- Department of Forestry, National Pingtung University of Science and Technology, Taipei, Taiwan
| | - Chen-Lung Ho
- Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Sheng-Yang Wang
- Department of Forestry, National Chung-Hsing University, Taichung, Taiwan
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan.
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242
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Atkins H, Sabharwal B, Boger L, Stegman N, Kula A, Wolfe AJ, Banerjee S, Putonti C. Evidence of Lactobacillus strains shared between the female urinary and vaginal microbiota. Microb Genom 2024; 10. [PMID: 38949867 DOI: 10.1099/mgen.0.001267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024] Open
Abstract
Lactobacillus species are common inhabitants of the 'healthy' female urinary and vaginal communities, often associated with a lack of symptoms in both anatomical sites. Given identification by prior studies of similar bacterial species in both communities, it has been hypothesized that the two microbiotas are in fact connected. Here, we carried out whole-genome sequencing of 49 Lactobacillus strains, including 16 paired urogenital samples from the same participant. These strains represent five different Lactobacillus species: L. crispatus, L. gasseri, L. iners, L. jensenii, and L. paragasseri. Average nucleotide identity (ANI), alignment, single-nucleotide polymorphism (SNP), and CRISPR comparisons between strains from the same participant were performed. We conducted simulations of genome assemblies and ANI comparisons and present a statistical method to distinguish between unrelated, related, and identical strains. We found that 50 % of the paired samples have identical strains, evidence that the urinary and vaginal communities are connected. Additionally, we found evidence of strains sharing a common ancestor. These results establish that microbial sharing between the urinary tract and vagina is not limited to uropathogens. Knowledge that these two anatomical sites can share lactobacilli in females can inform future clinical approaches.
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Affiliation(s)
- Haley Atkins
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA
| | - Baani Sabharwal
- Department of Molecular Environmental Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Leah Boger
- Data Science Program, Loyola University Chicago, Chicago, IL, USA
| | - Natalie Stegman
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA
| | - Alexander Kula
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Swarnali Banerjee
- Data Science Program, Loyola University Chicago, Chicago, IL, USA
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
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243
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Dong T, Su J, Li H, Du Y, Wang Y, Chen P, Duan H. Genome-Wide Identification of the WRKY Gene Family in Four Cotton Varieties and the Positive Role of GhWRKY31 in Response to Salt and Drought Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1814. [PMID: 38999654 PMCID: PMC11243856 DOI: 10.3390/plants13131814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
The WRKY gene family is ubiquitously distributed in plants, serving crucial functions in stress responses. Nevertheless, the structural organization and evolutionary dynamics of WRKY genes in cotton have not been fully elucidated. In this study, a total of 112, 119, 217, and 222 WRKY genes were identified in Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. These 670 WRKY genes were categorized into seven distinct subgroups and unequally distributed across chromosomes. Examination of conserved motifs, domains, cis-acting elements, and gene architecture collectively highlighted the evolutionary conservation and divergence within the WRKY gene family in cotton. Analysis of synteny and collinearity further confirmed instances of expansion, duplication, and loss events among WRKY genes during cotton evolution. Furthermore, GhWRKY31 transgenic Arabidopsis exhibited heightened germination rates and longer root lengths under drought and salt stress. Silencing GhWRKY31 in cotton led to reduced levels of ABA, proline, POD, and SOD, along with downregulated expression of stress-responsive genes. Yeast one-hybrid and molecular docking assays confirmed the binding capacity of GhWRKY31 to the W box of GhABF1, GhDREB2, and GhRD29. The findings collectively offer a systematic and comprehensive insight into the evolutionary patterns of cotton WRKYs, proposing a suitable regulatory framework for developing cotton cultivars with enhanced resilience to drought and salinity stress.
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Affiliation(s)
- Tianyu Dong
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Jiuchang Su
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Haoyuan Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Yajie Du
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Peilei Chen
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
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244
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Baker‐Austin C, Hervio‐Heath D, Martinez‐Urtaza J, Caro ES, Strauch E, Thébault A, Guerra B, Messens W, Simon AC, Barcia‐Cruz R, Suffredini E. Public health aspects of Vibrio spp. related to the consumption of seafood in the EU. EFSA J 2024; 22:e8896. [PMID: 39045511 PMCID: PMC11263920 DOI: 10.2903/j.efsa.2024.8896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
Vibrio parahaemolyticus, Vibrio vulnificus and non-O1/non-O139 Vibrio cholerae are the Vibrio spp. of highest relevance for public health in the EU through seafood consumption. Infection with V. parahaemolyticus is associated with the haemolysins thermostable direct haemolysin (TDH) and TDH-related haemolysin (TRH) and mainly leads to acute gastroenteritis. V. vulnificus infections can lead to sepsis and death in susceptible individuals. V. cholerae non-O1/non-O139 can cause mild gastroenteritis or lead to severe infections, including sepsis, in susceptible individuals. The pooled prevalence estimate in seafood is 19.6% (95% CI 13.7-27.4), 6.1% (95% CI 3.0-11.8) and 4.1% (95% CI 2.4-6.9) for V. parahaemolyticus, V. vulnificus and non-choleragenic V. cholerae, respectively. Approximately one out of five V. parahaemolyticus-positive samples contain pathogenic strains. A large spectrum of antimicrobial resistances, some of which are intrinsic, has been found in vibrios isolated from seafood or food-borne infections in Europe. Genes conferring resistance to medically important antimicrobials and associated with mobile genetic elements are increasingly detected in vibrios. Temperature and salinity are the most relevant drivers for Vibrio abundance in the aquatic environment. It is anticipated that the occurrence and levels of the relevant Vibrio spp. in seafood will increase in response to coastal warming and extreme weather events, especially in low-salinity/brackish waters. While some measures, like high-pressure processing, irradiation or depuration reduce the levels of Vibrio spp. in seafood, maintaining the cold chain is important to prevent their growth. Available risk assessments addressed V. parahaemolyticus in various types of seafood and V. vulnificus in raw oysters and octopus. A quantitative microbiological risk assessment relevant in an EU context would be V. parahaemolyticus in bivalve molluscs (oysters), evaluating the effect of mitigations, especially in a climate change scenario. Knowledge gaps related to Vibrio spp. in seafood and aquatic environments are identified and future research needs are prioritised.
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245
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Kim BY, Gellert HR, Church SH, Suvorov A, Anderson SS, Barmina O, Beskid SG, Comeault AA, Crown KN, Diamond SE, Dorus S, Fujichika T, Hemker JA, Hrcek J, Kankare M, Katoh T, Magnacca KN, Martin RA, Matsunaga T, Medeiros MJ, Miller DE, Pitnick S, Schiffer M, Simoni S, Steenwinkel TE, Syed ZA, Takahashi A, Wei KHC, Yokoyama T, Eisen MB, Kopp A, Matute D, Obbard DJ, O’Grady PM, Price DK, Toda MJ, Werner T, Petrov DA. Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. PLoS Biol 2024; 22:e3002697. [PMID: 39024225 PMCID: PMC11257246 DOI: 10.1371/journal.pbio.3002697] [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: 11/06/2023] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.
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Affiliation(s)
- Bernard Y. Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Hannah R. Gellert
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Samuel H. Church
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut United States of America
| | - Anton Suvorov
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Sean S. Anderson
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Olga Barmina
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Sofia G. Beskid
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Aaron A. Comeault
- School of Environmental and Natural Sciences, Bangor University, Bangor, United Kingdom
| | - K. Nicole Crown
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Sarah E. Diamond
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Steve Dorus
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Takako Fujichika
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - James A. Hemker
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Jan Hrcek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Toru Katoh
- Department of Biological Sciences, Hokkaido University, Sapporo, Japan
| | - Karl N. Magnacca
- Hawaii Invertebrate Program, Division of Forestry & Wildlife, Honolulu, Hawaii, United States of America
| | - Ryan A. Martin
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Teruyuki Matsunaga
- Department of Complexity Science and Engineering, The University of Tokyo, Tokyo, Japan
| | - Matthew J. Medeiros
- Pacific Biosciences Research Center, University of Hawaiʻi, Mānoa, Hawaii, United States of America
| | - Danny E. Miller
- Division of Genetic Medicine, Department of Pediatrics; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Scott Pitnick
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Michele Schiffer
- Daintree Rainforest Observatory, James Cook University, Townsville, Australia
| | - Sara Simoni
- Department of Biology, Stanford University, Stanford, California, United States of America
| | | | - Zeeshan A. Syed
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Kevin H-C. Wei
- Department of Zoology, The University of British Columbia, Vancouver, Canada
| | - Tsuya Yokoyama
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Michael B. Eisen
- Department of Cell and Molecular Biology, University of California Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Daniel Matute
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Darren J. Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Patrick M. O’Grady
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
| | - Donald K. Price
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | | | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
- CZ Biohub, Investigator, San Francisco, California, United States of America
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246
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Li S, Yin L, Duan L, Li J, Wang P, Gao S, Xian W, Li W. Diversity, abundance, and expression of proteorhodopsin genes in the northern South China Sea. ENVIRONMENTAL RESEARCH 2024; 259:119514. [PMID: 38950812 DOI: 10.1016/j.envres.2024.119514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/03/2024]
Abstract
Proteorhodopsins have been suggested as an important strategy among phototrophs to capture solar energy in marine environments. The goals of this study was to investigate the diversity of proteorhodopsin genes and to explore their abundance, distribution, and expression in the coastal surface waters of the northern South China Sea, one of the largest marginal seas of the western North Pacific Ocean. Using 21 metagenomes, we recovered proteorhodopsin genes from a wide range of prokaryotic taxa, and chlorophyll a contributed significantly to the community composition of proteorhodopsin-containing microbes. Most proteorhodopsin sequences were predicted to encode green light-absorbing proton pumps and green light-absorbing proteorhodopsin genes were more abundant than blue-absorbing ones. The variations in the conserved residues involved in ion pumping and several uncharacterized proteorhodopsins were observed. The gene abundance pattern of proteorhodopsin types were significantly influenced by the levels of total organic carbon and soluble reactive phosphorus. Gene expression analysis confirmed the importance of proteorhodopsin-based phototrophy and revealed different expressional patterns among major phyla. In tandem, we screened 2295 metagenome-assembled genomes to describe the taxonomic distribution of proteorhodopsins. Bacteroidota are the key lineages encoding proteorhodopsins, but proteorhodopsins were predicated from members of Proteobacteria, Marinisomatota, Myxococcota, Verrucomicrobiota and Thermoplasmatota. Our study expanded the diversity of proteorhodopsins and improve our understanding on the significance of proteorhodopsin-mediated phototrophy in the marine ecosystem.
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Affiliation(s)
- Shanhui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences & School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lingzi Yin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences & School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Duan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences & School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jialing Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences & School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences & School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shaoming Gao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences & School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wendong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences & School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China; Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316000, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences & School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China.
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247
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Carey ME, Thi Nguyen TN, Tran DHN, Dyson ZA, Keane JA, Pham Thanh D, Mylona E, Nair S, Chattaway M, Baker S. The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi. Commun Biol 2024; 7:775. [PMID: 38942806 PMCID: PMC11213900 DOI: 10.1038/s42003-024-06451-8] [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: 12/22/2023] [Accepted: 06/13/2024] [Indexed: 06/30/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is commonly associated with the H58 lineage, a lineage that arose comparatively recently before becoming globally disseminated. To better understand when and how H58 emerged and became dominant, we performed detailed phylogenetic analyses on contemporary genome sequences from S. Typhi isolated in the period spanning the emergence. Our dataset, which contains the earliest described H58 S. Typhi organism, indicates that ancestral H58 organisms were already multi-drug resistant (MDR). These organisms emerged spontaneously in India in 1987 and became radially distributed throughout South Asia and then globally in the ensuing years. These early organisms were associated with a single long branch, possessing mutations associated with increased bile tolerance, suggesting that the first H58 organism was generated during chronic carriage. The subsequent use of fluoroquinolones led to several independent mutations in gyrA. The ability of H58 to acquire and maintain AMR genes continues to pose a threat, as extensively drug-resistant (XDR; MDR plus resistance to ciprofloxacin and third generation cephalosporins) variants, have emerged recently in this lineage. Understanding where and how H58 S. Typhi originated and became successful is key to understand how AMR drives successful lineages of bacterial pathogens. Additionally, these data can inform optimal targeting of typhoid conjugate vaccines (TCVs) for reducing the potential for emergence and the impact of new drug-resistant variants. Emphasis should also be placed upon the prospective identification and treatment of chronic carriers to prevent the emergence of new drug resistant variants with the ability to spread efficiently.
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
- IAVI, Chelsea & Westminster Hospital, London, UK.
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | | | - Zoe A Dyson
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Elli Mylona
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Satheesh Nair
- United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Unit, London, UK
| | - Marie Chattaway
- United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Unit, London, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- IAVI, Chelsea & Westminster Hospital, London, UK
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248
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Shi Y, Masic V, Mosaiab T, Rajaratman P, Hartley-Tassell L, Sorbello M, Goulart CC, Vasquez E, Mishra BP, Holt S, Gu W, Kobe B, Ve T. Structural characterization of macro domain-containing Thoeris antiphage defense systems. SCIENCE ADVANCES 2024; 10:eadn3310. [PMID: 38924412 PMCID: PMC11204291 DOI: 10.1126/sciadv.adn3310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Thoeris defense systems protect bacteria from infection by phages via abortive infection. In these systems, ThsB proteins serve as sensors of infection and generate signaling nucleotides that activate ThsA effectors. Silent information regulator and SMF/DprA-LOG (SIR2-SLOG) containing ThsA effectors are activated by cyclic ADP-ribose (ADPR) isomers 2'cADPR and 3'cADPR, triggering abortive infection via nicotinamide adenine dinucleotide (NAD+) depletion. Here, we characterize Thoeris systems with transmembrane and macro domain (TM-macro)-containing ThsA effectors. We demonstrate that ThsA macro domains bind ADPR and imidazole adenine dinucleotide (IAD), but not 2'cADPR or 3'cADPR. Combining crystallography, in silico predictions, and site-directed mutagenesis, we show that ThsA macro domains form nucleotide-induced higher-order oligomers, enabling TM domain clustering. We demonstrate that ThsB can produce both ADPR and IAD, and we identify a ThsA TM-macro-specific ThsB subfamily with an active site resembling deoxy-nucleotide and deoxy-nucleoside processing enzymes. Collectively, our study demonstrates that Thoeris systems with SIR2-SLOG and TM-macro ThsA effectors trigger abortive infection via distinct mechanisms.
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Affiliation(s)
- Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Tamim Mosaiab
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Premraj Rajaratman
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Mitchell Sorbello
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cassia C. Goulart
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Eduardo Vasquez
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Biswa P. Mishra
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Stephanie Holt
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
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249
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Neumann EN, Bertozzi TM, Wu E, Serack F, Harvey JW, Brauer PP, Pirtle CP, Coffey A, Howard M, Kamath N, Lenz K, Guzman K, Raymond MH, Khalil AS, Deverman BE, Minikel EV, Vallabh SM, Weissman JS. Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor. Science 2024; 384:ado7082. [PMID: 38935715 DOI: 10.1126/science.ado7082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/02/2024] [Indexed: 06/29/2024]
Abstract
Prion disease is caused by misfolding of the prion protein (PrP) into pathogenic self-propagating conformations, leading to rapid-onset dementia and death. However, elimination of endogenous PrP halts prion disease progression. In this study, we describe Coupled Histone tail for Autoinhibition Release of Methyltransferase (CHARM), a compact, enzyme-free epigenetic editor capable of silencing transcription through programmable DNA methylation. Using a histone H3 tail-Dnmt3l fusion, CHARM recruits and activates endogenous DNA methyltransferases, thereby reducing transgene size and cytotoxicity. When delivered to the mouse brain by systemic injection of adeno-associated virus (AAV), Prnp-targeted CHARM ablates PrP expression across the brain. Furthermore, we have temporally limited editor expression by implementing a kinetically tuned self-silencing approach. CHARM potentially represents a broadly applicable strategy to suppress pathogenic proteins, including those implicated in other neurodegenerative diseases.
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Affiliation(s)
- Edwin N Neumann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tessa M Bertozzi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Elaine Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Fiona Serack
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John W Harvey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pamela P Brauer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Catherine P Pirtle
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alissa Coffey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Howard
- Comparative Medicine, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nikita Kamath
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kenney Lenz
- Comparative Medicine, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kenia Guzman
- Comparative Medicine, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael H Raymond
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Benjamin E Deverman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric Vallabh Minikel
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McCance Center for Brain Health and Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sonia M Vallabh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McCance Center for Brain Health and Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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250
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Khazani Asforooshani M, Elikaei A, Abed S, Shafiei M, Barzi SM, Solgi H, Badmasti F, Sohrabi A. A novel Enterococcus faecium phage EF-M80: unveiling the effects of hydrogel-encapsulated phage on wound infection healing. Front Microbiol 2024; 15:1416971. [PMID: 39006751 PMCID: PMC11239553 DOI: 10.3389/fmicb.2024.1416971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 06/13/2024] [Indexed: 07/16/2024] Open
Abstract
Background Enterococcus faecium is one of the members of ESKAPE pathogens. Due to its resistance to antimicrobial agents, treating this bacterium has become challenging. The development of innovative approaches to combat antibiotic resistance is necessary. Phage therapy has emerged as a promising method for curing antibiotic-resistant bacteria. Methods In this study, E. faecium phages were isolated from wastewater. Phage properties were characterized through in vitro assays (e.g. morphological studies, and physicochemical properties). In addition, whole genome sequencing was performed. A hydrogel-based encapsulated phage was obtained and its structure characteristics were evaluated. Wound healing activity of the hydrogel-based phage was assessed in a wound mice model. Results The purified phage showed remarkable properties including broad host range, tolerance to high temperature and pH and biofilm degradation feature as a stable and reliable therapeutic agent. Whole genome sequencing revealed that the genome of the EF-M80 phage had a length of 40,434 bp and harbored 65 open reading frames (ORFs) with a GC content of 34.9% (GenBank accession number is OR767211). Hydrogel-based encapsulated phage represented an optimized structure. Phage-loaded hydrogel-treated mice showed that the counting of neutrophils, fibroblasts, blood vessels, hair follicles and percentage of collagen growth were in favor of the wound healing process in the mice model. Conclusion These findings collectively suggest the promising capability of this phage-based therapeutic strategy for the treatment of infections associated with the antibiotic-resistant E. faecium. In the near future, we hope to expect the presence of bacteriophages in the list of antibacterial compounds used in the clinical settings.
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Affiliation(s)
- Mahshid Khazani Asforooshani
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Sahar Abed
- Department of Microbial Biotechnology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Morvarid Shafiei
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Hamid Solgi
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Aria Sohrabi
- Department of Epidemiology and Biostatistics, Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
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