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Santoro M, Occhibove F, López-Verdejo A, Rojas A, Solano-Barquero A. Paronatrema davidbowiei n. sp. (Trematoda: Syncoeliidae), a new parasite of the pelagic thresher (Alopias pelagicus) and its phylogenetic relationships within the suborder Hemiurata Skrjabin & Guschanskaja, 1954. Parasitol Int 2024; 103:102953. [PMID: 39181312 DOI: 10.1016/j.parint.2024.102953] [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: 06/25/2024] [Revised: 08/07/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
A new species of hemiurid trematode found on the gills and in the aorta of the pelagic thresher Alopias pelagicus from the eastern Pacific, off Costa Rica, is described based on an integrative taxonomic approach that includes the use of light and scanning electron microscopy, and 28S rDNA sequencing. Phylogenetic analysis was also performed to explore, for the first time, the relationships of a member of the subfamily Otiotrematinae within the suborder Hemiurata. Paronatrema davidbowiei n. sp. can be distinguished from the congeners by having tegumental spines on the dorsal surface of the forebody, papillae on the oral sucker, and different morphology or number of testicular follicles. BLAST analysis revealed that sequences of Paronatrema davidbowiei n. sp. had the highest degree of similarity with Hirudinella spp. (Hirudinellidae). Results from Maximum Likelihood and Bayesian phylogenetic analyses, returning trees with the exact same topology and strong branch support, distinguished between the two superfamilies included in the suborder Hemiurata: Azygioidea and Hemiuroidea. Our analysis placed the new species in a clade with Copiatestes filiferus, the only existing sequence of the family Syncoeliidae.
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Affiliation(s)
- Mario Santoro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy.
| | - Flavia Occhibove
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy
| | - Alejandro López-Verdejo
- Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Spain
| | - Alicia Rojas
- Center for Research in Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, 11501-2060 San Pedro de Montes de Oca, San José, Costa Rica
| | - Alberto Solano-Barquero
- Center for Research in Tropical Diseases (CIET), Faculty of Microbiology, University of Costa Rica, 11501-2060 San Pedro de Montes de Oca, San José, Costa Rica
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2
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Loginova OA, Spiridonov SE, Maslennikova OV, Bukina LA. Molecular Characterization of Echinococcus canadensis (Cestoda, Taeniidae) in Wolf from the Kirov Region. DOKL BIOCHEM BIOPHYS 2024; 518:305-308. [PMID: 38955913 DOI: 10.1134/s1607672924701011] [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: 04/20/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 07/04/2024]
Abstract
This work presents the results of studying the molecular characteristics of parasitic tapeworms Echinococcus canadensis. The helminths were discovered during the autopsy of a wolf (Canis lupus Linnaeus, 1758) killed by hunters in the Kirov oblast in 2021. A molecular phylogenetic study was performed by analyzing the sequence of a fragment of the first subunit of the mitochondrial cytochrome oxidase gene (CoxI). It was found that the detected echinococci belong to the G10 genotype of E. canadensis, which is common in wolves in the northern territories of the Holarctic. We discovered four positions at which the substitutions characteristic only of this genotype are revealed. A substitution at one of the positions that is characteristic exclusively for the representatives of the G10 genotype found in Russia and Finland was also discovered.
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Affiliation(s)
- O A Loginova
- Severtsov Institute of Ecology and Evolution, Moscow, Russia.
| | - S E Spiridonov
- Severtsov Institute of Ecology and Evolution, Moscow, Russia
| | | | - L A Bukina
- Vyatka State Agrotechnological University, Kirov, Russia
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3
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Santos JL, Nick F, Adhitama N, Fields PD, Stillman JH, Kato Y, Watanabe H, Ebert D. Trehalose mediates salinity-stress tolerance in natural populations of a freshwater crustacean. Curr Biol 2024; 34:4160-4169.e7. [PMID: 39168123 DOI: 10.1016/j.cub.2024.07.082] [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: 02/02/2024] [Revised: 06/10/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024]
Abstract
Salinization poses an increasing problem worldwide, threatening freshwater organisms and raising questions about their ability to adapt. We explored the mechanisms enabling a planktonic crustacean to tolerate elevated salinity. By gradually raising water salinity in clonal cultures from 185 Daphnia magna populations, we showed that salt tolerance strongly correlates with native habitat salinity, indicating local adaptation. A genome-wide association study (GWAS) further revealed a major effect of the Alpha,alpha-trehalose-phosphate synthase (TPS) gene, suggesting that trehalose production facilitates salinity tolerance. Salinity-tolerant animals showed a positive correlation between water salinity and trehalose concentrations, while intolerant animals failed to produce trehalose. Animals with a non-functional TPS gene, generated through CRISPR-Cas9, supported the trehalose role in salinity stress. Our study highlights how a keystone freshwater animal adapts to salinity stress using an evolutionary mechanism known in bacteria, plants, and arthropods.
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Affiliation(s)
- Joana L Santos
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.
| | - Fabienne Nick
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Nikko Adhitama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Japan
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Jonathon H Stillman
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland; Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132, USA; Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building 3140, Berkeley, CA 94720, USA
| | - Yasuhiko Kato
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Japan
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.
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Wang W, Weng J, Wei J, Zhang Q, Zhou Y, He Y, Zhang L, Li W, Zhang Y, Zhang Z, Li X. Whole genome sequencing insight into carbapenem-resistant and multidrug-resistant Acinetobacter baumannii harboring chromosome-borne blaOXA-23. Microbiol Spectr 2024; 12:e0050124. [PMID: 39101706 PMCID: PMC11370241 DOI: 10.1128/spectrum.00501-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/26/2024] [Indexed: 08/06/2024] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a significant threat to hospitalized patients as effective therapeutic options are scarce. Based on the genomic characteristics of the CRAB strain AB2877 harboring chromosome-borne blaOXA-23, which was isolated from the bronchoalveolar lavage fluid (BALF) of a patient in a respiratory intensive care unit (RICU), we systematically analyzed antibiotic resistance genes (ARGs) and the genetic context associated with ARGs carried by CRAB strains harboring chromosome-borne blaOXA-23 worldwide. Besides blaOXA-23, other ARGs were detected on the chromosome of the CRAB strain AB2877 belonging to ST208/1806 (Oxford MLST scheme). Several key genetic contexts associated with the ARGs were identified on the chromosome of the CRAB strain AB2877, including (1) the MDR region associated with blaOXA-23, tet(B)-tetR(B), aph(3'')-Ib, and aph(6)-Id (2); the resistance island AbGRI3 harboring armA and mph(E)-msr(E) (3); the Tn3-like composite transposon containing blaTEM-1D and aph(3')-Ia; and (4) the structure "ISAba1-blaADC-25." The first two genetic contexts were most common in ST195/1816, followed by ST208/1806. The last two genetic contexts were found most frequently in ST208/1806, followed by ST195/1816.IMPORTANCEThe blaOXA-23 gene can be carried by plasmid or chromosome, facilitating horizontal genetic transfer and increasing carbapenem resistance in healthcare settings. In this study, we focused on the genomic characteristics of CRAB strains harboring the chromosome-borne blaOXA-23 gene, and the important genetic contexts associated with blaOXA-23 and other ARGs were identified, and their prevalent clones worldwide were determined. Notably, although the predominant clonal CRAB lineages worldwide containing the MDR region associated with blaOXA-23, tet(B)-tetR(B), aph(3'')-Ib, and aph (6)-Id was ST195/1816, followed by ST208/1806, the CRAB strain AB2877 in our study belonged to ST208/1806. Our findings contribute to the knowledge regarding the dissemination of CRAB strains and the control of nosocomial infection.
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Affiliation(s)
- Wei Wang
- Department of Pulmonary and Critical Care Medicine, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
- Department of Critical Care Medicine, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Jiahui Weng
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jie Wei
- Department of Clinical Laboratory, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Qinghuan Zhang
- Department of Clinical Laboratory, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Yu Zhou
- Department of Anesthesiology, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Yanju He
- Department of Pulmonary and Critical Care Medicine, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Limei Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Wenting Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Yi Zhang
- Department of Pulmonary and Critical Care Medicine, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Zhiren Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
| | - Xiaobin Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, China
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Rivetti AV, Reischak D, de Oliveira CHS, Otaka JNP, Domingues CS, Freitas TDL, Cardoso FG, Montesino LO, da Silva ALS, Camillo SCA, Malta F, Amgarten D, Goés-Neto A, Aguiar ERGR, de Almeida IG, Pinto CA, Fonseca AA, Camargos MF. Phylodynamics of avian influenza A(H5N1) viruses from outbreaks in Brazil. Virus Res 2024; 347:199415. [PMID: 38880334 PMCID: PMC11239711 DOI: 10.1016/j.virusres.2024.199415] [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: 04/11/2024] [Revised: 05/23/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024]
Abstract
Our study identified strains of the A/H5N1 virus in analyzed samples of subsistence poultry, wild birds, and mammals, belonging to clade 2.3.4.4b, genotype B3.2, with very high genetic similarity to strains from Chile, Uruguay, and Argentina. This suggests a migratory route for wild birds across the Pacific, explaining the phylogenetic relatedness. The Brazilian samples displayed similarity to strains that had already been previously detected in South America. Phylogeographic analysis suggests transmission of US viruses from Europe and Asia, co-circulating with other lineages in the American continent. As mutations can influence virulence and host specificity, genomic surveillance is essential to detect those changes, especially in critical regions, such as hot spots in the HA, NA, and PB2 sequences. Mutations in the PB2 gene (D701N and Q591K) associated with adaptation and transmission in mammals were detected suggesting a potential zoonotic risk. Nonetheless, resistance to neuraminidase inhibitors (NAIs) was not identified, however, continued surveillance is crucial to detect potential resistance. Our study also mapped the spread of the virus in the Southern hemisphere, identifying possible entry routes and highlighting the importance of surveillance to prevent outbreaks and protect both human and animal populations.
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Affiliation(s)
- Anselmo Vasconcelos Rivetti
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/MG, Minas Gerais 33250220, Brazil.
| | - Dilmara Reischak
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/SP, São Paulo 13100-105, Brazil
| | | | - Juliana Nabuco Pereira Otaka
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/SP, São Paulo 13100-105, Brazil
| | - Christian Steffe Domingues
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/SP, São Paulo 13100-105, Brazil
| | - Talita de Lima Freitas
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/SP, São Paulo 13100-105, Brazil
| | - Fernanda Gomes Cardoso
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/SP, São Paulo 13100-105, Brazil
| | - Lucas Oliveira Montesino
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/SP, São Paulo 13100-105, Brazil
| | - Ana Luiza Savioli da Silva
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/SP, São Paulo 13100-105, Brazil
| | | | - Fernanda Malta
- Hospital Israelita Albert Einstein, São Paulo 05652-900, Brazil
| | - Deyvid Amgarten
- Hospital Israelita Albert Einstein, São Paulo 05652-900, Brazil
| | - Aristóteles Goés-Neto
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Minas Gerais 31270-901, Brazil
| | | | | | - Carla Amaral Pinto
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/MG, Minas Gerais 33250220, Brazil
| | - Antônio Augusto Fonseca
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/MG, Minas Gerais 33250220, Brazil
| | - Marcelo Fernandes Camargos
- Ministério da Agricultura e Pecuária, Laboratório Federal de Defesa Agropecuária/MG, Minas Gerais 33250220, Brazil
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6
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Ge Y, Lu J, Puiu D, Revsine M, Salzberg SL. Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595788. [PMID: 39071384 PMCID: PMC11275966 DOI: 10.1101/2024.05.24.595788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
In recent years, a growing number of publications have reported the presence of microbial species in human tumors and of mixtures of microbes that appear to be highly specific to different cancer types. Our recent re-analysis of data from three cancer types revealed that technical errors have caused erroneous reports of numerous microbial species found in sequencing data from The Cancer Genome Atlas (TCGA) project. Here we have expanded our analysis to cover all 5,734 whole-genome sequencing (WGS) data sets currently available from TCGA, covering 25 distinct types of cancer. We analyzed the microbial content using updated computational methods and databases, and compared our results to those from two major recent studies that focused on bacteria, viruses, and fungi in cancer. Our results expand upon and reinforce our recent findings, which showed that the presence of microbes is far smaller than had been previously reported, and that many species identified in TCGA data are either not present at all, or are known contaminants rather than microbes residing within tumors. As part of this expanded analysis, and to help others avoid being misled by flawed data, we have released a dataset that contains detailed read counts for bacteria, viruses, archaea, and fungi detected in all 5,734 TCGA samples, which can serve as a public reference for future investigations.
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Affiliation(s)
- Yuchen Ge
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, United States
- Department of Biomedical Engineering, Johns Hopkins University
| | - Jennifer Lu
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, United States
- Department of Pathology, Johns Hopkins School of Medicine
| | - Daniela Puiu
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, United States
- Department of Biomedical Engineering, Johns Hopkins University
| | - Mahler Revsine
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, United States
- Department of Computer Science, Johns Hopkins University
| | - Steven L. Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, United States
- Department of Biomedical Engineering, Johns Hopkins University
- Department of Computer Science, Johns Hopkins University
- Department of Biostatistics, Johns Hopkins University
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Lu Z, Tseng TT. Complete genome sequence of Escherichia coli O157:H7 phage Φ241. Microbiol Resour Announc 2024; 13:e0010624. [PMID: 39037317 PMCID: PMC11320906 DOI: 10.1128/mra.00106-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
We report the genome sequence of phage Φ241 infecting Escherichia coli O157:H7. Phage Φ241 was isolated from an industrial cucumber fermentation at high acidity (pH 3.7) and high salinity (5% NaCl). The phage genome consists of a 157,291 bp circular double-stranded DNA with 203 coding regions and 44.96% GC content.
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Affiliation(s)
- Zhongjing Lu
- Department of Molecular and Cellular Biology, College of Science and Mathematics, Kennesaw State University, Kennesaw, Georgia, USA
| | - Tsai-Tien Tseng
- Department of Molecular and Cellular Biology, College of Science and Mathematics, Kennesaw State University, Kennesaw, Georgia, USA
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Kawacka I, Olejnik-Schmidt A. Gene emrC Associated with Resistance to Quaternary Ammonium Compounds Is Common among Listeria monocytogenes from Meat Products and Meat Processing Plants in Poland. Antibiotics (Basel) 2024; 13:749. [PMID: 39200049 PMCID: PMC11350778 DOI: 10.3390/antibiotics13080749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 09/01/2024] Open
Abstract
(1) Background: L. monocytogenes is a food pathogen of great importance, characterized by a high mortality rate. Quaternary ammonium compounds (QACs), such as benzalkonium chloride (BC), are often used as disinfectants in food processing facilities. The effectiveness of disinfection procedures is crucial to food safety. (2) Methods: A collection of 153 isolates of L. monocytogenes from meat processing industry was analyzed for their sensitivity to BC using the agar diffusion method. Genes of interest were detected with PCR. (3) Results: Genes emrC, bcrABC, and qacH were found in 64 (41.8%), 6 (3.9%), and 1 isolate (0.7%), respectively, and 79 isolates (51.6%) were classified as having reduced sensitivity to BC. A strong correlation between carrying QACs resistance-related genes and phenotype was found (p-value < 0.0001). Among 51 isolates originating from bacon (collected over 13 months), 48 had the emrC gene, which could explain their persistent presence in a processing facility. Isolates with the ilsA gene (from LIPI-3) were significantly (p-value 0.006) less likely to carry QACs resistance-related genes. (4) Conclusions: Reduced sensitivity to QACs is common among L. monocytogenes from the meat processing industry. Persistent presence of these bacteria in a processing facility is presumably caused by emrC-induced QACs resistance.
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Affiliation(s)
- Iwona Kawacka
- Department of Food Biotechnology and Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
| | - Agnieszka Olejnik-Schmidt
- Department of Food Biotechnology and Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
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Baraf LM, Hung JY, Pratchett MS, Cowman PF. Comparative mitogenomics of marine angelfishes (F: Pomacanthidae). Ecol Evol 2024; 14:e70127. [PMID: 39119180 PMCID: PMC11307104 DOI: 10.1002/ece3.70127] [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: 03/27/2024] [Revised: 06/16/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
The targeted capture of ultraconserved elements (UCEs) has substantially increased the amount of genetic data available for phylogenomic reconstructions. These capture datasets frequently contain mitochondrial DNA as a by-product, often in the form of complete mitogenomes. These can be efficiently harvested to expand existing datasets without additional costs. Here, we present new mitochondrial genomes for six marine angelfish species (F: Pomacanthidae), assembled and annotated from off-target UCE reads. We provide the first comparative analysis of all mitochondrial genomes available for the Pomacanthidae. Results showed that the average length of pomacanthid mitogenomes is 16.8 kbp. Total GC and AT content varied between 44.5% and 46.3%, and 53.7% and 55.5%, respectively. The architecture of angelfish mitogenomes was comparable to that seen in other fish species with 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and the control region. All 13 PCGs evolved under purifying selection, highlighting a high level of selection pressure and gene expression to preserve genetic integrity. The ND6 and ATP8 genes had the highest ratio of non-synonymous (dN) to synonymous (dS) substitutions, indicating a relaxation of purifying selection constraints. Finally, these newly assembled mitogenomes will allow further investigations of the population genetics, systematics and evolutionary biology of one of the most prominent reef fish family in the aquarium trade.
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Affiliation(s)
- Lauriane M. Baraf
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Julia Y. Hung
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Morgan S. Pratchett
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Peter F. Cowman
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Biodiversity and Geosciences ProgramQueensland Museum TropicsTownsvilleQueenslandAustralia
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10
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Di Gregorio S, Niccolini L, Seggiani M, Strangis G, Barbani N, Vitiello V, Becarelli S, Petroni G, Yan X, Buttino I. Marine copepod culture as a potential source of bioplastic-degrading microbiome: The case of poly(butylene succinate-co-adipate). CHEMOSPHERE 2024; 362:142603. [PMID: 38885765 DOI: 10.1016/j.chemosphere.2024.142603] [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: 10/12/2023] [Revised: 05/21/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
The poly(butylene succinate-co-adipate) (PBSA) is emerging as environmentally sustainable polyester for applications in marine environment. In this work the capacity of microbiome associated with marine plankton culture to degrade PBSA, was tested. A taxonomic and functional characterization of the microbiome associated with the copepod Acartia tonsa, reared in controlled conditions, was analysed by 16S rDNA metabarcoding, in newly-formed adult stages and after 7 d of incubation. A predictive functional metagenomic profile was inferred for hydrolytic activities involved in bioplastic degradation with a particular focus on PBSA. The copepod-microbiome was also characterized in newly-formed carcasses of A. tonsa, and after 7 and 33 d of incubation in the plankton culture medium. Copepod-microbiome showed hydrolytic activities at all developmental stages of the alive copepods and their carcasses, however, the evenness of the hydrolytic bacterial community significantly increased with the time of incubation in carcasses. Microbial genera, never described in association with copepods: Devosia, Kordia, Lentibacter, Methylotenera, Rheinheimera, Marinagarivorans, Paraglaciecola, Pseudophaeobacter, Gaiella, Streptomyces and Kribbella sps., were retrieved. Kribbella sp. showed carboxylesterase activity and Streptomyces sp. showed carboxylesterase, triacylglycerol lipase and cutinase activities, that might be involved in PBSA degradation. A culturomic approach, adopted to isolate bacterial specimen from carcasses, led to the isolation of the bacterial strain, Vibrio sp. 01 tested for the capacity to promote the hydrolysis of the ester bonds. Granules of PBSA, incubated 82 d at 20 °C with Vibrio sp. 01, were characterized by scanning electron microscopy, infrared spectroscopy, thermogravimetric analysis, and differential scanning calorimetry, showing fractures compared to the control sample, and hydrolysis of ester bonds. These preliminary results are encouraging for further investigation on the ability of the microbiome associated with plankton to biodegrade polyesters, such as PBSA, and increasing knowledge on microorganisms involved in bioplastic degradation in marine environment.
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Affiliation(s)
- Simona Di Gregorio
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy
| | - Luca Niccolini
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy; Functional Biology and Plankton Genomic Lab. ISPRA - Italian Institute for Environmental Protection and Research, Via del Cedro n.38, 57122, Livorno, Italy
| | - Maurizia Seggiani
- Department of Civil and Industrial Engineering, University of Pisa, Largo Lucio Lazzarino 1, 56122, Pisa, Italy
| | - Giovanna Strangis
- Department of Civil and Industrial Engineering, University of Pisa, Largo Lucio Lazzarino 1, 56122, Pisa, Italy
| | - Niccoletta Barbani
- Department of Civil and Industrial Engineering, University of Pisa, Largo Lucio Lazzarino 1, 56122, Pisa, Italy
| | - Valentina Vitiello
- Functional Biology and Plankton Genomic Lab. ISPRA - Italian Institute for Environmental Protection and Research, Via del Cedro n.38, 57122, Livorno, Italy; Sino-Italian Joint Laboratory Functional Biology of Marine Biota, ISPRA, 57122, Livorno, Italy
| | - Simone Becarelli
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy
| | - Giulio Petroni
- Department of Biology, University of Pisa, Via Luca Ghini 13, 56123, Pisa, Italy
| | - Xiaojun Yan
- Sino-Italian Joint Laboratory Functional Biology of Marine Biota, ISPRA, 57122, Livorno, Italy; Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan City, 316022, Zhejiang, China
| | - Isabella Buttino
- Functional Biology and Plankton Genomic Lab. ISPRA - Italian Institute for Environmental Protection and Research, Via del Cedro n.38, 57122, Livorno, Italy; Sino-Italian Joint Laboratory Functional Biology of Marine Biota, ISPRA, 57122, Livorno, Italy.
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11
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Anders JL, Davey M, Van Moorter B, Fossøy F, Boessenkool S, Solberg EJ, Meisingset EL, Mysterud A, Rolandsen CM. Elucidating nematode diversity and prevalence in moose across a wide latitudinal gradient using DNA metabarcoding. Int J Parasitol Parasites Wildl 2024; 24:100962. [PMID: 39099677 PMCID: PMC11295938 DOI: 10.1016/j.ijppaw.2024.100962] [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: 06/07/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024]
Abstract
Parasitic nematodes are ubiquitous and can negatively impact their host by reducing fecundity or increasing mortality, yet the driver of variation in the parasite community across a wildlife host's geographic distribution remains elusive for most species. Based on an extensive collection of fecal samples (n = 264) from GPS marked moose (Alces alces), we used DNA metabarcoding to characterize the individual (sex, age class) and seasonal parasitic nematode community in relation to habitat use and migration behavior in five populations distributed across a wide latitudinal gradient (59.6°N to 70.5°N) in Norway. We detected 21 distinct nematode taxa with the six most common being Ostertagia spp., Nematodirella spp., Trichostongylus spp., T. axei, Elaphostrongylus alces, and an unclassified Strongylida. There was higher prevalence of livestock parasites in areas with larger sheep populations indicating a higher risk of spillover events. The individual level nematode richness was mostly consistent across study areas, while the number and type of nematode taxa detected at each study area varied considerably but did not follow a latitudinal gradient. While migration distance affected nematode beta-diversity across all sites, it had a positive effect on richness at only two of the five study areas suggesting population specific effects. Unexpectedly, nematode richness was higher in winter than summer when very few nematodes were detected. Here we provide the first extensive description of the parasitic nematode community of moose across a wide latitudinal range. Overall, the population-specific impact of migration on parasitism across the distribution range and variation in sympatry with other ruminants suggest local characteristics affect host-parasite relationships.
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Affiliation(s)
- Jason L. Anders
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Marie Davey
- Norwegian Institute for Nature Research (NINA), P. O. Box 5685 Sluppen, NO-7485 Trondheim, Norway
| | - Bram Van Moorter
- Norwegian Institute for Nature Research (NINA), Sognsveien 68, 0855 Oslo, Norway
| | - Frode Fossøy
- Norwegian Institute for Nature Research (NINA), P. O. Box 5685 Sluppen, NO-7485 Trondheim, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Erling J. Solberg
- Norwegian Institute for Nature Research (NINA), P. O. Box 5685 Sluppen, NO-7485 Trondheim, Norway
| | - Erling L. Meisingset
- Department of Forest and Forest Resources, Norwegian Institute of Bioeconomy Research, Tingvoll gard, NO-6630, Tingvoll, Norway
| | - Atle Mysterud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
- Norwegian Institute for Nature Research (NINA), P. O. Box 5685 Sluppen, NO-7485 Trondheim, Norway
| | - Christer M. Rolandsen
- Norwegian Institute for Nature Research (NINA), P. O. Box 5685 Sluppen, NO-7485 Trondheim, Norway
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12
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Lacy KD, Hart T, Kronauer DJC. Co-inheritance of recombined chromatids maintains heterozygosity in a parthenogenetic ant. Nat Ecol Evol 2024; 8:1522-1533. [PMID: 39014144 PMCID: PMC11310076 DOI: 10.1038/s41559-024-02455-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/30/2024] [Indexed: 07/18/2024]
Abstract
According to Mendel's second law, chromosomes segregate randomly in meiosis. Non-random segregation is primarily known for cases of selfish meiotic drive in females, in which particular alleles bias their own transmission into the oocyte. Here we report a rare example of unselfish meiotic drive for crossover inheritance in the clonal raider ant, Ooceraea biroi, in which both alleles are co-inherited at all loci across the entire genome. This species produces diploid offspring parthenogenetically via fusion of two haploid nuclei from the same meiosis. This process should cause rapid genotypic degeneration due to loss of heterozygosity, which results if crossover recombination is followed by random (Mendelian) segregation of chromosomes. However, by comparing whole genomes of mothers and daughters, we show that loss of heterozygosity is exceedingly rare, raising the possibility that crossovers are infrequent or absent in O. biroi meiosis. Using a combination of cytology and whole-genome sequencing, we show that crossover recombination is, in fact, common but that loss of heterozygosity is avoided because crossover products are faithfully co-inherited. This results from a programmed violation of Mendel's law of segregation, such that crossover products segregate together rather than randomly. This discovery highlights an extreme example of cellular 'memory' of crossovers, which could be a common yet cryptic feature of chromosomal segregation.
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Affiliation(s)
- Kip D Lacy
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA.
| | - Taylor Hart
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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13
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Zhang J, Schneller NM, Field MA, Chan CX, Miller DJ, Strugnell JM, Riginos C, Bay L, Cooke I. Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef. Mol Ecol 2024; 33:e17468. [PMID: 39046252 DOI: 10.1111/mec.17468] [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: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024]
Abstract
The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to assist evolutionary processes in corals require a comprehensive understanding of the distribution and structure of standing variation, however, efforts to map genomic variation in corals have so far focussed almost exclusively on SNPs, overlooking structural variants that have been shown to drive adaptive processes in other taxa. Here, we show that the reef-building coral, Acropora kenti, harbours at least five large, highly polymorphic structural variants, all of which exhibit signatures of strongly suppressed recombination in heterokaryotypes, a feature commonly associated with chromosomal inversions. Based on their high minor allele frequency, uniform distribution across habitats and elevated genetic load, we propose that these inversions in A. kenti are likely to be under balancing selection. An excess of SNPs with high impact on protein-coding genes within these loci elevates their importance both as potential targets for adaptive selection and as contributors to genetic decline if coral populations become fragmented or inbred in future.
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Affiliation(s)
- Jia Zhang
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Nadja M Schneller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Matt A Field
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Miller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Jan M Strugnell
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Line Bay
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Ira Cooke
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
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14
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Musese LJ, Kitegile AS, Kilawe CJ. Ectoparasites of wild rodents in forest sites invaded and uninvaded by Maesopsis eminii in Amani nature forest reserve, Tanzania. Int J Parasitol Parasites Wildl 2024; 24:100932. [PMID: 38601057 PMCID: PMC11002661 DOI: 10.1016/j.ijppaw.2024.100932] [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] [Received: 01/23/2024] [Revised: 03/22/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
Parasites are important component of communities in a forest ecosystem with profound effects on trophic interactions such as food web. Modification of the forest structure (e.g. changes in species composition and abundance of key species) can have a strong impact on the occurrence, diversity, and abundance of parasites, with subsequent repercussions for ecosystem functioning. In this study, we compared the occurrence and abundance of wild rodents' ectoparasites from forest sites invaded and uninvaded by an invasive tree, Maesopsis eminii in Amani Nature Forest Reserve, Tanzania. Three large plots (40 m × 100 m) were randomly established in each forest sites invaded and uninvaded by M. eminii. In each plot, 50 Sherman traps were systematically placed at 10 m interval for capturing wild rodents through a capture-mark-recapture technique. Wilcox rank sum test was used to compare for differences in the abundance of infested rodents and ectoparasites between the invaded and uninvaded forest sites. A total of 297 individual rodents were captured and screened for ectoparasites, including 174 rodents from uninvaded forest site and 123 rodents from invaded forest site. The number of infested rodents were significantly (W = 8592, P < 0.001) greater in uninvaded forest site (66.27%) than in the invaded forest site (36.2%). Furthermore, a significant greater number of Echinolaelaps echidninus (W = 1849, P < 0.01) and Dinopsyllus ellobius (W = 2800.5, P < 0.05) ectoparasites were found in uninvaded as compared to the invaded forest sites. The results of this study suggest that the invasion and dominance by, M. eminii in Amani Nature Reserve has created unfavorable conditions for rodents and ectoparasites and therefore impacting the diversity and function of the forest ecosystem. We recommend prevention of further introduction of the M. eminii outside their natural range and mitigating the impact of the established M. eminii in Amani Forest Nature Reserve.
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Affiliation(s)
- Leticia J. Musese
- Department of Wildlife Management, Sokoine University of Agriculture, Tanzania
- Department of Zoology and Wildlife Conservation, University of Dar es Salaam, Tanzania
| | - Amani S. Kitegile
- Department of Wildlife Management, Sokoine University of Agriculture, Tanzania
| | - Charles J. Kilawe
- Department of Ecosystems and Conservation, Sokoine University of Agriculture, Tanzania
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15
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Ghafari S, Alavi SM, Khaghani S. Potentially pathogenic culturable bacteria in hemodialysis waters. BMC Microbiol 2024; 24:276. [PMID: 39054498 PMCID: PMC11270894 DOI: 10.1186/s12866-024-03430-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/16/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Hemodialysis patients are at risk of acquiring healthcare-related infections due to using non-sterile water to prepare hemodialysis fluid. Therefore, microbiological control and monitoring of used water are of crucial importance. MATERIALS AND METHODS In this work, we identified bacterial populations occupying a hemodialysis water distribution system for almost a 6-month period in Ahvaz city, southwest of Iran. A total of 18 samples from three points were collected. We found high colony counts of bacteria on R2A agar. 31 bacteria with different morphological and biochemical characteristics were identified by molecular-genetic methods based on 16 S rRNA gene sequencing. Endotoxin concentrations were measured, using Endosafe® Rapid LAL Single-Test Vials. RESULTS A diverse bacterial community was identified, containing predominantly Gram-negative bacilli. The most frequently isolated genus was Sphingomonas. Five species including M. fortuitum, M. lentiflavum, M.szulgai, M. barrassiae, and M. gordonae was identified .Despite the presence of Gram-negative bacteria the endotoxin analysis of all samples revealed that their endotoxin values were below the detection limit. CONCLUSION The members of Sphingomonas genus along with Bosea and mycobacteria could be regarded as pioneers in surface colonization and biofilm creation. These bacteria with others like Pelomonas, Bradyrhizobium, staphylococcus, and Microbacterium may represent a potential health risk to patients under hemodialysis treatment.
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Affiliation(s)
- Shokouh Ghafari
- Cellular and Molecular Research Center, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Seyed Mohammad Alavi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Soheila Khaghani
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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16
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Girard EB, Didaskalou EA, Pratama AMA, Rattner C, Morard R, Renema W. Quantitative assessment of reef foraminifera community from metabarcoding data. Mol Ecol Resour 2024:e14000. [PMID: 39041197 DOI: 10.1111/1755-0998.14000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/20/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species-specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon-specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine-scale processes, such as seasonal and pollution-driven dynamics, that require high-throughput sampling treatment.
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Affiliation(s)
- Elsa B Girard
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Andi M A Pratama
- Marine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin University, Makassar, Indonesia
| | | | | | - Willem Renema
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
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17
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Gupta G, Labrie S, Filteau M. Systematic Evaluation of Biotic and Abiotic Factors in Antifungal Microorganism Screening. Microorganisms 2024; 12:1396. [PMID: 39065164 PMCID: PMC11279232 DOI: 10.3390/microorganisms12071396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Microorganisms have significant potential to control fungal contamination in various foods. However, the identification of strains that exhibit robust antifungal activity poses challenges due to highly context-dependent responses. Therefore, to fully exploit the potential of isolates as antifungal agents, it is crucial to systematically evaluate them in a variety of biotic and abiotic contexts. Here, we present an adaptable and scalable method using a robotic platform to study the properties of 1022 isolates obtained from maple sap. We tested the antifungal activity of isolates alone or in pairs on M17 + lactose (LM17), plate count agar (PCA), and sucrose-allantoin (SALN) culture media against Kluyveromyces lactis, Candida boidinii, and Saccharomyces cerevisiae. Microorganisms exhibited less often antifungal activity on SALN and PCA than LM17, suggesting that the latter is a better screening medium. We also analyzed the results of ecological interactions between pairs. Isolates that showed consistent competitive behaviors were more likely to show antifungal activity than expected by chance. However, co-culture rarely improved antifungal activity. In fact, an interaction-mediated suppression of activity was more prevalent in our dataset. These findings highlight the importance of incorporating both biotic and abiotic factors into systematic screening designs for the bioprospection of microorganisms with environmentally robust antifungal activity.
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Affiliation(s)
- Gunjan Gupta
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve Labrie
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
| | - Marie Filteau
- Département des Sciences des Aliments, Université Laval, Quebec City, QC G1V 0A6, Canada; (G.G.); (S.L.)
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
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18
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Markee A, Godfrey RK, Frandsen PB, Weng YM, Triant DA, Kawahara AY. De Novo Long-Read Genome Assembly and Annotation of the Luna Moth (Actias luna) Fully Resolves Repeat-Rich Silk Genes. Genome Biol Evol 2024; 16:evae148. [PMID: 38957923 PMCID: PMC11258402 DOI: 10.1093/gbe/evae148] [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: 03/29/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
We present the first long-read de novo assembly and annotation of the luna moth (Actias luna) and provide the full characterization of heavy chain fibroin (h-fibroin), a long and highly repetitive gene (>20 kb) essential in silk fiber production. There are >160,000 described species of moths and butterflies (Lepidoptera), but only within the last 5 years have we begun to recover high-quality annotated whole genomes across the order that capture h-fibroin. Using PacBio HiFi reads, we produce the first high-quality long-read reference genome for this species. The assembled genome has a length of 532 Mb, a contig N50 of 16.8 Mb, an L50 of 14 contigs, and 99.4% completeness (BUSCO). Our annotation using Bombyx mori protein and A. luna RNAseq evidence captured a total of 20,866 genes at 98.9% completeness with 10,267 functionally annotated proteins and a full-length h-fibroin annotation of 2,679 amino acid residues.
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Affiliation(s)
- Amanda Markee
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Yi-Ming Weng
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Deborah A Triant
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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19
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López-Verdejo A, Occhibove F, Uberti BD, Montero FE, Santoro M. Mass mortality event of round sardinella Sardinella aurita Valenciennes associated with Glugea Thélohan, 1891 microsporidian infection off the southern Italian coast. JOURNAL OF FISH DISEASES 2024:e13995. [PMID: 38953156 DOI: 10.1111/jfd.13995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024]
Abstract
Intracellular parasites of the genus Glugea Thélohan, 1891 (Microsporidia) comprise about 34 putative species capable of causing high morbidity and mortality in freshwater and marine teleost fishes. In this study, we report on the first mass mortality event associated with Glugea sp. infecting free-ranging round sardinella Sardinella aurita in the southern Tyrrhenian Sea (Italy). Here, we describe the ultrastructure of mature spores of this microsporidian and characterize it molecularly, as well as report its phylogenetic position. Most of the affected fish showed an irregular swelling of its abdomen. At necropsy, a variable number of xenomas, spherical to ellipsoidal in shape, were found in the peritoneal cavity strongly attached to the viscera of all fish. Histological analysis revealed varying severity of chronic inflammation along with occasional necrosis in visceral organs associated with multiple xenoma proliferation. These pathological findings were considered the main cause of this mass mortality event. Morphologically, the present material was closely related to G. sardinellesis and G. thunni. The phylogenetically closest taxa to the newly SSU rDNA sequence were G. thunni and an erroneusly identified G. plecoglossi, which were very closely related to each other, also suggesting that all these sequences might belong to the same species.
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Affiliation(s)
- Alejandro López-Verdejo
- Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Spain
| | - Flavia Occhibove
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | | | - Francisco E Montero
- Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Spain
| | - Mario Santoro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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20
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Miura T, Kadoya SS, Miura Y, Takino H, Akiba M, Sano D, Masuda T. Pepper mild mottle virus intended for use as a process indicator for drinking water treatment: Present forms and quantitative relations to norovirus and rotavirus in surface water. WATER RESEARCH 2024; 257:121713. [PMID: 38733963 DOI: 10.1016/j.watres.2024.121713] [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: 11/06/2023] [Revised: 03/19/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Pepper mild mottle virus (PMMoV) has been proposed as a potential indicator of human enteric viruses in environmental water and for viral removal during drinking water treatment. To investigate the occurrence and present forms of PMMoV and quantitative relations to norovirus GII and rotavirus A (RVA) in surface waters, 147 source water samples were collected from 21 drinking water treatment plants (DWTPs) in Japan between January 2018 and January 2021, and the concentrations of viruses in suspended and dissolved fractions were measured using real-time RT-PCR. PMMoV was detected in 81-100 % of samples in each sample month and observed concentrations ranged from 3.0 to 7.0 log10 copies/L. The concentrations of PMMoV were higher in dissolved fraction compared to suspended fractions, while different partitioning was observed for NoV GII depending on seasons. The concentrations of PMMoV were basically higher than those of norovirus GII (1.9-5.3 log10 copies/L) and RVA (1.9-6.6 log10 copies/L), while in 18 samples, RVA presented higher concentrations than PMMoV. Partial regions of VP7, VP4, and VP6 of the RVA in the 18 samples were amplified using nested PCR, and the genotypes were determined using an amplicon-based next-generation sequencing approach. We found that these source water samples included not only human RVA but also various animal RVA and high genetic diversity due to the existence of animal RVA was associated with a higher RVA concentration than PMMoV. Our findings suggest that PMMoV can be used as an indicator of norovirus GII and human RVA in drinking water sources and that the indicator performance should be evaluated by comparing to zoonotic viruses as well as human viruses.
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Affiliation(s)
- Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan.
| | - Syun-Suke Kadoya
- Department of Civil and Environmental Engineering, Tohoku University, Japan; Department of Urban Engineering, The University of Tokyo, Japan
| | - Yohei Miura
- Department of Civil and Environmental Engineering, Tohoku University, Japan
| | - Hiroyuki Takino
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Michihiro Akiba
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Japan
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21
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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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22
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Lopez-Verdejo A, Palomba M, Crocetta F, Santoro M. Integrative taxonomy of metazoan parasites of the bluntnose sixgill shark Hexanchus griseus (Bonnaterre, 1788) in the Mediterranean Sea, with the resurrection of Grillotia acanthoscolex Rees, 1944 (Cestoda: Trypanorhyncha). JOURNAL OF FISH BIOLOGY 2024; 104:1754-1763. [PMID: 38450741 DOI: 10.1111/jfb.15703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/26/2024] [Accepted: 02/13/2024] [Indexed: 03/08/2024]
Abstract
Appropriate diagnoses of parasites of apex marine predators are crucial to understand their biodiversity, host specificity, biogeography, and life cycles. Such diagnoses are also informative of ecological and biological characteristics of both host and environment in which the hosts and their parasites live. We here (i) investigate the parasite fauna of a bluntnose sixgill shark Hexanchus griseus (Bonnaterre, 1788) obtained from the Gulf of Naples (Tyrrhenian Sea), (ii) characterize molecularly all its metazoan parasites, and (iii) resurrect and report the main morphological features and phylogenetic position of Grillotia acanthoscolex, a cestode species previously synonymized with Grillotia adenoplusia. A rich parasite fauna represented by eight different taxa was found, including two monogeneans (Protocotyle grisea and Protocotyle taschenbergi), one digenean (Otodistomum veliporum), four cestodes (Crossobothrium dohrnii, Clistobothrium sp., G. acanthoscolex, and G. adenoplusia), and one copepod (Protodactylina pamelae). Sequencing of these samples accounts for an important molecular baseline to widen the knowledge on the parasitic fauna of bluntnose sixgill sharks worldwide and to reconstruct their correct food chains. The bluntnose sixgill shark was found to be a definitive host for all endoparasites found here, confirming that it occupies an apex trophic level in the Mediterranean Sea. The taxa composition of the trophic parasite fauna confirms that the bluntnose sixgill shark mostly feeds on teleost fish species. However, the occurrence of two phillobothrid cestodes (C. dohrnii and Clistobothrium sp.) suggests that it also feeds on squids. Finally, we emphasize the importance of using integrative taxonomic approaches in the study of parasites from definitive and intermediate hosts to elucidate biology and ecology of taxa generally understudied in the Mediterranean Sea.
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Affiliation(s)
- Alejandro Lopez-Verdejo
- Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Spain
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marialetizia Palomba
- Department of Biological and Ecological Sciences, University of Tuscia, Viterbo, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Fabio Crocetta
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Mario Santoro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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23
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Ferreira RC, Alves GV, Ramon M, Antoneli F, Briones MRS. Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data. Viruses 2024; 16:856. [PMID: 38932149 PMCID: PMC11209150 DOI: 10.3390/v16060856] [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: 03/13/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals, and, therefore, the identification of viral genome remnants in Neanderthal sequence reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequence reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double-stranded DNA viruses that may establish lifelong latency and can produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide identity to extant viral genomes and variable regions in coding regions with substantial divergence to extant close relatives. Sequence reads mapped to extant viral genomes showed deamination patterns of ancient DNA, and these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10-5 to 10-8 substitutions/site/year). Analysis of random effects showed that the Neanderthal mapping to genomes of extant persistent viruses is above what is expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment.
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Affiliation(s)
- Renata C. Ferreira
- Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP 04039-032, Brazil (F.A.)
- Epigene LLC, São Paulo, SP 04537-080, Brazil
| | - Gustavo V. Alves
- Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP 04039-032, Brazil (F.A.)
| | | | - Fernando Antoneli
- Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP 04039-032, Brazil (F.A.)
| | - Marcelo R. S. Briones
- Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP 04039-032, Brazil (F.A.)
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24
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Kawacka I, Olejnik-Schmidt A. High Prevalence of Virulence-Associated Genes and Length Polymorphism in actA and inlB Genes Identified in Listeria monocytogenes Isolates from Meat Products and Meat-Processing Environments in Poland. Pathogens 2024; 13:444. [PMID: 38921742 PMCID: PMC11206756 DOI: 10.3390/pathogens13060444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024] Open
Abstract
Listeria monocytogenes is a human pathogen that has the ability to cause listeriosis, a disease with possible fatal outcomes. The typical route of infection is ingestion of the bacteria with contaminated food. In this study, 13 virulence-associated genes were examined with PCR in the genomes of 153 L. monocytogenes isolates collected from meat products and processing environments in Poland. All isolates possessed genes from LIPI-1-hly, actA, plcA, plcB and mpl-as well as four internalins: inlA, inlB, inlC, inlJ. Invasion-associated protein iap, as well as genes prfA and sigB, encoding regulatory proteins, were also detected in all isolates. Gene flaA, encoding flagellin, was detected in 113 (74%) isolates. This was the only gene that was not detected in all isolates, as its presence is serotype-dependent. Gene actA showed polymorphism with longer and shorter variants in PCR amplicons. Two isolates were characterized by truncated inlB genes, lacking 141 bp in their sequence, which was confirmed by gene sequencing. All isolates were positive in hemolysis assays, proving the synthesis of functional PrfA and Hly proteins. Four genotypes of L. monocytogenes based on actA polymorphism and two genotypes based on inlB polymorphism were distinguished within the isolates' collection.
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Affiliation(s)
- Iwona Kawacka
- Department of Food Biotechnology and Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
| | - Agnieszka Olejnik-Schmidt
- Department of Food Biotechnology and Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
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25
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Zhong J, Guo L, Wang Y, Jiang X, Wang C, Xiao Y, Wang Y, Zhou F, Wu C, Chen L, Wang X, Wang J, Cao B, Li M, Ren L. Gut Microbiota Improves Prognostic Prediction in Critically Ill COVID-19 Patients Alongside Immunological and Hematological Indicators. RESEARCH (WASHINGTON, D.C.) 2024; 7:0389. [PMID: 38779486 PMCID: PMC11109594 DOI: 10.34133/research.0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
The gut microbiota undergoes substantial changes in COVID-19 patients; yet, the utility of these alterations as prognostic biomarkers at the time of hospital admission, and its correlation with immunological and hematological parameters, remains unclear. The objective of this study is to investigate the gut microbiota's dynamic change in critically ill patients with COVID-19 and evaluate its predictive capability for clinical outcomes alongside immunological and hematological parameters. In this study, anal swabs were consecutively collected from 192 COVID-19 patients (583 samples) upon hospital admission for metagenome sequencing. Simultaneously, blood samples were obtained to measure the concentrations of 27 cytokines and chemokines, along with hematological and biochemical indicators. Our findings indicate a significant correlation between the composition and dynamics of gut microbiota with disease severity and mortality in COVID-19 patients. Recovered patients exhibited a higher abundance of Veillonella and denser interactions among gut commensal bacteria compared to deceased patients. Furthermore, the abundance of gut commensal bacteria exhibited a negative correlation with the concentration of proinflammatory cytokines and organ damage markers. The gut microbiota upon admission showed moderate prognostic prediction ability with an AUC of 0.78, which was less effective compared to predictions based on immunological and hematological parameters (AUC 0.80 and 0.88, respectively). Noteworthy, the integration of these three datasets yielded a higher predictive accuracy (AUC 0.93). Our findings suggest the gut microbiota as an informative biomarker for COVID-19 prognosis, augmenting existing immune and hematological indicators.
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Affiliation(s)
- Jiaxin Zhong
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Guo
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital,
Capital Medical University, Beijing, China
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases,
Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xuan Jiang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Xiao
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Zhou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital,
Capital Medical University, Beijing, China
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases,
Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Chao Wu
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lan Chen
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinming Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital,
Capital Medical University, Beijing, China
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases,
Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - LiLi Ren
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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26
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Vogel AL, Thompson KJ, Straub D, Musat F, Gutierrez T, Kleindienst S. Genetic redundancy in the naphthalene-degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations. FEMS Microbiol Ecol 2024; 100:fiae060. [PMID: 38614960 PMCID: PMC11099662 DOI: 10.1093/femsec/fiae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024] Open
Abstract
Polycyclic aromatic hydrocarbon (PAH) contamination in marine environments range from low-diffusive inputs to high loads. The influence of PAH concentration on the expression of functional genes [e.g. those encoding ring-hydroxylating dioxygenases (RHDs)] has been overlooked in PAH biodegradation studies. However, understanding marker-gene expression under different PAH loads can help to monitor and predict bioremediation efficiency. Here, we followed the expression (via RNA sequencing) of Cycloclasticus pugetii strain PS-1 in cell suspension experiments under different naphthalene (100 and 30 mg L-1) concentrations. We identified genes encoding previously uncharacterized RHD subunits, termed rhdPS1α and rhdPS1β, that were highly transcribed in response to naphthalene-degradation activity. Additionally, we identified six RHD subunit-encoding genes that responded to naphthalene exposure. By contrast, four RHD subunit genes were PAH-independently expressed and three other RHD subunit genes responded to naphthalene starvation. Cycloclasticus spp. could, therefore, use genetic redundancy in key PAH-degradation genes to react to varying PAH loads. This genetic redundancy may restrict the monitoring of environmental hydrocarbon-degradation activity using single-gene expression. For Cycloclasticus pugetii strain PS-1, however, the newly identified rhdPS1α and rhdPS1β genes might be potential target genes to monitor its environmental naphthalene-degradation activity.
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Affiliation(s)
- Anjela L Vogel
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Katharine J Thompson
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Daniel Straub
- Eberhard Karls University of Tübingen, Quantitative Biology Center (QBiC), Auf der Morgenstelle 10, Tübingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Florin Musat
- Aarhus University, Department of Biology, Section for Microbiology, Ny Munkegade 116, Aarhus C 8000, Denmark
- Babeş-Bolyai University, Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Str. Republicii nr 44, Cluj-Napoca 400015, Romania
| | - Tony Gutierrez
- Heriot-Watt University, Institute of Mechanical Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Edinburgh EH14 4AS, UK
| | - Sara Kleindienst
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
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27
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Tian Q, Zhang P, Zhai Y, Wang Y, Zou Q. Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data. Genome Biol Evol 2024; 16:evae102. [PMID: 38748485 PMCID: PMC11135637 DOI: 10.1093/gbe/evae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2024] [Indexed: 05/30/2024] Open
Abstract
The advent of high-throughput sequencing technologies has not only revolutionized the field of bioinformatics but has also heightened the demand for efficient taxonomic classification. Despite technological advancements, efficiently processing and analyzing the deluge of sequencing data for precise taxonomic classification remains a formidable challenge. Existing classification approaches primarily fall into two categories, database-based methods and machine learning methods, each presenting its own set of challenges and advantages. On this basis, the aim of our study was to conduct a comparative analysis between these two methods while also investigating the merits of integrating multiple database-based methods. Through an in-depth comparative study, we evaluated the performance of both methodological categories in taxonomic classification by utilizing simulated data sets. Our analysis revealed that database-based methods excel in classification accuracy when backed by a rich and comprehensive reference database. Conversely, while machine learning methods show superior performance in scenarios where reference sequences are sparse or lacking, they generally show inferior performance compared with database methods under most conditions. Moreover, our study confirms that integrating multiple database-based methods does, in fact, enhance classification accuracy. These findings shed new light on the taxonomic classification of high-throughput sequencing data and bear substantial implications for the future development of computational biology. For those interested in further exploring our methods, the source code of this study is publicly available on https://github.com/LoadStar822/Genome-Classifier-Performance-Evaluator. Additionally, a dedicated webpage showcasing our collected database, data sets, and various classification software can be found at http://lab.malab.cn/~tqz/project/taxonomic/.
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Affiliation(s)
- Qinzhong Tian
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003 China
| | - Pinglu Zhang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003 China
| | - Yixiao Zhai
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003 China
| | - Yansu Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003 China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003 China
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28
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López-Verdejo A, Occhibove F, Degli Uberti B, Crocetta F, Santoro M. Philometroides giginosantoroi n. sp. (Nematoda: Philometridae), a new muscle-infecting species in the Mediterranean moray ( Muraena helena) revealed using integrative taxonomy. Parasitology 2024; 151:615-625. [PMID: 38736290 DOI: 10.1017/s0031182024000581] [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: 05/14/2024]
Abstract
Philometroides Yamaguti, 1935 is a genus of dracunculoid nematodes of the family Philometridae Baylis & Daubney, 1926 comprising tissue-infecting species worldwide. In the present study, a new species of Philometroides is described from the Tyrrhenian Sea (central-western Mediterranean Sea) using integrative approaches such as light and scanning microscopy, histopathology and 18S rRNA sequencing. Philometroides giginosantoroi n. sp. found in the skeletal muscles of the Mediterranean moray Muraena helena can be distinguished from its congeners by a combination of morphological traits and in particular by having the oral aperture with 3 large sclerotized triangular oesophageal teeth. The molecular analyses and phylogenetic reconstructions support its status as a new taxon and placed it within a clade of tissue-infecting species, although also confirmed mismatches in the generic assignment of several species. Philometroides giginosantoroi n. sp. is the second species of the genus found in the Mediterranean Sea and in general in the European marine waters and the third species of the family known to infect the family Muraenidae.
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Affiliation(s)
- Alejandro López-Verdejo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy
- Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, C/Catedrático José Beltrán 2, 46980 Paterna, Spain
| | - Flavia Occhibove
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy
| | - Barbara Degli Uberti
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy
| | - Fabio Crocetta
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy
| | - Mario Santoro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy
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29
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St John E, Reysenbach AL. Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae. Syst Appl Microbiol 2024; 47:126507. [PMID: 38703419 DOI: 10.1016/j.syapm.2024.126507] [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: 12/15/2023] [Revised: 03/02/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
Deep-sea hydrothermal vents host archaeal and bacterial thermophilic communities, including taxonomically and functionally diverse Thermoproteota. Despite their prevalence in high-temperature submarine communities, Thermoproteota are chronically under-represented in genomic databases and issues have emerged regarding their nomenclature, particularly within the Aeropyrum-Thermodiscus-Caldisphaera. To resolve some of these problems, we identified 47 metagenome-assembled genomes (MAGs) within this clade, from 20 previously published deep-sea hydrothermal vent and submarine volcano metagenomes, and 24 MAGs from public databases. Using phylogenomic analysis, Genome Taxonomy Database Toolkit (GTDB-Tk) taxonomic assessment, 16S rRNA gene phylogeny, average amino acid identity (AAI) and functional gene patterns, we re-evaluated of the taxonomy of the Aeropyrum-Thermodiscus-Caldisphaera. At least nine genus-level clades were identified with two or more MAGs. In accordance with SeqCode requirements and recommendations, we propose names for three novel genera, viz. Tiamatella incendiivivens, Hestiella acidicharens and Calypsonella navitae. A fourth genus was also identified related to Thermodiscus maritimus, for which no available sequenced genome exists. We propose the novel species Thermodiscus eudorianus to describe our high-quality Thermodiscus MAG, which represents the type genome for the genus. All three novel genera and T. eudorianus are likely anaerobic heterotrophs, capable of fermenting protein-rich carbon sources, while some Tiamatella, Calypsonella and T. eudorianus may also reduce polysulfides, thiosulfate, sulfur and/or selenite, and the likely acidophile, Hestiella, may reduce nitrate and/or perchlorate. Based on phylogenomic evidence, we also propose the family Acidilobaceae be amended to include Caldisphaera, Aeropyrum, Thermodiscus and Stetteria and the novel genera described here.
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Affiliation(s)
- Emily St John
- Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA.
| | - Anna-Louise Reysenbach
- Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA.
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Kang I, Roda A, Misiaszek B, Sparks T, Diaz R. Detection of Ochyromera ligustri (Coleoptera: Curculionidae: Curculioninae) in Ligustrum spp. (Oleaceae) Using Newly Developed PCR Primers. INSECTS 2024; 15:320. [PMID: 38786876 PMCID: PMC11122171 DOI: 10.3390/insects15050320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/10/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Ligustrum spp. (Oleaceae) have become invasive species in the US and negatively affect native plant diversity and richness in forests. Ochyromera ligustri (Coleoptera: Curculionidae) is considered a potential biological control agent in the US because adults feed on the foliage and larvae are seed-feeders of Ligustrum spp. To discover the relationships between O. ligustri and Ligustrum spp., fruit dissections or rearing and field observations are required. In the current research project, novel PCR primers were developed to rapidly detect the DNA of O. ligustri in molecular analyses without rearing and observation. The developed PCR primers worked even with 0.01 ng of DNA and did not amplify the DNA of the other five curculionid species tested. When the novel primers were tested with three Ligustrum spp. species common in the southeastern US, the DNA of O. ligustri was detected from all three species. We expect that the novel primers will be utilized to find out the presence and impact of O. ligustri on Ligustrum spp rapidly and accurately.
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Affiliation(s)
- Ilgoo Kang
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (I.K.); (B.M.); (T.S.)
- Department of Entomology, College of Ecology and Environmental Science, Kyungpook National University, Sangju 37228, Gyeongsangbuk-do, Republic of Korea
| | - Amy Roda
- Animal and Plant Health Inspection Service, Plant Protection and Quarantine, United States Department of Agriculture, Miami, FL 33158, USA;
| | - Brandi Misiaszek
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (I.K.); (B.M.); (T.S.)
| | - Tanner Sparks
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (I.K.); (B.M.); (T.S.)
| | - Rodrigo Diaz
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (I.K.); (B.M.); (T.S.)
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Trzebny A, Nahimova O, Dabert M. High temperatures and low humidity promote the occurrence of microsporidians (Microsporidia) in mosquitoes (Culicidae). Parasit Vectors 2024; 17:187. [PMID: 38605410 PMCID: PMC11008030 DOI: 10.1186/s13071-024-06254-0] [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: 10/26/2023] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND In the context of climate change, a growing concern is that vector-pathogen or host-parasite interactions may be correlated with climatic factors, especially increasing temperatures. In the present study, we used a mosquito-microsporidian model to determine the impact of environmental factors such as temperature, humidity, wind and rainfall on the occurrence rates of opportunistic obligate microparasites (Microsporidia) in hosts from a family that includes important disease vectors (Culicidae). METHODS In our study, 3000 adult mosquitoes collected from the field over 3 years were analysed. Mosquitoes and microsporidia were identified using PCR and sequencing of the hypervariable V5 region of the small subunit ribosomal RNA gene and a shortened fragment of the cytochrome c oxidase subunit I gene, respectively. RESULTS DNA metabarcoding was used to identify nine mosquito species, all of which were hosts of 12 microsporidian species. The prevalence of microsporidian DNA across all mosquito samples was 34.6%. Microsporidian prevalence in mosquitoes was more frequent during warm months (> 19 °C; humidity < 65%), as was the co-occurrence of two or three microsporidian species in a single host individual. During warm months, microsporidian occurrence was noted 1.6-fold more often than during the cold periods. Among the microsporidians found in the mosquitoes, five (representing the genera Enterocytospora, Vairimorpha and Microsporidium) were positively correlated with an increase in temperature, whereas one (Hazardia sp.) was significantly correlated with a decrease in temperature. Threefold more microsporidian co-occurrences were recorded in the warm months than in the cold months. CONCLUSIONS These results suggest that the susceptibility of mosquitoes to parasite occurrence is primarily determined by environmental conditions, such as, for example, temperatures > 19 °C and humidity not exceeding 62%. Collectively, our data provide a better understanding of the effects of the environment on microsporidian-mosquito interactions.
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Affiliation(s)
- Artur Trzebny
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
| | - Olena Nahimova
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
- Genetics and Cytology Department, School of Biology, V.N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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Webster VL, Hemmings S, Pérez M, Fisher MC, Brown MJF, Farrer RA. Revealing the genome of the microsporidian Vairimorpha bombi, a potential driver of bumble bee declines in North America. G3 (BETHESDA, MD.) 2024; 14:jkae029. [PMID: 38334143 PMCID: PMC10989860 DOI: 10.1093/g3journal/jkae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
Pollinators are vital for food security and the maintenance of terrestrial ecosystems. Bumblebees are important pollinators across northern temperate, arctic, and alpine ecosystems, yet are in decline across the globe. Vairimorpha bombi is a parasite belonging to the fungal class Microsporidia that has been implicated in the rapid decline of bumblebees in North America, where it may be an emerging infectious disease. To investigate the evolutionary basis of pathogenicity of V. bombi, we sequenced and assembled its genome using Oxford Nanopore and Illumina technologies and performed phylogenetic and genomic evolutionary analyses. The genome assembly for V. bombi is 4.73 Mb, from which we predicted 1,870 protein-coding genes and 179 tRNA genes. The genome assembly has low repetitive content and low GC content. V. bombi's genome assembly is the smallest of the Vairimorpha and closely related Nosema genera, but larger than those found in the Encephalitozoon and Ordospora sister clades. Orthology and phylogenetic analysis revealed 18 core conserved single-copy microsporidian genes including the histone acetyltransferase (HAT) GCN5. Surprisingly, V. bombi was unique to the microsporidia in not encoding the second predicted HAT ESA1. The V. bombi genome assembly annotation included 265 unique genes (i.e. not predicted in other microsporidia genome assemblies), 20% of which encode a secretion signal, which is a significant enrichment. Intriguingly, of the 36 microsporidian genomes we analyzed, 26 also had a significant enrichment of secreted signals encoded by unique genes, ranging from 6 to 71% of those predicted genes. These results suggest that microsporidia are under selection to generate and purge diverse and unique genes encoding secreted proteins, potentially contributing to or facilitating infection of their diverse hosts. Furthermore, V. bombi has 5/7 conserved spore wall proteins (SWPs) with its closest relative V. ceranae (that primarily infects honeybees), while also uniquely encoding four additional SWPs. This gene class is thought to be essential for infection, providing both environmental protection and recognition and uptake into the host cell. Together, our results show that SWPs and unique genes encoding a secretion signal are rapidly evolving in the microsporidia, suggesting that they underpin key pathobiological traits including host specificity and pathogenicity.
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Affiliation(s)
- Victoria L Webster
- Department of Biological Sciences, Royal Holloway University of London, London TW20 0EX, UK
| | - Samuel Hemmings
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK
| | - Marta Pérez
- Department of Biological Sciences, Royal Holloway University of London, London TW20 0EX, UK
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK
| | - Mark J F Brown
- Department of Biological Sciences, Royal Holloway University of London, London TW20 0EX, UK
| | - Rhys A Farrer
- MRC Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, UK
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Möller L, Vainshtein Y, Meyer B, Neidhardt J, Eren AM, Sohn K, Rabus R. Rich microbial and depolymerising diversity in Antarctic krill gut. Microbiol Spectr 2024; 12:e0403523. [PMID: 38466097 PMCID: PMC10986584 DOI: 10.1128/spectrum.04035-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/13/2024] [Indexed: 03/12/2024] Open
Abstract
With almost a quadrillion individuals, the Antarctic krill processes five million tons of organic carbon every day during austral summer. This high carbon flux requires a broad range of hydrolytic enzymes to decompose the diverse food-derived biopolymers. While krill itself possesses numerous such enzymes, it is unclear, to what extent the endogenous microbiota contribute to the hydrolytic potential of the gut environment. Here we applied amplicon sequencing, shotgun metagenomics, cultivation, and physiological assays to characterize the krill gut microbiota. The broad bacterial diversity (273 families, 919 genera, and 2,309 species) also included a complex potentially anaerobic sub-community. Plate-based assays with 198 isolated pure cultures revealed widespread capacities to utilize lipids (e.g., tributyrin), followed by proteins (casein) and to a lesser extent by polysaccharides (e.g., alginate and chitin). While most isolates affiliated with the genera Pseudoalteromonas and Psychrobacter, also Rubritalea spp. (Verrucomicrobia) were observed. The krill gut microbiota growing on marine broth agar plates possess 13,012 predicted hydrolyses; 15-fold more than previously predicted from a transcriptome-proteome compendium of krill. Cultivation-independent and -dependent approaches indicated members of the families Flavobacteriaceae and Pseudoalteromonadaceae to dominate the capacities for lipid/protein hydrolysis and to provide a plethora of carbohydrate-active enzymes, sulfatases, and laminarin- or porphyrin-depolymerizing hydrolases. Notably, also the potential to hydrolyze plastics such as polyethylene terephthalate and polylactatide was observed, affiliating mostly with Moraxellaceae. Overall, this study shows extensive microbial diversity in the krill gut, and suggests that the microbiota likely play a significant role in the nutrient acquisition of the krill by enriching its hydrolytic enzyme repertoire.IMPORTANCEThe Antarctic krill (Euphausia superba) is a keystone species of the Antarctic marine food web, connecting the productivity of phyto- and zooplankton with the nutrition of the higher trophic levels. Accordingly, krill significantly contributes to biomass turnover, requiring the decomposition of seasonally varying plankton-derived biopolymers. This study highlights the likely role of the krill gut microbiota in this ecosystem function by revealing the great number of diverse hydrolases that microbes contribute to the krill gut environment. The here resolved repertoire of hydrolytic enzymes could contribute to the overall nutritional resilience of krill and to the general organic matter cycling under changing environmental conditions in the Antarctic sea water. Furthermore, the krill gut microbiome could serve as a valuable resource of cold-adapted hydrolytic enzymes for diverse biotechnological applications.
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Affiliation(s)
- Lars Möller
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Yevhen Vainshtein
- In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Bettina Meyer
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University Oldenburg (HIFMB), Oldenburg, Germany
- Biosciences, Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - John Neidhardt
- Department of Human Medicine, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - A. Murat Eren
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University Oldenburg (HIFMB), Oldenburg, Germany
- HIFMB-MPG Bridging Group for Marine Genomics, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute (AWI), Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Kai Sohn
- In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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Posteraro B, De Maio F, Motro Y, Menchinelli G, De Lorenzis D, Marano RBM, Aljanazreh B, Errico FM, Massaria G, Spanu T, Posteraro P, Moran-Gilad J, Sanguinetti M. In-depth characterization of multidrug-resistant NDM-1 and KPC-3 co-producing Klebsiella pneumoniae bloodstream isolates from Italian hospital patients. Microbiol Spectr 2024; 12:e0330523. [PMID: 38411998 PMCID: PMC10986569 DOI: 10.1128/spectrum.03305-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/04/2024] [Indexed: 02/28/2024] Open
Abstract
Bloodstream infection (BSI) caused by carbapenem-resistant Klebsiella pneumoniae (KP) poses significant challenges, particularly when the infecting isolate carries multiple antimicrobial resistance (AMR) genes/determinants. This study, employing short- and long-read whole-genome sequencing, characterizes six New Delhi metallo-β-lactamase (NDM) 1 and KP carbapenemase (KPC) 3 co-producing KP isolates, the largest cohort investigated in Europe to date. Five [sequence type (ST) 512] and one (ST11) isolates were recovered from patients who developed BSI from February to August 2022 or February 2023 at two different hospitals in Rome, Italy. Phylogenetic analysis revealed two distinct clusters among ST512 isolates and a separate cluster for the ST11 isolate. Beyond blaNDM-1 and blaKPC-3, various AMR genes, indicative of a multidrug resistance phenotype, including colistin resistance, were found. Each cluster-representative ST512 isolate harbored a blaNDM-1 plasmid (IncC) and a blaKPC-3 plasmid [IncFIB(pQil)/IncFII(K)], while the ST11 isolate harbored a blaNDM-1 plasmid [IncFII(pKPX1)] and a blaKPC-3 plasmid [IncFIB(K)/IncFII(K)]. The blaNDM-1 plasmids carried genes conferring resistance to clinically relevant antimicrobial agents, and the aminoglycoside resistance gene aac(6')-Ib was found on different plasmids. Colistin resistance-associated mgrB/pmrB gene mutations were present in all isolates, and the yersiniabactin-encoding ybt gene was unique to the ST11 isolate. In conclusion, our findings provide insights into the genomic context of blaNDM-1/blaKPC-3 carbapenemase-producing KP isolates.IMPORTANCEThis study underscores the critical role of genomic surveillance as a proactive measure to restrict the spread of carbapenemase-producing KP isolates, especially when key antimicrobial resistance genes, such as blaNDM-1/blaKPC-3, are plasmid borne. In-depth characterization of these isolates may help identify plasmid similarities contributing to their intra-hospital/inter-hospital adaptation and transmission. Despite the lack of data on patient movements, it is possible that carbapenem-resistant isolates were selected to co-produce KP carbapenemase and New Delhi metallo-β-lactamase via plasmid acquisition. Studies employing long-read whole-genome sequencing should be encouraged to address the emergence of KP clones with converging phenotypes of virulence and resistance to last-resort antimicrobial agents.
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Affiliation(s)
- Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Flavio De Maio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Yair Motro
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Giulia Menchinelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Desy De Lorenzis
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Roberto B. M. Marano
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Bessan Aljanazreh
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Federica Maria Errico
- GVM - Ospedale San Carlo di Nancy, Laboratorio di Analisi Chimico-Cliniche e Microbiologiche, Rome, Italy
| | | | - Teresa Spanu
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Patrizia Posteraro
- GVM - Ospedale San Carlo di Nancy, Laboratorio di Analisi Chimico-Cliniche e Microbiologiche, Rome, Italy
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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Parker EM, Mollenkopf DF, Ballash GA, Li C, Wittum TE. Transcontinental Dissemination of Enterobacterales Harboring blaNDM-1 in Retail Frozen Shrimp. Foodborne Pathog Dis 2024. [PMID: 38563789 DOI: 10.1089/fpd.2023.0161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
The global food trade provides a means of disseminating antimicrobial resistant (AMR) bacteria and genes. Using selective media, carbapenem-resistant species of Enterobacterales (Providencia sp. and Citrobacter sp.), were detected in a single package of imported frozen shrimp purchased from a grocery store in Ohio, USA. Polymerase chain reaction confirmed that both isolates harbored blaNDM-1 genes. Following PacBio long read sequencing, the sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline. The blaNDM-1 genes were found in IncC plasmids, each with different antimicrobial resistance island configuration. We found that the blaNDM-1 AMR islands had close relationships with previously reported environmental, food, and clinical isolates detected in Asia and the United States, highlighting the importance of the food chain in the global dissemination of antimicrobial resistance.
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Affiliation(s)
- Elizabeth M Parker
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Dixie F Mollenkopf
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Gregory A Ballash
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Cong Li
- Center for Veterinary Medicine, Office of Applied Science, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Thomas E Wittum
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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Djotan AKG, Matsushita N, Fukuda K. Year-round dynamics of arbuscular mycorrhizal fungi communities in the roots and surrounding soils of Cryptomeria japonica. MYCORRHIZA 2024; 34:119-130. [PMID: 38509266 PMCID: PMC10998819 DOI: 10.1007/s00572-024-01143-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) live simultaneously inside and outside of host plant roots for a functional mycorrhizal symbiosis. Still, the year-round dynamics and relationships between soil properties and AMF communities of trees in forest ecosystems remain unclear. We collected paired root and soil samples of the same Cryptomeria japonica trees at two forest sites (five trees at each site) every 2 months over a year. Total DNA was extracted from roots and soil separately and soil physicochemical properties were measured. With Illumina's next-generation amplicon sequencing targeting the small subunit of fungal ribosomal DNA, we clarified seasonal dynamics of soil properties and AMF communities. Soil pH and total phosphorus showed significant seasonality while total carbon, nitrogen, and C/N did not. Only pH was a good predictor of the composition and dynamics of the AMF community. The total AMF community (roots + soil) showed significant seasonality because of variation from May to September. Root and soil AMF communities were steady year-round, however, with similar species richness but contained significantly different AMF assemblages in any sampling month. Despite the weak seasonality in the communities, the top two dominant OTUs showed significant but different shifts between roots and soils across seasons with strong antagonistic relationships. In conclusion, few dominant AMF taxa are dynamically shifting between the roots and soils of C. japonica to respond to seasonal and phenological variations in their microhabitats. AMF inhabiting forest ecosystems may have high environmental plasticity to sustain a functional symbiosis regardless of seasonal variations that occur in the soil.
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Affiliation(s)
- Akotchiffor Kevin Geoffroy Djotan
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Kenji Fukuda
- Graduate School of Agricultural and Life Sciences (Laboratory of Forest Botany), University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
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Sansom SE, Shimasaki T, Dangana T, Lin MY, Schoeny ME, Fukuda C, Moore NM, Yelin RD, Bassis CM, Rhee Y, Cornejo Cisneros E, Bell P, Lolans K, Aboushaala K, Young VB, Hayden MK. Comparison of Daily versus Admission and Discharge Surveillance Cultures for Multidrug-Resistant Organism Detection in an Intensive Care Unit. J Infect Dis 2024:jiae162. [PMID: 38546721 DOI: 10.1093/infdis/jiae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Admission and discharge screening of patients for asymptomatic gut colonization with multidrug-resistant organisms (MDROs) is a traditional approach to active surveillance, but its sensitivity for detecting colonization is uncertain. METHODS Daily rectal or fecal swab samples and clinical data were collected over 12 months from patients in one 25-bed intensive care unit (ICU) in Chicago, IL USA and tested for the following multidrug-resistant organisms (MDROs): vancomycin-resistant enterococci (VRE); third-generation cephalosporin-resistant Enterobacterales, including extended-spectrum β-lactamase-producing Enterobacterales (ESBL); and carbapenem-resistant Enterobacterales (CRE). MDRO detection by (1) admission/discharge surveillance cultures or (2) clinical cultures were compared to daily surveillance cultures. Samples underwent 16S rRNA gene sequencing to measure the relative abundance of operational taxonomic units (OTUs) corresponding to each MDRO. RESULTS Compared with daily surveillance cultures, admission/discharge cultures detected 91% of prevalent MDRO colonization and 63% of incident MDRO colonization among medical ICU patients. Only a minority (7%) of MDRO carriers were identified by clinical cultures. Higher relative abundance of MDRO-associated OTUs and specific antibiotic exposures were independently associated with higher probability of MDRO detection by culture. CONCLUSION Admission and discharge surveillance cultures underestimated MDRO acquisitions in an ICU. These limitations should be considered when designing sampling strategies for epidemiologic studies that use culture-based surveillance.
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Affiliation(s)
- Sarah E Sansom
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Teppei Shimasaki
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Thelma Dangana
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Michael Y Lin
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | | | - Christine Fukuda
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Nicholas M Moore
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Rachel D Yelin
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Christine M Bassis
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI USA
| | - Yoona Rhee
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Enrique Cornejo Cisneros
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Pamela Bell
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Karen Lolans
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Khaled Aboushaala
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI USA
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI USA
| | - Mary K Hayden
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
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Santoro M, López-Verdejo A, Angulo A, Rojas A, Cortés J, Pacheco-Chaves B, Solano-Barquero A. Integrative taxonomy of Anaporrhutum mundae sp. nov. (Trematoda: Gorgoderidae), a parasite of the Munda round ray Urotrygon munda (Urotrygonidae) in Costa Rica. J Helminthol 2024; 98:e28. [PMID: 38516701 DOI: 10.1017/s0022149x2400018x] [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: 03/23/2024]
Abstract
A new species of trematode of anaporrhutine gorgoderid, from the gill chambers of the Munda round ray Urotrygon munda in Costa Rica is described, based on an integrative taxonomic approach that includes the use of light and scanning electron microscopy, ITS2 and 28S rDNA sequencing, and phylogenetic analysis. Anaporrhutum mundae sp. nov. can be distinguished from congeneric species by a combination of morphological traits and particularly by having the genital pore opening at the level of the intestinal bifurcation. The new species also can be distinguished from all other species of Anaporrhutum, except A. euzeti Curran, Blend & Overstreet, 2003, by having fewer testicular follicles per testis. Anaporrhutum mundae sp. nov. also differs from A. euzeti in its forebody shape and by having different morphology and location of the vitellaria. The study of the tegumental surface of A. mundae sp. nov., as revealed by scanning electron microscopy, allowed detection of new morphological characters for a member of Anaporrhutinae that may be of taxonomic value. These are: a stylet cavity dorsal to the oral sucker with a large penetration gland opening on each side of the cavity and small penetration gland openings located ventral to the stylet cavity, arranged in a circle around the mouth. This represents the first record of an Anaporrhutum species from Costa Rica. Further, A. mundae sp. nov. represents the first parasite described or reported in this host.
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Affiliation(s)
- Mario Santoro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121Naples, Italy
| | - Alejandro López-Verdejo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121Naples, Italy
- Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, C/Catedrático José Beltrán 2, 46980Paterna, Spain
| | - Arturo Angulo
- Escuela de Biología, Museo de Zoología, Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET), and Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, 11501-2060 San Pedro de Montes de Oca, San José, Costa Rica
| | - Alicia Rojas
- Center for Research in Tropical Diseases, Faculty of Microbiology, University of Costa Rica, 11501-2060 San Pedro de Montes de Oca, San José, Costa Rica
| | - Jorge Cortés
- Escuela de Biología, Museo de Zoología, Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET), and Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, 11501-2060 San Pedro de Montes de Oca, San José, Costa Rica
| | - Bernald Pacheco-Chaves
- Departamento de Investigación, Instituto Costarricense de Pesca y Acuicultura, Barrio El Cocal, Puntarenas 333-5400, Costa Rica
| | - Alberto Solano-Barquero
- Center for Research in Tropical Diseases, Faculty of Microbiology, University of Costa Rica, 11501-2060 San Pedro de Montes de Oca, San José, Costa Rica
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Pedersen KM, von Beeren C, Oggioni A, Blüthgen N. Mammal dung-dung beetle trophic networks: an improved method based on gut-content DNA. PeerJ 2024; 12:e16627. [PMID: 38500531 PMCID: PMC10946388 DOI: 10.7717/peerj.16627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 11/16/2023] [Indexed: 03/20/2024] Open
Abstract
Background Dung beetles provide many important ecosystem services, including dung decomposition, pathogen control, soil aeration, and secondary seed dispersal. Yet, the biology of most dung beetles remains unknown. Natural diets are poorly studied, partly because previous research has focused on choice or attraction experiments using few, easily accessible dung types from zoo animals, farm animals, or humans. This way, many links within natural food webs have certainly been missed. In this work, we aimed to establish a protocol to analyze the natural diets of dung beetles using DNA gut barcoding. Methods First, the feasibility of gut-content DNA extraction and amplification of 12s rDNA from six different mammal dung types was tested in the laboratory. We then applied the method to beetles caught in pitfall traps in Ecuador and Germany by using 12s rDNA primers. For a subset of the dung beetles caught in the Ecuador sampling, we also used 16s rDNA primers to see if these would improve the number of species we could identify. We predicted the likelihood of amplifying DNA using gut fullness, DNA concentration, PCR primer, collection method, and beetle species as predictor variables in a dominance analysis. Based on the gut barcodes, we generated a dung beetle-mammal network for both field sites (Ecuador and Germany) and analyzed the levels of network specificity. Results We successfully amplified mammal DNA from dung beetle gut contents for 128 specimens, which included such prominent species as Panthera onca (jaguar) and Puma concolor (puma). The overall success rate of DNA amplification was 53%. The best predictors for amplification success were gut fullness and DNA concentration, suggesting the success rate can be increased by focusing on beetles with a full gut. The mammal dung-dung beetle networks differed from purely random network models and showed a moderate degree of network specialization (H2': Ecuador = 0.49; Germany = 0.41). Conclusion We here present a reliable method of extracting and amplifying gut-content DNA from dung beetles. Identifying mammal dung via DNA reference libraries, we created mammal dung-dung beetle trophic networks. This has benefits over previous methods because we inventoried the natural mammal dung resources of dung beetles instead of using artificial mammal baits. Our results revealed higher levels of specialization than expected and more rodent DNA than expected in Germany, suggesting that the presented method provides more detailed insights into mammal dung-dung beetle networks. In addition, the method could have applications for mammal monitoring in many ecosystems.
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Affiliation(s)
- Karen M. Pedersen
- Biology, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | | | - Arianna Oggioni
- Biology, Technical University of Darmstadt, Darmstadt, Hessen, Germany
| | - Nico Blüthgen
- Biology, Technical University of Darmstadt, Darmstadt, Hessen, Germany
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Ortiz-Velez A, Kelley S. Data-driven mathematical and visualization approaches for removing rare features for Compositional Data Analysis (CoDA). NAR Genom Bioinform 2024; 6:lqad110. [PMID: 38187087 PMCID: PMC10768885 DOI: 10.1093/nargab/lqad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 11/25/2023] [Accepted: 12/20/2023] [Indexed: 01/09/2024] Open
Abstract
Sparse feature tables, in which many features are present in very few samples, are common in big biological data (e.g. metagenomics). Ignoring issues of zero-laden datasets can result in biased statistical estimates and decreased power in downstream analyses. Zeros are also a particular issue for compositional data analysis using log-ratios since the log of zero is undefined. Researchers typically deal with this issue by removing low frequency features, but the thresholds for removal differ markedly between studies with little or no justification. Here, we present CurvCut, an unsupervised data-driven approach with human confirmation for rare-feature removal. CurvCut implements two distinct approaches for determining natural breaks in the feature distributions: a method based on curvature analysis borrowed from thermodynamics and the Fisher-Jenks statistical method. Our results show that CurvCut rapidly identifies data-specific breaks in these distributions that can be used as cutoff points for low-frequency feature removal that maximizes feature retention. We show that CurvCut works across different biological data types and rapidly generates clear visual results that allow researchers to confirm and apply feature removal cutoffs to individual datasets.
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Affiliation(s)
- Adrian Ortiz-Velez
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA 92182, USA
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Scott T Kelley
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA 92182, USA
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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Yadav K, Saurav GK, Rana VS, Rawat N, Anjali, Jamwal R, Singh OP, Bandyopadhyay A, Rajagopal R. Polyubiquitin protein of Aedes aegypti as an interacting partner of dengue virus envelope protein. MEDICAL AND VETERINARY ENTOMOLOGY 2024; 38:48-58. [PMID: 37807654 DOI: 10.1111/mve.12696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
Dengue virus (DENV) is an arbovirus that comprises four antigenically different serotypes. Aedes aegypti (Diptera: Culicidae) acts as the principal vector for DENV transmission, and vector control is crucial for dengue fever epidemic management. To design effective vector control strategies, a comprehensive understanding of the insect vector and virus interaction is required. Female Ae. aegypti ingests DENV during the acquisition of a blood meal from an infected human. DENV enters the insect midgut, replicates inside it and reaches the salivary gland for transmitting DENV to healthy humans during the subsequent feeding cycles. DENV must interact with the proteins present in the midgut and salivary glands to gain entry and accomplish successful replication and transmission. Ae. aegypti midgut cDNA library was prepared, and yeast two-hybrid screening was performed against the envelope protein domain III (EDIII) protein of DENV-2. The polyubiquitin protein was selected from the various candidate proteins for subsequent analysis. Polyubiquitin gene was amplified, and the protein was purified in a heterologous expression system for in vitro interaction studies. In vitro pull-down assay presented a clear interaction between polyubiquitin protein and EDIII. To further confirm this interaction, a dot blot assay was employed, and polyubiquitin protein was found to interact with DENV particles. Our results enable us to suggest that polyubiquitin plays an important role in DENV infection within mosquitoes.
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Affiliation(s)
- Karuna Yadav
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Gunjan Kumar Saurav
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
- Department of Zoology, Rajiv Gandhi University, Doimukh, Arunachal Pradesh, India
| | - Vipin Singh Rana
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
- Department of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Nitish Rawat
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Anjali
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Rohit Jamwal
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | | | - Anannya Bandyopadhyay
- Protein Homeostasis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Raman Rajagopal
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
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Chen C, Wang W, Zhang J, Zhang L, Zhao J, Deng J, Li W, Li X, Zhuo W, Huang L, Chen J. Genomic characteristics of two strains of ESBL-producing Klebsiella pneumoniae ST268 isolated from different samples of one patient. J Glob Antimicrob Resist 2024; 36:319-325. [PMID: 38266958 DOI: 10.1016/j.jgar.2024.01.007] [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: 05/29/2023] [Revised: 11/20/2023] [Accepted: 01/13/2024] [Indexed: 01/26/2024] Open
Abstract
OBJECTIVES This study reports the whole-genome sequences of two strains of extended-spectrum beta-lactamase (ESBL)-producing and multidrug-resistant (MDR) K. pneumoniae ST268 and explores their acquired antibiotic resistance genes (ARGs) and the mobile genetic elements (MGEs). METHODS Two strains of K. pneumoniae ST268 were isolated from different samples of one patient. Assessment of antimicrobial susceptibility was performed, and then whole-genome sequencing was conducted. Acquired ARGs, insertion sequences, and transposons harboured by the two strains of K. pneumoniae ST268 were identified, and then the genetic contexts associated with the ARGs were analysed systematically. RESULTS Two strains of K. pneumoniae ST268 were found to carry the 118.6-kb hybrid IncFIIK:IncQ1:repBR1701 plasmid. All the acquired ARGs carried by the IncF plasmid were found to be situated on the 25.3-kb MDR region bracketed by ISKpn19 and IS26, which was widely present in the plasmids in 14 STs of strains in K. pneumoniae but also in IncF plasmids from Shigella flexneri and Klebsiella quasipneumoniae. Notably, the IncF plasmids harbouring the 25.3-kb MDR region were geographically distributed mainly in China, and the pKP161637-1/pKP160802-1 in our study was the first report on the IncF plasmid carrying the 25.3-kb MDR region bracketed in K. pneumoniae ST268. CONCLUSIONS Two strains of ESBL-producing K. pneumoniae ST268 with a MDR IncF plasmid were identified in a hospital in China. The ARGs were identified on the 25.3-kb MDR region, bracketed by ISKpn19 and IS26, of the IncF plasmids, which were present not only in the K. pneumoniae but also in the S. flexneri and K. quasipneumoniae.
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Affiliation(s)
- Chao Chen
- Department of Neurology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wei Wang
- Department of Pulmonary and Critical Care Medicine, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Jiechang Zhang
- Department of Cardiology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Limei Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Jianhua Zhao
- Department of Neurosurgery, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Jinming Deng
- Department of Neurology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wang Li
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Xiaobin Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wenyan Zhuo
- Department of Neurology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China.
| | - Lian Huang
- Department of Neurology, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Jing Chen
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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Kim ST, Conklin SD, Redan BW, Ho KK. Determination of the Nutrient and Toxic Element Content of Wild-Collected and Cultivated Seaweeds from Hawai'i. ACS FOOD SCIENCE & TECHNOLOGY 2024; 4:595-605. [PMID: 38528908 PMCID: PMC10961648 DOI: 10.1021/acsfoodscitech.3c00476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
For centuries, Hawaiians have gathered seaweed for food, medicine, and ceremonial purposes. Seaweed contains nutrients, but some varieties can accumulate toxic elements. We measured target macrominerals (Na, Mg, P, K, Ca), microminerals (B, V, Mn, Co, Cu, Zn, Mo), and nonessential/toxic elements (As, Sr, Cd, Sn, Hg, Pb, and U) in a sample of wild-collected and cultivated seaweeds from Hawai'i. The samples consisted of brown (Sargassum aquifolium, Sargassum echinocarpum), red (Gracilaria parvispora, Halymenia formosa, Halymenia hawaiiana), and green (Ulva ohnoi) seaweed. Elemental composition was determined by inductively coupled plasma (ICP)-atomic emission spectroscopy and ICP-mass spectrometry (MS). Speciation of As was conducted by using liquid chromatography-ICP-MS. S. echinocarpum per 80 g serving was high in Ca (~37% daily value [DV]), U. ohnoi was high in Mg (~40%DV), H. formosa was high in Fe (~40%DV), and G. parvispora was high in Mn (~128%DV). In this study, the highest amounts of toxic elements were observed in S. aquifolium and S. echinocarpum (27.6 mg inorganic As/kg fdw), G. parvispora (43.3 mg Pb/kg fdw) and H. formosa (46.6 mg Pb/kg fdw). These results indicate that although seaweeds from Hawai'i contain a variety of nutrients, some species can accumulate high amounts of toxic elements.
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Affiliation(s)
- Samuel T. Kim
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, 96822, United States
| | - Sean D. Conklin
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, 20740, United States
| | - Benjamin W. Redan
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Food Safety, Bedford Park, IL, 60501, United States
| | - Kacie K.H.Y. Ho
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, 96822, United States
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Zhao T, Gussak A, van der Hee B, Brugman S, van Baarlen P, Wells JM. Identification of plasminogen-binding sites in Streptococcus suis enolase that contribute to bacterial translocation across the blood-brain barrier. Front Cell Infect Microbiol 2024; 14:1356628. [PMID: 38456079 PMCID: PMC10919400 DOI: 10.3389/fcimb.2024.1356628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/06/2024] [Indexed: 03/09/2024] Open
Abstract
Streptococcus suis is an emerging zoonotic pathogen that can cause invasive disease commonly associated with meningitis in pigs and humans. To cause meningitis, S. suis must cross the blood-brain barrier (BBB) comprising blood vessels that vascularize the central nervous system (CNS). The BBB is highly selective due to interactions with other cell types in the brain and the composition of the extracellular matrix (ECM). Purified streptococcal surface enolase, an essential enzyme participating in glycolysis, can bind human plasminogen (Plg) and plasmin (Pln). Plg has been proposed to increase bacterial traversal across the BBB via conversion to Pln, a protease which cleaves host proteins in the ECM and monocyte chemoattractant protein 1 (MCP1) to disrupt tight junctions. The essentiality of enolase has made it challenging to unequivocally demonstrate its role in binding Plg/Pln on the bacterial surface and confirm its predicted role in facilitating translocation of the BBB. Here, we report on the CRISPR/Cas9 engineering of S. suis enolase mutants eno261, eno252/253/255, eno252/261, and eno434/435 possessing amino acid substitutions at in silico predicted binding sites for Plg. As expected, amino acid substitutions in the predicted Plg binding sites reduced Plg and Pln binding to S. suis but did not affect bacterial growth in vitro compared to the wild-type strain. The binding of Plg to wild-type S. suis enhanced translocation across the human cerebral microvascular endothelial cell line hCMEC/D3 but not for the eno mutant strains tested. To our knowledge, this is the first study where predicted Plg-binding sites of enolase have been mutated to show altered Plg and Pln binding to the surface of S. suis and attenuation of translocation across an endothelial cell monolayer in vitro.
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Affiliation(s)
| | | | | | | | | | - Jerry M. Wells
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, Netherlands
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Ryu H, Bi TM, Pulliam TH, Sarkar K, Church CD, Kumar N, Mayer-Blackwell K, Jani S, Ramchurren N, Hansen UK, Hadrup SR, Fling SP, Koelle DM, Nghiem P, Newell EW. Merkel cell polyomavirus-specific and CD39 +CLA + CD8 T cells as blood-based predictive biomarkers for PD-1 blockade in Merkel cell carcinoma. Cell Rep Med 2024; 5:101390. [PMID: 38340724 PMCID: PMC10897544 DOI: 10.1016/j.xcrm.2023.101390] [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: 07/03/2023] [Revised: 11/29/2023] [Accepted: 12/21/2023] [Indexed: 02/12/2024]
Abstract
Merkel cell carcinoma is a skin cancer often driven by Merkel cell polyomavirus (MCPyV) with high rates of response to anti-PD-1 therapy despite low mutational burden. MCPyV-specific CD8 T cells are implicated in anti-PD-1-associated immune responses and provide a means to directly study tumor-specific T cell responses to treatment. Using mass cytometry and combinatorial tetramer staining, we find that baseline frequencies of blood MCPyV-specific cells correlated with response and survival. Frequencies of these cells decrease markedly during response to therapy. Phenotypes of MCPyV-specific CD8 T cells have distinct expression patterns of CD39, cutaneous lymphocyte-associated antigen (CLA), and CD103. Correspondingly, overall bulk CD39+CLA+ CD8 T cell frequencies in blood correlate with MCPyV-specific cell frequencies and similarly predicted favorable clinical outcomes. Conversely, frequencies of CD39+CD103+ CD8 T cells are associated with tumor burden and worse outcomes. These cell subsets can be useful as biomarkers and to isolate blood-derived tumor-specific T cells.
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Affiliation(s)
- Heeju Ryu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Timothy M Bi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Korok Sarkar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Candice D Church
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Nandita Kumar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Saumya Jani
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nirasha Ramchurren
- Cancer Immunotherapy Trails Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ulla K Hansen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Steven P Fling
- Cancer Immunotherapy Trails Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA; Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Benaroya Research Institute, Seattle, WA, USA
| | - Paul Nghiem
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA.
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Schirmer M, Stražar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host Microbe 2024; 32:209-226.e7. [PMID: 38215740 PMCID: PMC10923022 DOI: 10.1016/j.chom.2023.12.013] [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: 03/13/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
Understanding the role of the microbiome in inflammatory diseases requires the identification of microbial effector molecules. We established an approach to link disease-associated microbes to microbial metabolites by integrating paired metagenomics, stool and plasma metabolomics, and culturomics. We identified host-microbial interactions correlated with disease activity, inflammation, and the clinical course of ulcerative colitis (UC) in the Predicting Response to Standardized Colitis Therapy (PROTECT) pediatric inception cohort. In severe disease, metabolite changes included increased dipeptides and tauro-conjugated bile acids (BAs) and decreased amino-acid-conjugated BAs in stool, whereas in plasma polyamines (N-acetylputrescine and N1-acetylspermidine) increased. Using patient samples and Veillonella parvula as a model, we uncovered nitrate- and lactate-dependent metabolic pathways, experimentally linking V. parvula expansion to immunomodulatory tryptophan metabolite production. Additionally, V. parvula metabolizes immunosuppressive thiopurine drugs through xdhA xanthine dehydrogenase, potentially impairing the therapeutic response. Our findings demonstrate that the microbiome contributes to disease-associated metabolite changes, underscoring the importance of these interactions in disease pathology and treatment.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
| | - Martin Stražar
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Eric M Brown
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emily Temple
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Deik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Bullock
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Jeanfavre
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kerry Pierce
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shen Jin
- Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | | | - Marie-Madlen Pust
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Zach Costliow
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Anne M Griffiths
- Division of Gastroenterology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thomas Walters
- Division of Gastroenterology, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Brendan M Boyle
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey Hyams
- Connecticut Children's Medical Center, Division of Digestive Diseases, Hartford, CT 06106, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Clary B Clish
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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47
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Lacy KD, Hart T, Kronauer DJ. Unselfish meiotic drive maintains heterozygosity in a parthenogenetic ant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579553. [PMID: 38405725 PMCID: PMC10888755 DOI: 10.1101/2024.02.09.579553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
According to Mendel's second law, chromosomes segregate randomly in meiosis. Nonrandom segregation is primarily known for cases of selfish meiotic drive in females, in which particular alleles bias their own transmission into the oocyte1,2. Here, we report a rare example of unselfish meiotic drive for crossover inheritance in the clonal raider ant, Ooceraea biroi. This species produces diploid offspring parthenogenetically via fusion of two haploid nuclei from the same meiosis3. This process should cause rapid genotypic degeneration due to loss of heterozygosity, which results if crossover recombination is followed by random (Mendelian) segregation of chromosomes4,5. However, by comparing whole genomes of mothers and daughters, we show that loss of heterozygosity is exceedingly rare, raising the possibility that crossovers are infrequent or absent in O. biroi meiosis. Using a combination of cytology and whole genome sequencing, we show that crossover recombination is, in fact, common, but that loss of heterozygosity is avoided because crossover products are faithfully co-inherited. This results from a programmed violation of Mendel's law of segregation, such that crossover products segregate together rather than randomly. This discovery highlights an extreme example of cellular "memory" of crossovers, which could be a common yet cryptic feature of chromosomal segregation.
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Affiliation(s)
- Kip D. Lacy
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - Taylor Hart
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - Daniel J.C. Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
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48
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Bai H, Li C, Lai X, Hu X, Li L, Chen W. Case Report: Successful Treatment of Cerebral Phaeohyphomycosis with Voriconazole: A Case Report and Literature Review. Am J Trop Med Hyg 2024; 110:274-278. [PMID: 38227961 PMCID: PMC10859812 DOI: 10.4269/ajtmh.23-0122] [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: 02/24/2023] [Accepted: 07/21/2023] [Indexed: 01/18/2024] Open
Abstract
Fonsecaea monophora is a species of Fonsecaea that belongs to Chaetothyriales. It is usually isolated from tropical and subtropical regions, causing reactive inflammation, skin abscesses, and pain. Cerebral infection caused by F. monophora is rare but often fatal. Diagnosing this disease at an early stage is difficult, and appropriate antifungal therapy is often delayed as a result. We report the case of a 53-year-old woman with type 2 diabetes who presented with a headache 2 months ago and progressive right-sided weakness of 1 month's duration. Magnetic resonance imaging revealed a space-occupying lesion in the left frontal lobe and corpus callosum. The cystic mass was removed by surgical intervention, and the identification of the sample based on sequencing of the internal transcribed spaced region in BLAST-N search showed that the sequences producing most significant alignments were F. monophora or similar (query cover 99%, E value 0.0, per ident 99.84). The patient was treated with a 3-month course of twice daily voriconazole, leading to complete recovery.
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Affiliation(s)
- Hao Bai
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, China
| | - Chao Li
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiangyu Lai
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiaogang Hu
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, China
| | - Lixian Li
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, China
| | - Wanyi Chen
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, China
- College of Bioengineering, Chongqing University, Chongqing, China
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49
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Wang L, Guan Y, Lin X, Wei J, Zhang Q, Zhang L, Tan J, Jiang J, Ling C, Cai L, Li X, Liang X, Wei W, Li RM. Whole-Genome Sequencing of an Escherichia coli ST69 Strain Harboring blaCTX-M-27 on a Hybrid Plasmid. Infect Drug Resist 2024; 17:365-375. [PMID: 38318209 PMCID: PMC10840416 DOI: 10.2147/idr.s427571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/29/2023] [Indexed: 02/07/2024] Open
Abstract
Objective Escherichia coli is a common Gram-negative human pathogen. The emergence of E. coli with multiple-antibiotic-resistant phenotypes has become a serious health concern. This study reports the whole-genome sequences of third-generation cephalosporin-resistant (3GC-R) and multidrug-resistant (MDR) E. coli EC6868 and explores the acquired antibiotic-resistance genes (ARGs) as well as their genetic contexts. Methods E. coli EC6868 was isolated from a vaginal secretion sample of a pregnant patient in China. The antimicrobial susceptibility was assessed, and whole-genome sequencing was conducted. The acquired ARGs, insertion sequence (IS) elements, and integrons within the genome of E. coli EC6868 were identified, and the genetic contexts associated with the ARGs were analyzed systematically. Results E. coli EC6868 was determined to belong to ST69 and harbored a 144.9-kb IncF plasmid (pEC6868-1) with three replicons (Col156, IncFIBAP001918, and IncFII). The ESBL gene blaCTX-M-27 was located on the structure "∆ISEcp1-blaCTX-M-27-IS903B", which was widely present in the species of Enterobacteriales. Other ARGs carried by plasmid pEC6868-1 were mainly located on the 18.9-kb IS26-composite transposon (five copies of intact IS26 and one copy of truncated IS26) composing of IS26-mphA-mrx(A)-mphR(A)-IS6100, ∆TnAs3-eamA-tet(A)-tetR(A)-aph(6)-Id-aph(3")-Ib-sul2-IS26, and a class 1 integron, which was widely present on IncF plasmids of E. coli, mainly distributed in ST131, ST38, and ST405. Notably, pEC6868 in our study was the first report on a plasmid harboring the 18.9-kb structure in E. coli ST69 in China. Conclusion The 3GC-R E. coli ST69 strain with an MDR IncF plasmid carrying blaCTX-M-27 and other ARGs, conferring resistance to aminoglycosides, macrolides, sulfonamides, tetracycline, and trimethoprim, was identified in a hospital in China. Mobile genetic elements including ISEcp1, IS903B, IS26, Tn3, IS6100 and class 1 integron were found within the MDR region, which could play important roles in the global dissemination of these resistance genes.
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Affiliation(s)
- Ling Wang
- Department of Obstetrics, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Yuee Guan
- Department of Cardiology, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Xu Lin
- Department of Gastrointestinal Surgery, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Jie Wei
- Department of Clinical Laboratory, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Qinghuan Zhang
- Department of Clinical Laboratory, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Limei Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Jing Tan
- Department of Obstetrics, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Jie Jiang
- Department of Obstetrics, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Caiqin Ling
- Department of Obstetrics, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Lei Cai
- Department of Obstetrics, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Xiaobin Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Xiong Liang
- Department of Obstetrics, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Wei Wei
- Department of Cardiothoracic Surgery, Zhuhai Hospital Affiliated with Jinan University (Zhuhai People’s Hospital), Zhuhai, 519000, People’s Republic of China
| | - Rui-Man Li
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, People’s Republic of China
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van der Reis AL, Sewell MA, Nelson WA. Investigating seed bank potential of crustose coralline algae using DNA metabarcoding. JOURNAL OF PHYCOLOGY 2024; 60:195-202. [PMID: 37864777 DOI: 10.1111/jpy.13403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023]
Abstract
To examine the potential for the autogenic ecosystem engineers, crustose coralline algae (CCA), to serve as seed banks or refugia for life stages of other species, it is critical to develop sampling protocols that reflect the diversity of life present. In this pilot study on two shallow water species of CCA collected from Raoul Island (Kermadec Islands; Rangitāhua) New Zealand, we investigated two preservation methods (ethanol vs. silica gel), sampled inner and outer regions of the crusts, and used DNA metabarcoding and seven genes/gene regions (16S rRNA, 18S rRNA, 23S rRNA, cox1, rbcL, and tufA genes and the ITS rRNA region) to develop a protocol for taxa identification. The results revealed immense diversity, with typically more taxa identified within the inner layers than the outer layers. As highlighted in other metabarcoding studies and in earlier work on rhodoliths (nodose coralline algae), reference databases are incomplete, and to some extent, the use of multiple markers mitigates this issue. Specifically, the 23S rRNA and rbcL genes are currently more suitable for identifying algae, while the cox1 gene fares better at capturing the diversity present inclusive of algae. Further investigation of these autogenic ecosystem engineers that likely act as marine seed banks is needed.
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Affiliation(s)
| | - Mary A Sewell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Wendy A Nelson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Auckland War Memorial Museum Tāmaki Paenga Hira, Auckland, New Zealand
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