99901
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Yin SJ, Lee J, Lim G, Chen Z, Qian GY, Si YX, Park YD. A study of Pb 2+ induced unfolding and aggregation of arginine kinase from Euphausia superba: kinetics and computational simulation integrating study. J Biomol Struct Dyn 2021; 40:8206-8215. [PMID: 33847251 DOI: 10.1080/07391102.2021.1908168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Arginine kinase is a crucial phosphagen kinase in invertebrates, which is associated to the environmental stress response, plays a key role in cellular energy metabolism. In this study, we investigated the Pb2+-induced inhibition and aggregation of Euphausia superba arginine kinase (ESAK) and found that significantly inactivated ESAK in a dose-dependent manner (IC50 = 0.058 ± 0.002 mM). Spectrofluorimetry results showed that Pb2+ induced tertiary structural changes via the internal polarity increased and the non-polarity decreased in ESAK and directly induced ESAK aggregation. The ESAK aggregation process induced by Pb2+ occurred with multi-phase kinetics. The addition of osmolytes did not show protective effect on Pb2+-induced inactivation of ESAK. The computational molecular dynamics (MD) simulation showed that three Pb2+ interrupt the entrance of the active site of ESAK and it could be the reason on the loss of activity of ESAK. Several important residues of ESAK were detected that were importantly contributed the conformation and catalytic function of ESAK. Our study showed that Pb2+-induced misfolding of ESAK and the complete loss of activity irreversibly, which cannot be recovered by osmolytes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shang-Jun Yin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, P.R. China
| | - Jinhyuk Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Sciences and Technology, Daejeon, Korea
| | - Gyutae Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Zhongfa Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, P.R. China
| | - Guo-Ying Qian
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, P.R. China
| | - Yue-Xiu Si
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, P.R. China
| | - Yong-Doo Park
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, P.R. China.,Skin Diseases Research Center, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, P.R. China.,Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, P. R. China
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99902
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Wong AYW, Johnsson ATA, Ininbergs K, Athlin S, Özenci V. Comparison of Four Streptococcus pneumoniae Urinary Antigen Tests Using Automated Readers. Microorganisms 2021; 9:microorganisms9040827. [PMID: 33924729 PMCID: PMC8070120 DOI: 10.3390/microorganisms9040827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 01/13/2023] Open
Abstract
Streptococcus pneumoniae urinary antigen tests (UATs) may be interpreted using automatic readers to potentially automate sample incubation and provide standardized results reading. Here, we evaluated four UATs the BinaxNOW S. pneumoniae Antigen Card (Abbott, Chicago, IL, USA), ImmuView S. pneumoniae and Legionella (SSI Diagnostica, Hillerød, Denmark), STANDARD F S. pneumoniae Ag FIA (SD Biosensor, Gyeonggi, South Korea), and Sofia S. pneumoniae FIA (Quidel Corporation, San Diego, CA, USA) with their respective benchtop readers for their ability to detect S. pneumoniae urinary antigen. We found that these assays had a sensitivity of 76.9–86.5%, and specificity of 84.2–89.7%, with no significant difference found among the four UATs. The assays had a high level of agreement with each other, with 84.5% of samples testing consistently across all four assays. The automatically and visually read test results from the two immunochromatographic assays, BinaxNOW and ImmuView, were compared and showed excellent agreement between the two types of reading. Immunofluorescent-based assays, Sofia and STANDARD F, had significantly less time to detect compared to the two immunochromatographic assays due to having less assay setup procedures and shorter sample incubation times. In conclusion, the four UATs performed similarly in the detection of S. pneumoniae urinary antigen, and readers can bring increased flexibility to running UATs in the clinical routine.
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Affiliation(s)
- Alicia Yoke Wei Wong
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, 141 86 Stockholm, Sweden;
- Correspondence: (A.Y.W.W.); (V.Ö.)
| | | | - Karolina Ininbergs
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, 141 86 Stockholm, Sweden;
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, 171 76 Stockholm, Sweden
| | - Simon Athlin
- Faculty of Medicine and Health, School of Medical Sciences, Örebro University, 701 82 Örebro, Sweden;
| | - Volkan Özenci
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, 141 86 Stockholm, Sweden;
- Department of Clinical Microbiology, Karolinska University Hospital, Huddinge, 141 86 Stockholm, Sweden;
- Correspondence: (A.Y.W.W.); (V.Ö.)
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99903
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Abstract
BACKGROUND Antimicrobial resistance (AMR) is a global challenge that requires a "One Health" approach to achieve better public health outcomes for people, animals, and the environment. Numerous bibliometric studies were published on AMR in humans. However, none was published in food-producing animals. The current study aimed at assessing and analyzing scientific publications on AMR in food-producing animals. METHOD A validated search query was developed and entered in Scopus advanced search function to retrieve and quantitatively analyze relevant documents. Bibliometric indicators and mapping were presented. The study period was from 2000 to 2019. RESULTS The search query retrieved 2852 documents. During the period from 2015 to 2019, approximately 48% of the retrieved documents were published. The article about the discovery of plasmid-mediated colistin resistance in pigs received the highest number of citations (n = 1970). The Journal of Food Protection (n = 123; 4.3%) ranked first in the number of publications while the Applied and Environmental Microbiology journal ranked first in the number of citations per document. The USA led with 576 (20.2%) documents followed by China (n = 375; 13.1%). When the number of publications was standardized by income and population size, India (n = 51.5) ranked first followed by China (n = 38.3) and Brazil (n = 13.4). The growth of publications from China exceeded that of the USA in the last 3 years of the study period. Research collaboration in this field was inadequate. Mapping author keywords showed that E. coli, Salmonella, poultry, Campylobacter, chicken, cattle, and resistant genes were most frequent. The retrieved documents existed in five research themes. The largest research theme was about AMR in Salmonella in food-producing animals. The most recent research theme was about the dissemination and molecular transfer of AMR genes into the environment and among different bacterial strains. CONCLUSION Hot spots of research on AMR in food-producing animals match the world regions of reported hot spots of AMR in animals. Research collaboration in this field is of great importance, especially with low- and middle-income countries. Data on AMR need to be collected nationally and internationally to implement the "One Health" approach in the fight against AMR.
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Affiliation(s)
- Waleed M Sweileh
- Department of Physiology, Pharmacology/Toxicology, Division of Biomedical Sciences, College of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine.
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99904
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Poimala A, Parikka P, Hantula J, Vainio EJ. Viral diversity in Phytophthora cactorum population infecting strawberry. Environ Microbiol 2021; 23:5200-5221. [PMID: 33848054 DOI: 10.1111/1462-2920.15519] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/18/2021] [Accepted: 04/08/2021] [Indexed: 01/31/2023]
Abstract
Eighty-eight Phytophthora cactorum strains isolated from crown or leather rot of strawberry in 1971-2019 were screened for viruses using RNA-seq and RT-PCR. Remarkably, all but one isolate were virus-infected, most of them harbouring more than one virus of different genera or species. The most common virus occurring in 94% of the isolates was the Phytophthora cactorum RNA virus 1 (PcRV1) resembling members of Totiviridae. Novel viruses related to members of Endornaviridae, named Phytophthora cactorum alphaendornaviruses 1-3 (PcAEV1-3), were found in 57% of the isolates. Four isolates hosted viruses with affinities to Bunyaviridae, named Phytophthora cactorum bunyaviruses 1-3 (PcBV1-3), and a virus resembling members of the proposed genus 'Ustivirus', named Phytophthora cactorum usti-like virus (PcUV1), was found in a single isolate. Most of the virus species were represented by several distinct strains sharing ≥81.4% aa sequence identity. We found no evidence of spatial differentiation but some temporal changes in the P. cactorum virus community were observed. Some isolates harboured two or more closely related strains of the same virus (PcAEV1 or PcRV1) sharing 86.6%-96.4% nt identity in their polymerase sequence. This was surprising as viruses with such a high similarity are typically mutually exclusive.
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Affiliation(s)
- Anna Poimala
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity, Latokartanonkaari 9, Helsinki, FI-00790, Finland
| | - Päivi Parikka
- Natural Resources Institute Finland (Luke), Plant Health, Humppilantie 18, Jokioinen, 31600, Finland
| | - Jarkko Hantula
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity, Latokartanonkaari 9, Helsinki, FI-00790, Finland
| | - Eeva J Vainio
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity, Latokartanonkaari 9, Helsinki, FI-00790, Finland
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99905
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Mooney BC, Mantz M, Graciet E, Huesgen PF. Cutting the line: manipulation of plant immunity by bacterial type III effector proteases. J Exp Bot 2021; 72:3395-3409. [PMID: 33640987 DOI: 10.1093/jxb/erab095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Pathogens and their hosts are engaged in an evolutionary arms race. Pathogen-derived effectors promote virulence by targeting components of a host's innate immune system, while hosts have evolved proteins that sense effectors and trigger a pathogen-specific immune response. Many bacterial effectors are translocated into host cells using type III secretion systems. Type III effector proteases irreversibly modify host proteins by cleavage of peptide bonds and are prevalent among both plant and animal bacterial pathogens. In plants, the study of model effector proteases has yielded important insights into the virulence mechanisms employed by pathogens to overcome their host's immune response, as well as into the mechanisms deployed by their hosts to detect these effector proteases and counteract their effects. In recent years, the study of a larger number of effector proteases, across a wider range of pathogens, has yielded novel insights into their functions and recognition. One key limitation that remains is the lack of methods to detect protease cleavage at the proteome-wide level. We review known substrates and mechanisms of plant pathogen type III effector proteases and compare their functions with those of known type III effector proteases of mammalian pathogens. Finally, we discuss approaches to uncover their function on a system-wide level.
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Affiliation(s)
- Brian C Mooney
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Melissa Mantz
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Emmanuelle Graciet
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
- Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
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99906
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Olejniczak-Staruch I, Ciążyńska M, Sobolewska-Sztychny D, Narbutt J, Skibińska M, Lesiak A. Alterations of the Skin and Gut Microbiome in Psoriasis and Psoriatic Arthritis. Int J Mol Sci 2021; 22:ijms22083998. [PMID: 33924414 PMCID: PMC8069836 DOI: 10.3390/ijms22083998] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous scientific studies in recent years have shown significant skin and gut dysbiosis among patients with psoriasis. A significant decrease in microbiome alpha-diversity (abundance of different bacterial taxa measured in one sample) as well as beta-diversity (microbial diversity in different samples) was noted in psoriasis skin. It has been proven that the representation of Cutibacterium, Burkholderia spp., and Lactobacilli is decreased and Corynebacterium kroppenstedii, Corynebacterium simulans, Neisseria spp., and Finegoldia spp. increased in the psoriasis skin in comparison to healthy skin. Alterations in the gut microbiome in psoriasis are similar to those observed in patients with inflammatory bowel disease. In those two diseases, the F. prausnitzii, Bifidobacterium spp., Lactobacillus spp., Parabacteroides and Coprobacillus were underrepresented, while the abundance of Salmonella sp., Campylobacter sp., Helicobacter sp., Escherichia coli, Alcaligenes sp., and Mycobacterium sp. was increased. Several research studies provided evidence for the significant influence of psoriasis treatments on the skin and gut microbiome and a positive influence of orally administered probiotics on the course of this dermatosis. Further research is needed to determine the influence of the microbiome on the development of inflammatory skin diseases. The changes in microbiome under psoriasis treatment can serve as a potential biomarker of positive response to the administered therapy.
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Affiliation(s)
- Irmina Olejniczak-Staruch
- Department of Dermatology, Pediatric Dermatology and Dermatological Oncology, Medical University of Lodz, 91-347 Lodz, Poland; (D.S.-S.); (J.N.); (M.S.); (A.L.)
- Dermoklinika Centrum Medyczne, 90-436 Lodz, Poland
- Correspondence: ; Tel.: +48-42-230-9657
| | - Magdalena Ciążyńska
- Department of Proliferative Diseases, Nicolaus Copernicus Multidisciplinary Centre for Oncology and Traumatology, 93-513 Lodz, Poland;
| | - Dorota Sobolewska-Sztychny
- Department of Dermatology, Pediatric Dermatology and Dermatological Oncology, Medical University of Lodz, 91-347 Lodz, Poland; (D.S.-S.); (J.N.); (M.S.); (A.L.)
| | - Joanna Narbutt
- Department of Dermatology, Pediatric Dermatology and Dermatological Oncology, Medical University of Lodz, 91-347 Lodz, Poland; (D.S.-S.); (J.N.); (M.S.); (A.L.)
| | - Małgorzata Skibińska
- Department of Dermatology, Pediatric Dermatology and Dermatological Oncology, Medical University of Lodz, 91-347 Lodz, Poland; (D.S.-S.); (J.N.); (M.S.); (A.L.)
| | - Aleksandra Lesiak
- Department of Dermatology, Pediatric Dermatology and Dermatological Oncology, Medical University of Lodz, 91-347 Lodz, Poland; (D.S.-S.); (J.N.); (M.S.); (A.L.)
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99907
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Griggs RG, Steenwerth KL, Mills DA, Cantu D, Bokulich NA. Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing. Front Microbiol 2021; 12:673810. [PMID: 33927711 PMCID: PMC8076609 DOI: 10.3389/fmicb.2021.673810] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/22/2021] [Indexed: 01/05/2023] Open
Abstract
Microbiomes are integral to viticulture and winemaking – collectively termed winegrowing – where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.
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Affiliation(s)
- Reid G Griggs
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States
| | - Kerri L Steenwerth
- USDA-ARS, Crops Pathology and Genetics Research Unit, Department of Land, Air and Water Resources, University of California, Davis, Davis, CA, United States
| | - David A Mills
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States.,Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States.,Foods for Health Institute, University of California, Davis, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States
| | - Nicholas A Bokulich
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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99908
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Le Sénéchal C, Puges M, Barthe C, Costaglioli P, Tokarski C, Buré C, Vilain S. Analysis of the Phospholipid Profile of the Collection Strain PAO1 and Clinical Isolates of Pseudomonas aeruginosa in Relation to Their Attachment Capacity. Int J Mol Sci 2021; 22:ijms22084003. [PMID: 33924531 PMCID: PMC8068974 DOI: 10.3390/ijms22084003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 11/24/2022] Open
Abstract
Bacteria form multicellular and resistant structures named biofilms. Biofilm formation starts with the attachment phase, and the molecular actors involved in this phase, except adhesins, are poorly characterized. There is growing evidence that phospholipids are more than simple structural bricks. They are involved in bacterial adaptive physiology, but little is known about their role in biofilm formation. Here, we report a mass spectrometry analysis of the phospholipid (PL) profile of several strains of Pseudomonas aeruginosa isolated from cystic fibrosis patients. The aim of our study was to evaluate a possible link between the PL profile of a strain and its attachment phenotype. Our results showed that PL profile is strongly strain-dependent. The PL profile of P. aeruginosa PAO1, a collection strain, was different from those of 10 clinical isolates characterized either by a very low or a very high attachment capacity. We observed also that the clinical strain’s PL profiles varied even more importantly between isolates. By comparing groups of strains having similar attachment capacities, we identified one PL, PE 18:1-18:1, as a potential molecular actor involved in attachment, the first step in biofilm formation. This PL represents a possible target in the fight against biofilms.
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Affiliation(s)
- Caroline Le Sénéchal
- CNRS, Bordeaux INP, CBMN, University Bordeaux, UMR 5248, F-33600 Pessac, France; (C.L.S.); (C.B.); (P.C.); (C.T.); (C.B.)
| | - Mathilde Puges
- Infectious and Tropical Diseases Department, CHU of Bordeaux, F-33000 Bordeaux, France;
| | - Christophe Barthe
- CNRS, Bordeaux INP, CBMN, University Bordeaux, UMR 5248, F-33600 Pessac, France; (C.L.S.); (C.B.); (P.C.); (C.T.); (C.B.)
| | - Patricia Costaglioli
- CNRS, Bordeaux INP, CBMN, University Bordeaux, UMR 5248, F-33600 Pessac, France; (C.L.S.); (C.B.); (P.C.); (C.T.); (C.B.)
| | - Caroline Tokarski
- CNRS, Bordeaux INP, CBMN, University Bordeaux, UMR 5248, F-33600 Pessac, France; (C.L.S.); (C.B.); (P.C.); (C.T.); (C.B.)
| | - Corinne Buré
- CNRS, Bordeaux INP, CBMN, University Bordeaux, UMR 5248, F-33600 Pessac, France; (C.L.S.); (C.B.); (P.C.); (C.T.); (C.B.)
| | - Sébastien Vilain
- CNRS, Bordeaux INP, CBMN, University Bordeaux, UMR 5248, F-33600 Pessac, France; (C.L.S.); (C.B.); (P.C.); (C.T.); (C.B.)
- Correspondence:
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99909
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Huang W, Kane MA. MAPLE: A Microbiome Analysis Pipeline Enabling Optimal Peptide Search and Comparative Taxonomic and Functional Analysis. J Proteome Res 2021; 20:2882-2894. [PMID: 33848166 DOI: 10.1021/acs.jproteome.1c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metaproteomics by mass spectrometry (MS) is a powerful approach to profile a large number of proteins expressed by all organisms in a highly complex biological or ecological sample, which is able to provide a direct and quantitative assessment of the functional makeup of a microbiota. The human gastrointestinal microbiota has been found playing important roles in human physiology and health, and metaproteomics has been shown to shed light on multiple novel associations between microbiota and diseases. MS-powered proteomics generally relies on genome data to define search space. However, metaproteomics, which simultaneously analyzes all proteins from hundreds to thousands of species, faces significant challenges regarding database search and interpretation of results. To overcome these obstacles, we have developed a user-friendly microbiome analysis pipeline (MAPLE, freely downloadable at http://maple.rx.umaryland.edu/), which is able to define an optimal search space by inferring proteomes specific to samples following the principle of parsimony. MAPLE facilitates highly comparable or better peptide identification compared to a sample-specific metagenome-guided search. In addition, we implemented an automated peptide-centric enrichment analysis function in MAPLE to address issues of traditional protein-centric comparison, enabling straightforward and comprehensive comparison of taxonomic and functional makeup between microbiota.
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Affiliation(s)
- Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland 21201, United States
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99910
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Zeng Z, Boeren S, Bhandula V, Light SH, Smid EJ, Notebaart RA, Abee T. Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes. mSystems 2021; 6:e01349-20. [PMID: 33850044 DOI: 10.1128/mSystems.01349-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Ethanolamine (EA) is a valuable microbial carbon and nitrogen source derived from cell membranes. EA catabolism is suggested to occur in a cellular metabolic subsystem called a bacterial microcompartment (BMC), and the activation of EA utilization (eut) genes is linked to bacterial pathogenesis. Despite reports showing that the activation of eut is regulated by a vitamin B12-binding riboswitch and that upregulation of eut genes occurs in mice, it remains unknown whether EA catabolism is BMC dependent in Listeria monocytogenes Here, we provide evidence for BMC-dependent anaerobic EA utilization via metabolic analysis, proteomics, and electron microscopy. First, we show vitamin B12-induced activation of the eut operon in L. monocytogenes coupled to the utilization of EA, thereby enabling growth. Next, we demonstrate BMC formation connected with EA catabolism with the production of acetate and ethanol in a molar ratio of 2:1. Flux via the ATP-generating acetate branch causes an apparent redox imbalance due to the reduced regeneration of NAD+ in the ethanol branch resulting in a surplus of NADH. We hypothesize that the redox imbalance is compensated by linking eut BMCs to anaerobic flavin-based extracellular electron transfer (EET). Using L. monocytogenes wild-type, BMC mutant, and EET mutant strains, we demonstrate an interaction between BMCs and EET and provide evidence for a role of Fe3+ as an electron acceptor. Taken together, our results suggest an important role of BMC-dependent EA catabolism in L. monocytogenes growth in anaerobic environments like the human gastrointestinal tract, with a crucial role for the flavin-based EET system in redox balancing.IMPORTANCE Listeria monocytogenes is a foodborne pathogen causing severe illness, and as such, it is crucial to understand the molecular mechanisms contributing to pathogenicity. One carbon source that allows L. monocytogenes to grow in humans is ethanolamine (EA), which is derived from phospholipids present in eukaryotic cell membranes. It is hypothesized that EA utilization occurs in bacterial microcompartments (BMCs), self-assembling subcellular proteinaceous structures and analogs of eukaryotic organelles. Here, we demonstrate that BMC-driven utilization of EA in L. monocytogenes results in increased energy production essential for anaerobic growth. However, exploiting BMCs and the encapsulated metabolic pathways also requires the balancing of oxidative and reductive pathways. We now provide evidence that L. monocytogenes copes with this by linking BMC activity to flavin-based extracellular electron transfer (EET) using iron as an electron acceptor. Our results shed new light on an important molecular mechanism that enables L. monocytogenes to grow using host-derived phospholipid degradation products.
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99911
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Murray GGR, Charlesworth J, Miller EL, Casey MJ, Lloyd CT, Gottschalk M, Tucker AW(D, Welch JJ, Weinert LA. Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence. Mol Biol Evol 2021; 38:1570-1579. [PMID: 33313861 PMCID: PMC8042751 DOI: 10.1093/molbev/msaa323] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). Although genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, that is, host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of nonfunctional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a consistent correlate of pathogenicity in bacteria.
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Affiliation(s)
- Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jane Charlesworth
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Eric L Miller
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Haverford College, Haverford, PA, USA
| | - Michael J Casey
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- School of Mathematical Sciences, University of Southampton, Southampton, United Kingdom
| | - Catrin T Lloyd
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Marcelo Gottschalk
- Département de Pathologie et Microbiologie, Université de Montréal, Montréal, QC, Canada
| | | | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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99912
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Jaber AA, Chowdhury ZM, Bhattacharjee A, Mourin M, Keya CA, Bhuyan ZA. Elucidating molecular mechanisms of acquired resistance to BRAF inhibitors in melanoma using a microfluidic device and deep sequencing. Genomics Inform 2021; 19:e48. [PMID: 35172476 PMCID: PMC8752979 DOI: 10.5808/gi.21040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/05/2021] [Indexed: 11/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes small envelope protein (E) that plays a major role in viral assembly, release, pathogenesis, and host inflammation. Previous studies demonstrated that pyrazine ring containing amiloride analogs inhibit this protein in different types of coronavirus including SARS-CoV-1 small envelope protein E (SARS-CoV-1 E). SARS-CoV-1 E has 93.42% sequence identity with SARS-CoV-2 E and shared a conserved domain NS3/small envelope protein (NS3_envE). Amiloride analog hexamethylene amiloride (HMA) can inhibit SARS-CoV-1 E. Therefore, we performed molecular docking and dynamics simulations to explore whether amiloride analogs are effective in inhibiting SARS-CoV-2 E. To do so, SARS-CoV-1 E and SARS-CoV-2 E proteins were taken as receptors while HMA and 3-amino-5-(azepan-1-yl)-N-(diaminomethylidene)-6-pyrimidin-5-ylpyrazine-2-carboxamide (3A5NP2C) were selected as ligands. Molecular docking simulation showed higher binding affinity scores of HMA and 3A5NP2C for SARS-CoV-2 E than SARS-CoV-1 E. Moreover, HMA and 3A5NP2C engaged more amino acids in SARS-CoV-2 E. Molecular dynamics simulation for 1 μs (1,000 ns) revealed that these ligands could alter the native structure of the proteins and their flexibility. Our study suggests that suitable amiloride analogs might yield a prospective drug against coronavirus disease 2019.
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Affiliation(s)
- Abdullah All Jaber
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh.,Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Arittra Bhattacharjee
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh.,Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka-1349, Bangladesh
| | - Muntahi Mourin
- Department of Microbiology, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh
| | - Zaied Ahmed Bhuyan
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka-1229, Bangladesh
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99913
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Feng W, Han X, Hu H, Chang M, Ding L, Xiang H, Chen Y, Li Y. 2D vanadium carbide MXenzyme to alleviate ROS-mediated inflammatory and neurodegenerative diseases. Nat Commun 2021; 12:2203. [PMID: 33850133 PMCID: PMC8044242 DOI: 10.1038/s41467-021-22278-x] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 02/25/2021] [Indexed: 02/02/2023] Open
Abstract
Reactive oxygen species (ROS) are generated and consumed in living organism for normal metabolism. Paradoxically, the overproduction and/or mismanagement of ROS have been involved in pathogenesis and progression of various human diseases. Here, we reported a two-dimensional (2D) vanadium carbide (V2C) MXene nanoenzyme (MXenzyme) that can mimic up to six naturally-occurring enzymes, including superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), glutathione peroxidase (GPx), thiol peroxidase (TPx) and haloperoxidase (HPO). Based on these enzyme-mimicking properties, the constructed 2D V2C MXenzyme not only possesses high biocompatibility but also exhibits robust in vitro cytoprotection against oxidative stress. Importantly, 2D V2C MXenzyme rebuilds the redox homeostasis without perturbing the endogenous antioxidant status and relieves ROS-induced damage with benign in vivo therapeutic effects, as demonstrated in both inflammation and neurodegeneration animal models. These findings open an avenue to enable the use of MXenzyme as a remedial nanoplatform to treat ROS-mediated inflammatory and neurodegenerative diseases.
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Affiliation(s)
- Wei Feng
- grid.39436.3b0000 0001 2323 5732School of Life Sciences, Shanghai University, Shanghai, P. R. China ,grid.9227.e0000000119573309State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Xiuguo Han
- grid.412987.10000 0004 0630 1330Department of Orthopedic Surgery, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
| | - Hui Hu
- grid.412528.80000 0004 1798 5117Institute of Diagnostic and Interventional Radiology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, P. R. China ,grid.440785.a0000 0001 0743 511XMedmaterial Research Center, Jiangsu University Affiliated People’s Hospital, Zhenjiang, China
| | - Meiqi Chang
- grid.9227.e0000000119573309State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Li Ding
- grid.9227.e0000000119573309State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Huijing Xiang
- grid.39436.3b0000 0001 2323 5732School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Yu Chen
- grid.39436.3b0000 0001 2323 5732School of Life Sciences, Shanghai University, Shanghai, P. R. China ,grid.9227.e0000000119573309State Key Laboratory of High Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Yuehua Li
- grid.412528.80000 0004 1798 5117Institute of Diagnostic and Interventional Radiology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, P. R. China
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99914
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Wu J, Gu J, Shen L, Jia X, Yin Y, Chen Y, Wang S, Mao L. The role of host cell Rab GTPases in influenza A virus infections. Future Microbiol 2021; 16:445-452. [PMID: 33847136 DOI: 10.2217/fmb-2020-0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Influenza A virus (IAV) is a crucial cause of respiratory infections in humans worldwide. Therefore, studies should clarify adaptation mechanisms of IAV and critical factors of the viral pathogenesis in human hosts. GTPases of the Rab family are the largest branch of the Ras-like small GTPase superfamily, and they regulate almost every step during vesicle-mediated trafficking. Evidence has shown that Rab proteins participate in the lifecycle of IAV. In this mini-review, we outline the regulatory mechanisms of different Rab proteins in the lifecycle of IAV. Understanding the role of Rab proteins in IAV infections is important to develop broad-spectrum host-targeted antiviral strategies.
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Affiliation(s)
- Jing Wu
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jiaqi Gu
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Li Shen
- Clinical Laboratory, Zhenjiang Center for Disease Control & Prevention, Jiangsu, China
| | - Xiaonan Jia
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yiqian Yin
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yiwen Chen
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shengjun Wang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Lingxiang Mao
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
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99915
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Zoaiter M, Nasser R, Hage-Sleiman R, Abdel-Sater F, Badran B, Zeaiter Z. Helicobacter pylori outer membrane vesicles induce expression and secretion of oncostatin M in AGS gastric cancer cells. Braz J Microbiol 2021; 52:1057-66. [PMID: 33851342 DOI: 10.1007/s42770-021-00490-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 04/06/2021] [Indexed: 01/01/2023] Open
Abstract
Helicobacter pylori, a human pathogen that colonizes the stomach of 50% of the world's population, is associated with gastritis, gastric adenocarcinoma, and mucosa-associated lymphoid tissue (MALT) lymphoma. Diseases are characterized by severe inflammatory responses in the stomach that are induced by various chemokines and cytokines. Recently, oncostatin M (OSM), an IL-6 family cytokine, was detected in early gastric cancer biopsies. In this study, we showed that Helicobacter pylori induced secretion of OSM and overexpression of its type II receptor OSMRβ (OSM/OSMRβ) in a human gastric adenocarcinoma cell line (AGS) over 24 h of infection. Furthermore, we showed that the induction of OSM and OSMRβ was carried out by heat-sensitive Helicobacter pylori outer membrane vesicle (OMV) protein. Collectively, our results established, for the first time, a direct relation between Helicobacter pylori OMVs and the OSM/OSMRβ signaling axis.
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99916
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Feng S, Hong Z, Zhang G, Li J, Tian GB, Zhou H, Huang X. Mycobacterium PPE31 Contributes to Host Cell Death. Front Cell Infect Microbiol 2021; 11:629836. [PMID: 33928042 PMCID: PMC8078103 DOI: 10.3389/fcimb.2021.629836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/23/2021] [Indexed: 12/03/2022] Open
Abstract
Genome scale mutagenesis identifies many genes required for mycobacterial infectivity and survival, but their contributions and mechanisms of action within the host are poorly understood. Using CRISPR interference, we created a knockdown of ppe31Mm gene in Mycobacterium marinum (M. marinum), which reduced the resistance to acid medium. To further explore the function of PPE31, the ppe31 mutant strain was generated in M. marinum and Mycobacterium tuberculosis (M. tuberculosis), respectively. Macrophages infected with the ppe31Mm mutant strain caused a reduced inflammatory mediator expressions. In addition, macrophages infected with M. marinum Δppe31Mm had decreased host cell death dependent on JNK signaling. Consistent with these results, deletion of ppe31Mtb from M. tuberculosis increased the sensitivity to acid medium and reduced cell death in macrophages. Furthermore, we demonstrate that both ppe31 mutants from M. marinum and M. tuberculosis resulted in reduced survival in macrophages, and the survivability of M. marinum was deceased in zebrafish due to loss of ppe31Mm. Our findings confirm that PPE31 as a virulence associated factor that modulates innate immune responses to mycobacterial infection.
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Affiliation(s)
- Siyuan Feng
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Zhongsi Hong
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China
| | - Guoliang Zhang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Jiachen Li
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Guo-Bao Tian
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Haibo Zhou
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Xi Huang
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.,The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China.,Sino-French Hoffmann Institute of Immunology, College of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
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99917
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Lv L, Gu S, Jiang H, Yan R, Chen Y, Chen Y, Luo R, Huang C, Lu H, Zheng B, Zhang H, Xia J, Tang L, Sheng G, Li L. Gut mycobiota alterations in patients with COVID-19 and H1N1 infections and their associations with clinical features. Commun Biol 2021; 4:480. [PMID: 33850296 PMCID: PMC8044104 DOI: 10.1038/s42003-021-02036-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
The relationship between gut microbes and COVID-19 or H1N1 infections is not fully understood. Here, we compared the gut mycobiota of 67 COVID-19 patients, 35 H1N1-infected patients and 48 healthy controls (HCs) using internal transcribed spacer (ITS) 3-ITS4 sequencing and analysed their associations with clinical features and the bacterial microbiota. Compared to HCs, the fungal burden was higher. Fungal mycobiota dysbiosis in both COVID-19 and H1N1-infected patients was mainly characterized by the depletion of fungi such as Aspergillus and Penicillium, but several fungi, including Candida glabrata, were enriched in H1N1-infected patients. The gut mycobiota profiles in COVID-19 patients with mild and severe symptoms were similar. Hospitalization had no apparent additional effects. In COVID-19 patients, Mucoromycota was positively correlated with Fusicatenibacter, Aspergillus niger was positively correlated with diarrhoea, and Penicillium citrinum was negatively correlated with C-reactive protein (CRP). In H1N1-infected patients, Aspergillus penicilloides was positively correlated with Lachnospiraceae members, Aspergillus was positively correlated with CRP, and Mucoromycota was negatively correlated with procalcitonin. Therefore, gut mycobiota dysbiosis occurs in both COVID-19 patients and H1N1-infected patients and does not improve until the patients are discharged and no longer require medical attention. Lv et al. associate the gut mycobiota with clinical features and the bacterial microbiota by comparing COVID-19 patients to those infected with H1N1 and healthy controls. They find that gut mycobiota dysbiosis occurs in both COVID-19 patients and those infected with H1N1 and that it does not improve until patients no longer require medical attention, providing insights into a better healthcare guideline.
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Affiliation(s)
- Longxian Lv
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Silan Gu
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Huiyong Jiang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ren Yan
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yanfei Chen
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yunbo Chen
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Rui Luo
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Chenjie Huang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Haifeng Lu
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hua Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jiafeng Xia
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lingling Tang
- Department of Infectious Diseases, Shulan (Hangzhou) Hospital, Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Guoping Sheng
- Department of Infectious Diseases, Shulan (Hangzhou) Hospital, Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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99918
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Chen Z, Zhong X, Zheng M, Liu WS, Fei Y, Ding K, Li Y, Liu Y, Chao Y, Tang YT, Wang S, Qiu R. Indicator species drive the key ecological functions of microbiota in a river impacted by acid mine drainage generated by rare earth elements mining in South China. Environ Microbiol 2021; 24:919-937. [PMID: 33848048 DOI: 10.1111/1462-2920.15501] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/03/2021] [Indexed: 01/04/2023]
Abstract
Acid mine drainage (AMD) generated by rare earth elements (REEs) deposits exploration contains high concentrations of REEs, ammonium and sulfates, which is quite different from typical metallic AMD. Currently, microbial responses and ecological functions in REEs-AMD impacted rivers are unknown. Here, 16S rRNA analysis and genome-resolved metagenomics were performed on microbial community collected from a REEs-AMD contaminated river. The results showed that REEs-AMD significantly changed river microbial diversity and shaped unique indicator species (e.g. Thaumarchaeota, Methylophilales, Rhodospirillales and Burkholderiales). The main environmental factors regulating community were pH, ammonium and REEs, among which high concentration of REEs increased REEs-dependent enzyme-encoding genes (XoxF and ExaF/PedH). Additionally, we reconstructed 566 metagenome-assembled genomes covering 70.4% of identifying indicators. Genome-centric analysis revealed that the abundant archaea Thaumarchaeota and Xanthomonadaceae were often involved in nitrification and denitrification, while family Burkholderiaceae were capable of sulfide oxidation coupled with dissimilatory nitrate reduction to ammonium. These indicators play crucial roles in nitrogen and sulfur cycling as well as REEs immobilization in REEs-AMD contaminated rivers. This study confirmed the potential dual effect of REEs on microbial community at the functional gene level. Our investigation on the ecological roles of indicators further provided new insights for the development of REEs-AMD bioremediation.
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Affiliation(s)
- Ziwu Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xi Zhong
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mengyuan Zheng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yingheng Fei
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Kengbo Ding
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yaying Li
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ye Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510275, China.,Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
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99919
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Chiang C, Dvorkin S, Chiang JJ, Potter RB, Gack MU. The Small t Antigen of JC Virus Antagonizes RIG-I-Mediated Innate Immunity by Inhibiting TRIM25's RNA Binding Ability. mBio 2021; 12:e00620-21. [PMID: 33849980 PMCID: PMC8092259 DOI: 10.1128/mbio.00620-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
JC polyomavirus (JCV), a DNA virus that leads to persistent infection in humans, is the causative agent of progressive multifocal leukoencephalopathy, a lethal brain disease that affects immunocompromised individuals. Almost nothing is currently known about how JCV infection is controlled by the innate immune response and, further, whether JCV has evolved mechanisms to antagonize antiviral immunity. Here, we show that the innate immune sensors retinoic acid-inducible gene I (RIG-I) and cGMP-AMP synthase (cGAS) control JCV replication in human astrocytes. We further identify that the small t antigen (tAg) of JCV functions as an interferon (IFN) antagonist by suppressing RIG-I-mediated signal transduction. JCV tAg interacts with the E3 ubiquitin ligase TRIM25, thereby preventing its ability to bind RNA and to induce the K63-linked ubiquitination of RIG-I, which is known to facilitate RIG-I-mediated cytokine responses. Antagonism of RIG-I K63-linked ubiquitination and antiviral signaling is also conserved in the tAg of the related polyomavirus BK virus (BKV). These findings highlight how JCV and BKV manipulate a key innate surveillance pathway, which may stimulate research into designing novel therapies.IMPORTANCE The innate immune response is the first line of defense against viral pathogens, and in turn, many viruses have evolved strategies to evade detection by the host's innate immune surveillance machinery. Investigation of the interplay between viruses and the innate immune response provides valuable insight into potential therapeutic targets against viral infectious diseases. JC polyomavirus (JCV) is associated with a lifelong, persistent infection that can cause a rare neurodegenerative disease, called progressive multifocal leukoencephalopathy, in individuals that are immunosuppressed. The molecular mechanisms of JCV infection and persistence are not well understood, and very little is currently known about the relevance of innate immunity for the control of JCV replication. Here, we define the intracellular innate immune sensors responsible for controlling JCV infection and also demonstrate a novel mechanism by which a JCV-encoded protein acts as an antagonist of the type I interferon-mediated innate immune response.
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Affiliation(s)
- Cindy Chiang
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, Florida, USA
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Steve Dvorkin
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Jessica J Chiang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rachel B Potter
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, Florida, USA
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
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99920
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Kastan JP, Tremblay MW, Brown MC, Trimarco JD, Dobrikova EY, Dobrikov MI, Gromeier M. Enterovirus 2A pro Cleavage of the YTHDF m 6A Readers Implicates YTHDF3 as a Mediator of Type I Interferon-Driven JAK/STAT Signaling. mBio 2021; 12:e00116-21. [PMID: 33849973 DOI: 10.1128/mBio.00116-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Enteroviruses (EV) deploy two proteases that mediate viral polyprotein cleavage and host cell manipulation. Here, we report that EV 2A proteases cleave all three members of the YTHDF protein family, cytosolic N 6-methyladenosine (m6A) "readers" that regulate target mRNA fate. YTHDF protein cleavage occurs very early during infection, before viral translation is detected or cytopathogenic effects are observed. Preemptive YTHDF protein depletion enhanced viral translation and replication but only in cells with restrained viral translation, signs of inefficient 2A protease activity, and protective innate host immune responses. This effect corresponded with repression of interferon (IFN)-stimulated gene (ISG) induction, while type I/III IFN production was not significantly altered. Moreover, YTHDF3 depletion impaired JAK/STAT signaling in cells treated with type I, but not type II, IFN. YTHDF3 depletion's stimulatory effect on viral dynamics was dampened by JAK/STAT blockade and enhanced by type I IFN pretreatment of cells. We propose that EV 2A proteases cleave YTHDF proteins to antagonize ISG induction in infected cells.IMPORTANCE It is believed that ∼7,000 messenger RNAs (mRNAs) are subject to N 6-methyladenosine modification. The biological significance of this remains mysterious. The YTHDF m6A readers are three related proteins with high affinity for m6A-modified mRNA, yet their biological functions remain obscure. We discovered that polio/enteroviruses elicit very early proteolysis of YTHDF1 to 3 in infected cells. Our research demonstrates that YTHDF3 acts as a positive regulator of antiviral JAK/STAT signaling in response to positive single-strand RNA virus infection, enabling type I interferon (IFN)-mediated gene regulatory programs to unfurl in infected cells. Our observation of viral degradation of the YTHDF proteins demonstrates that they are key response modifiers in the innate antiviral immune response.
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99921
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Liu J, Cvirkaite-Krupovic V, Baquero DP, Yang Y, Zhang Q, Shen Y, Krupovic M. Virus-induced cell gigantism and asymmetric cell division in archaea. Proc Natl Acad Sci U S A 2021; 118:e2022578118. [PMID: 33782110 PMCID: PMC8054024 DOI: 10.1073/pnas.2022578118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Archaeal viruses represent one of the most mysterious parts of the global virosphere, with many virus groups sharing no evolutionary relationship to viruses of bacteria or eukaryotes. How these viruses interact with their hosts remains largely unexplored. Here we show that nonlytic lemon-shaped virus STSV2 interferes with the cell cycle control of its host, hyperthermophilic and acidophilic archaeon Sulfolobus islandicus, arresting the cell cycle in the S phase. STSV2 infection leads to transcriptional repression of the cell division machinery, which is homologous to the eukaryotic endosomal sorting complexes required for transport (ESCRT) system. The infected cells grow up to 20-fold larger in size, have 8,000-fold larger volume compared to noninfected cells, and accumulate massive amounts of viral and cellular DNA. Whereas noninfected Sulfolobus cells divide symmetrically by binary fission, the STSV2-infected cells undergo asymmetric division, whereby giant cells release normal-sized cells by budding, resembling the division of budding yeast. Reinfection of the normal-sized cells produces a new generation of giant cells. If the CRISPR-Cas system is present, the giant cells acquire virus-derived spacers and terminate the virus spread, whereas in its absence, the cycle continues, suggesting that CRISPR-Cas is the primary defense system in Sulfolobus against STSV2. Collectively, our results show how an archaeal virus manipulates the cell cycle, transforming the cell into a giant virion-producing factory.
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Affiliation(s)
- Junfeng Liu
- Archaeal Virology Unit, Institut Pasteur, 75015 Paris, France
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, 266237 Qingdao, China
| | | | - Diana P Baquero
- Archaeal Virology Unit, Institut Pasteur, 75015 Paris, France
| | - Yunfeng Yang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, 266237 Qingdao, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500 Kunming, China
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, 266237 Qingdao, China;
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, 75015 Paris, France;
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99922
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Abstract
Plasma membrane integrity is essential for cellular homeostasis. In vivo, cells experience plasma membrane damage from a multitude of stressors in the extra- and intra-cellular environment. To avoid lethal consequences, cells are equipped with repair pathways to restore membrane integrity. Here, we assess plasma membrane damage and repair from a whole-body perspective. We highlight the role of tissue-specific stressors in health and disease and examine membrane repair pathways across diverse cell types. Furthermore, we outline the impact of genetic and environmental factors on plasma membrane integrity and how these contribute to disease pathogenesis in different tissues.
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Affiliation(s)
- Dustin A Ammendolia
- Cell Biology Program, Hospital for Sick Children, 686 Bay Street PGCRL, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - William M Bement
- Center for Quantitative Cell Imaging and Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John H Brumell
- Cell Biology Program, Hospital for Sick Children, 686 Bay Street PGCRL, Toronto, ON, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada. .,Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A1, Canada. .,SickKids IBD Centre, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
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99923
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García-López R, Cornejo-Granados F, Lopez-Zavala AA, Cota-Huízar A, Sotelo-Mundo RR, Gómez-Gil B, Ochoa-Leyva A. OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters. Genes (Basel) 2021; 12:genes12040564. [PMID: 33924545 PMCID: PMC8070570 DOI: 10.3390/genes12040564] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/03/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
The interplay between shrimp immune system, its environment, and microbiota contributes to the organism’s homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of L. vannamei from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method’s choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.
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Affiliation(s)
- Rodrigo García-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
| | - Alonso A. Lopez-Zavala
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora (UNISON), Blvd., Rosales y Luis, Encinas, Hermosillo, Sonora 83000, Mexico;
| | - Andrés Cota-Huízar
- Camarones el Renacimiento S.P.R. de R.I. Justino Rubio 26, Colonia Ejidal, Higuera de Zaragoza, Sinaloa 81330, Mexico;
| | - Rogerio R. Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora 83304, Mexico;
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. Mazatlán, Sinaloa 82100, Mexico;
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
- Correspondence: ; Tel.: +52-777-3291614
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99924
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Lemay-St-Denis C, Diwan SS, Pelletier JN. The Bacterial Genomic Context of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases Highlights an Emerging Threat to Public Health. Antibiotics (Basel) 2021; 10:antibiotics10040433. [PMID: 33924456 PMCID: PMC8103504 DOI: 10.3390/antibiotics10040433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 01/21/2023] Open
Abstract
Type B dihydrofolate reductase (dfrb) genes were identified following the introduction of trimethoprim in the 1960s. Although they intrinsically confer resistance to trimethoprim (TMP) that is orders of magnitude greater than through other mechanisms, the distribution and prevalence of these short (237 bp) genes is unknown. Indeed, this knowledge has been hampered by systematic biases in search methodologies. Here, we investigate the genomic context of dfrbs to gain information on their current distribution in bacterial genomes. Upon searching publicly available databases, we identified 61 sequences containing dfrbs within an analyzable genomic context. The majority (70%) of those sequences also harbor virulence genes and 97% of the dfrbs are found near a mobile genetic element, representing a potential risk for antibiotic resistance genes. We further identified and confirmed the TMP-resistant phenotype of two new members of the family, dfrb10 and dfrb11. Dfrbs are found both in Betaproteobacteria and Gammaproteobacteria, a majority (59%) being in Pseudomonas aeruginosa. Previously labelled as strictly plasmid-borne, we found 69% of dfrbs in the chromosome of pathogenic bacteria. Our results demonstrate that the intrinsically TMP-resistant dfrbs are a potential emerging threat to public health and justify closer surveillance of these genes.
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Affiliation(s)
- Claudèle Lemay-St-Denis
- Department of Biochemistry and Molecular Medecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Sarah-Slim Diwan
- Department of Biochemistry and Molecular Medecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Joelle N Pelletier
- Department of Biochemistry and Molecular Medecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
- Chemistry Department, Université de Montréal, Montréal, QC H2V 0B3, Canada
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99925
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Loftie-Eaton W, Crabtree A, Perry D, Millstein J, Baytosh J, Stalder T, Robison BD, Forney LJ, Top EM. Contagious Antibiotic Resistance: Plasmid Transfer among Bacterial Residents of the Zebrafish Gut. Appl Environ Microbiol 2021; 87:e02735-20. [PMID: 33637574 DOI: 10.1128/AEM.02735-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/20/2021] [Indexed: 01/12/2023] Open
Abstract
By characterizing the trajectories of antibiotic resistance gene transfer in bacterial communities such as the gut microbiome, we will better understand the factors that influence this spread of resistance. Our aim was to investigate the host network of a multidrug resistance broad-host-range plasmid in the culturable gut microbiome of zebrafish. This was done through in vitro and in vivo conjugation experiments with Escherichia coli as the donor of the plasmid pB10::gfp When this donor was mixed with the extracted gut microbiome, only transconjugants of Aeromonas veronii were detected. In separate matings between the same donor and four prominent isolates from the gut microbiome, the plasmid transferred to two of these four isolates, A. veronii and Plesiomonas shigelloides, but not to Shewanella putrefaciens and Vibrio mimicus When these A. veronii and P. shigelloides transconjugants were the donors in matings with the same four isolates, the plasmid now also transferred from A. veronii to S. putrefaciens P. shigelloides was unable to donate the plasmid, and V. mimicus was unable to acquire it. Finally, when the E. coli donor was added in vivo to zebrafish through their food, plasmid transfer was observed in the gut, but only to Achromobacter, a rare member of the gut microbiome. This work shows that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome depends on the donor-recipient species combinations and therefore their spatial arrangement. It also suggests that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.IMPORTANCE To understand how antibiotic resistance plasmids end up in human pathogens, it is crucial to learn how, where, and when they are transferred and maintained in members of bacterial communities such as the gut microbiome. To gain insight into the network of plasmid-mediated antibiotic resistance sharing in the gut microbiome, we investigated the transferability and maintenance of a multidrug resistance plasmid among the culturable bacteria of the zebrafish gut. We show that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome can depend on which species are involved, as some are important nodes in the plasmid-host network and others are dead ends. Our findings also suggest that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.
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99926
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Viotti C, Bach C, Maillard F, Ziegler-Devin I, Mieszkin S, Buée M. Sapwood and heartwood affect differentially bacterial and fungal community structure and successional dynamics during Quercus petraea decomposition. Environ Microbiol 2021; 23:6177-6193. [PMID: 33848050 DOI: 10.1111/1462-2920.15522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
In forests, bacteria and fungi are key players in wood degradation. Still, studies focusing on bacterial and fungal successions during the decomposition process depending on the wood types (i.e. sapwood and heartwood) remain scarce. This study aimed to understand the effect of wood type on the dynamics of microbial ecological guilds in wood decomposition. Using Illumina metabarcoding, bacterial and fungal communities were monitored every 3 months for 3 years from Quercus petraea wood discs placed on forest soil. Wood density and microbial enzymes involved in biopolymer degradation were measured. We observed rapid changes in the bacterial and fungal communities and microbial ecological guilds associated with wood decomposition throughout the experiment. Bacterial and fungal succession dynamics were very contrasted between sapwood and heartwood. The initial microbial communities were quickly replaced by new bacterial and fungal assemblages in the sapwood. Conversely, some initial functional guilds (i.e. endophytes and yeasts) persisted all along the experiment in heartwood and finally became dominant, possibly limiting the development of saprotrophic fungi. Our data also suggested a significant role of bacteria in nitrogen cycle during wood decomposition.
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Affiliation(s)
- Chloé Viotti
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - Cyrille Bach
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - François Maillard
- Department of Plant and Microbial Biology University of Minnesota St. Paul, Saint Paul, Minnesota, 55108, USA
| | | | - Sophie Mieszkin
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
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99927
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Butler AM, Durkin MJ, Keller MR, Ma Y, Dharnidharka VR, Powderly WG, Olsen MA. Risk of antibiotic treatment failure in premenopausal women with uncomplicated urinary tract infection. Pharmacoepidemiol Drug Saf 2021; 30:1360-1370. [PMID: 33783918 DOI: 10.1002/pds.5237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 11/11/2022]
Abstract
PURPOSE Acute uncomplicated urinary tract infections (UTIs) are among the most common indications for antibiotic prescriptions in otherwise healthy women. We compared the risk of treatment failure of antibiotic regimens for outpatient treatment of UTI in real-world practice. METHODS We identified non-pregnant, premenopausal women diagnosed with uncomplicated, lower tract UTI and prescribed an oral antibiotic with activity against common uropathogens. We used propensity score-weighted Kaplan-Meier functions to estimate 30-day risks and risk differences (RD) for pyelonephritis and UTI-related antibiotic prescription switch. RESULTS Of 1 140 602 patients, the distribution of index prescriptions was 44% fluoroquinolones (non-first-line), 28% trimethoprim-sulfamethoxazole (TMP/SMX) (first-line), 24% nitrofurantoin (first-line), 3% narrow-spectrum β-lactams (non-first-line), 1% broad-spectrum β-lactams (non-first-line), and 1% amoxicillin/ampicillin (non-recommended). Compared to the risk of pyelonephritis for nitrofurantoin (0.3%), risks were higher for TMP/SMX (RD, 0.2%; 95% CI, 0.2%-0.2%) and broad-spectrum β-lactams (RD, 0.2%; 95% CI, 0.1%-0.4%). Compared to the risk of prescription switch for nitrofurantoin (12.7%), the risk was higher for TMP/SMX (RD 1.6%; 95% CI 1.3%-1.7%) but similar for broad-spectrum β-lactams (RD -0.7%; 95% CI -1.4%-0.1%) and narrow-spectrum β-lactams (RD -0.3%; 95% CI -0.8%-0.2%). Subgroup analyses suggest TMP/SMX treatment failure may be due in part to increasing uropathogen resistance over time. CONCLUSIONS The risk of treatment failure differed by antibiotic agent, with higher risk associated with TMP/SMX versus nitrofurantoin, and lower or similar risk associated with broad- versus narrow-spectrum β-lactams. Given serious safety warnings for fluoroquinolones, these results suggest that nitrofurantoin may be preferable as the first-line agent for outpatient treatment of uncomplicated UTI.
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Affiliation(s)
- Anne M Butler
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael J Durkin
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Matthew R Keller
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Yinjiao Ma
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Vikas R Dharnidharka
- Department of Pediatrics, Division of Pediatric Nephrology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - William G Powderly
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Margaret A Olsen
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Surgery, Division of Public Health Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
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99928
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Genovese C, D'Angeli F, Bellia F, Distefano A, Spampinato M, Attanasio F, Nicolosi D, Di Salvatore V, Tempera G, Lo Furno D, Mannino G, Milardo F, Li Volti G. In Vitro Antibacterial, Anti-Adhesive and Anti-Biofilm Activities of Krameria lappacea (Dombey) Burdet & B.B. Simpson Root Extract against Methicillin-Resistant Staphylococcus aureus Strains. Antibiotics (Basel) 2021; 10:428. [PMID: 33924336 DOI: 10.3390/antibiotics10040428] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/08/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) represents a serious threat to public health, due to its large variety of pathogenetic mechanisms. Accordingly, the present study aimed to investigate the anti-MRSA activities of Krameria lappacea, a medicinal plant native to South America. Through Ultra-High-Performance Liquid Chromatography coupled with High-Resolution Mass spectrometry, we analyzed the chemical composition of Krameria lappacea root extract (KLRE). The antibacterial activity of KLRE was determined by the broth microdilution method, also including the minimum biofilm inhibitory concentration and minimum biofilm eradication concentration. Besides, we evaluated the effect on adhesion and invasion of human lung carcinoma A549 cell line by MRSA strains. The obtained results revealed an interesting antimicrobial action of this extract, which efficiently inhibit the growth, biofilm formation, adhesion and invasion of MRSA strains. Furthermore, the chemical analysis revealed the presence in the extract of several flavonoid compounds and type-A and type-B proanthocyanidins, which are known for their anti-adhesive effects. Taken together, our findings showed an interesting antimicrobial activity of KLRE, giving an important contribution to the current knowledge on the biological activities of this plant.
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99929
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Welter DK, Ruaud A, Henseler ZM, De Jong HN, van Coeverden de Groot P, Michaux J, Gormezano L, Waters JL, Youngblut ND, Ley RE. Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts. mSystems 2021; 6:e00258-21. [PMID: 33850039 DOI: 10.1128/mSystems.00258-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the phylum Gammaproteobacteria, family Moraxellaceae, the genus Psychrobacter includes strains from a broad ecological distribution including animal bodies as well as sea ice and other nonhost environments. To elucidate the relationship between these ecological niches and Psychrobacter's evolutionary history, we performed tandem genomic analyses with phenotyping of 85 Psychrobacter accessions. Phylogenomic analysis of the family Moraxellaceae reveals that basal members of the Psychrobacter clade are Moraxella spp., a group of often-pathogenic organisms. Psychrobacter exhibited two broad growth patterns in our phenotypic screen: one group that we called the "flexible ecotype" (FE) had the ability to grow between 4 and 37°C, and the other, which we called the "restricted ecotype" (RE), could grow between 4 and 25°C. The FE group includes phylogenetically basal strains, and FE strains exhibit increased transposon copy numbers, smaller genomes, and a higher likelihood to be bile salt resistant. The RE group contains only phylogenetically derived strains and has increased proportions of lipid metabolism and biofilm formation genes, functions that are adaptive to cold stress. In a 16S rRNA gene survey of polar bear fecal samples, we detect both FE and RE strains, but in in vivo colonizations of gnotobiotic mice, only FE strains persist. Our results indicate the ability to grow at 37°C, seemingly necessary for mammalian gut colonization, is an ancestral trait for Psychrobacter, which likely evolved from a pathobiont.IMPORTANCE Host-associated microbes are generally assumed to have evolved from free-living ones. The evolutionary transition of microbes in the opposite direction, from host associated toward free living, has been predicted based on phylogenetic data but not studied in depth. Here, we provide evidence that the genus Psychrobacter, particularly well known for inhabiting low-temperature, high-salt environments such as sea ice, permafrost soils, and frozen foodstuffs, has evolved from a mammalian-associated ancestor. We show that some Psychrobacter strains retain seemingly ancestral genomic and phenotypic traits that correspond with host association while others have diverged to psychrotrophic or psychrophilic lifestyles.
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99930
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Fioriti S, Coccitto SN, Cedraro N, Simoni S, Morroni G, Brenciani A, Mangiaterra G, Vignaroli C, Vezzulli L, Biavasco F, Giovanetti E. Linezolid Resistance Genes in Enterococci Isolated from Sediment and Zooplankton in Two Italian Coastal Areas. Appl Environ Microbiol 2021; 87:e02958-20. [PMID: 33608287 DOI: 10.1128/AEM.02958-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/08/2021] [Indexed: 12/19/2022] Open
Abstract
Linezolid is a last-resort antibiotic for the treatment of severe infections caused by multidrug-resistant Gram-positive organisms; although linezolid resistance remains uncommon, the number of linezolid-resistant enterococci has increased in recent years due to worldwide spread of acquired resistance genes (cfr, optrA, and poxtA) in clinical, animal, and environmental settings. In this study, we investigated the occurrence of linezolid-resistant enterococci in marine samples from two coastal areas in Italy. Isolates grown on florfenicol-supplemented Slanetz-Bartley agar plates were investigated for their carriage of optrA, poxtA, and cfr genes; optrA was found in one Enterococcus faecalis isolate, poxtA was found in three Enterococcus faecium isolates and two Enterococcus hirae isolates, and cfr was not found. Two of the three poxtA-carrying E. faecium isolates and the two E. hirae isolates showed related pulsed-field gel electrophoresis (PFGE) profiles. Two E. faecium isolates belonged to the new sequence type 1710, which clustered in clonal complex 94, encompassing nosocomial strains. S1 PFGE/hybridization assays showed a double (chromosome and plasmid) location of poxtA and a plasmid location of optrA Whole-genome sequencing revealed that poxtA was contained in a Tn6657-like element carried by two plasmids (pEfm-EF3 and pEh-GE2) of similar size, found in different species, and that poxtA was flanked by two copies of IS1216 in both plasmids. In mating experiments, all but one strain (E. faecalis EN3) were able to transfer the poxtA gene to E. faecium 64/3. The occurrence of linezolid resistance genes in enterococci from marine samples is of great concern and highlights the need to improve practices aimed at limiting the transmission of linezolid-resistant strains to humans from environmental reservoirs.IMPORTANCE Linezolid is one of the few antimicrobials available to treat severe infections due to drug-resistant Gram-positive bacteria; therefore, the emergence of linezolid-resistant enterococci carrying transferable resistance determinants is of great concern for public health. Linezolid resistance genes (cfr, optrA, and poxtA), often plasmid located, can be transmitted via horizontal gene transfer and have the potential to spread globally. This study highlights the detection of enterococci carrying linezolid resistance genes from sediment and zooplankton samples from two coastal urban areas in Italy. The presence of clinically relevant resistant bacteria, such as linezolid-resistant enterococci, in marine environments could reflect their spillover from human and/or animal reservoirs and could indicate that coastal seawaters also might represent a source of these resistance genes.
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99931
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Alavi Darazam I, Shokouhi S, Pourhoseingholi MA, Naghibi Irvani SS, Mokhtari M, Shabani M, Amirdosara M, Torabinavid P, Golmohammadi M, Hashemi S, Azimi A, Jafarazadeh Maivan MH, Rezaei O, Zali A, Hajiesmaeili M, Shabanpour Dehbsneh H, Hoseyni Kusha A, Taleb Shoushtari M, Khalili N, Soleymaninia A, Gachkar L, Khoshkar A. Role of interferon therapy in severe COVID-19: the COVIFERON randomized controlled trial. Sci Rep 2021; 11:8059. [PMID: 33850184 DOI: 10.1038/s41598-021-86859-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/17/2021] [Indexed: 12/15/2022] Open
Abstract
Type 1 Interferons (IFNs) have been associated with positive effects on Coronaviruses. Previous studies point towards the superior potency of IFNβ compared to IFNα against viral infections. We conducted a three-armed, individually-randomized, open-label, controlled trial of IFNβ1a and IFNβ1b, comparing them against each other and a control group. Patients were randomly assigned in a 1:1:1 ratio to IFNβ1a (subcutaneous injections of 12,000 IU on days 1, 3, 6), IFNβ1b (subcutaneous injections of 8,000,000 IU on days 1, 3, 6), or the control group. All three arms orally received Lopinavir/Ritonavir (400 mg/100 mg twice a day for ten days) and a single dose of Hydroxychloroquine 400 mg on the first day. Our utilized primary outcome measure was Time To Clinical Improvement (TTCI) defined as the time from enrollment to discharge or a decline of two steps on the clinical seven-step ordinal scale, whichsoever came first. A total of 60 severely ill patients with positive RT-PCR and Chest CT scans underwent randomization (20 patients to each arm). In the Intention-To-Treat population, IFNβ1a was associated with a significant difference against the control group, in the TTCI; (HR; 2.36, 95% CI 1.10–5.17, P-value = 0.031) while the IFNβ1b indicated no significant difference compared with the control; HR; 1.42, (95% CI 0.63–3.16, P-value = 0.395). The median TTCI for both of the intervention groups was five days vs. seven days for the control group. The mortality was numerically lower in both of the intervention groups (20% in the IFNβ1a group and 30% in the IFNβ1b group vs. 45% in the control group). There were no significant differences between the three arms regarding the adverse events. In patients with laboratory-confirmed SARS-CoV-2 infection, as compared with the base therapeutic regiment, the benefit of a significant reduction in TTCI was observed in the IFNβ1a arm. This finding needs further confirmation in larger studies. Trial Registration Number: ClinicalTrials.gov, NCT04343768. (Submitted: 08/04/2020; First Online: 13/04/2020) (Registration Number: NCT04343768).
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99932
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Barros CHN, Hiebner DW, Fulaz S, Vitale S, Quinn L, Casey E. Synthesis and self-assembly of curcumin-modified amphiphilic polymeric micelles with antibacterial activity. J Nanobiotechnology 2021; 19:104. [PMID: 33849570 PMCID: PMC8045376 DOI: 10.1186/s12951-021-00851-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The ubiquitous nature of bacterial biofilms combined with the enhanced resistance towards antimicrobials has led to the development of an increasing number of strategies for biofilm eradication. Such strategies must take into account the existence of extracellular polymeric substances, which obstruct the diffusion of antibiofilm agents and assists in the maintenance of a well-defended microbial community. Within this context, nanoparticles have been studied for their drug delivery efficacy and easily customised surface. Nevertheless, there usually is a requirement for nanocarriers to be used in association with an antimicrobial agent; the intrinsically antimicrobial nanoparticles are most often made of metals or metal oxides, which is not ideal from ecological and biomedical perspectives. Based on this, the use of polymeric micelles as nanocarriers is appealing as they can be easily prepared using biodegradable organic materials. RESULTS In the present work, micelles comprised of poly(lactic-co-glycolic acid) and dextran are prepared and then functionalised with curcumin. The effect of the functionalisation in the micelle's physical properties was elucidated, and the antibacterial and antibiofilm activities were assessed for the prepared polymeric nanoparticles against Pseudomonas spp. cells and biofilms. It was found that the nanoparticles have good penetration into the biofilms, which resulted in enhanced antibacterial activity of the conjugated micelles when compared to free curcumin. Furthermore, the curcumin-functionalised micelles were efficient at disrupting mature biofilms and demonstrated antibacterial activity towards biofilm-embedded cells. CONCLUSION Curcumin-functionalised poly(lactic-co-glycolic acid)-dextran micelles are novel nanostructures with an intrinsic antibacterial activity tested against two Pseudomonas spp. strains that have the potential to be further exploited to deliver a secondary bioactive molecule within its core.
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Affiliation(s)
- Caio H N Barros
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
- National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland
| | - Dishon W Hiebner
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Stephanie Fulaz
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Stefania Vitale
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Laura Quinn
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Eoin Casey
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland.
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99933
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Mok WK, Tan YX, Chen WN. Evaluating the potential of Bacillus subtilis fermented okara as a functional food ingredient through in vitro digestion and fermentation. FOOD BIOTECHNOL 2021. [DOI: 10.1080/08905436.2021.1909615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Wai Kit Mok
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yong Xing Tan
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore, Singapore
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
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99934
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Kong LF, Yan KQ, Xie ZX, He YB, Lin L, Xu HK, Liu SQ, Wang DZ. Metaproteomics Reveals Similar Vertical Distribution of Microbial Transport Proteins in Particulate Organic Matter Throughout the Water Column in the Northwest Pacific Ocean. Front Microbiol 2021; 12:629802. [PMID: 33841356 PMCID: PMC8034268 DOI: 10.3389/fmicb.2021.629802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/18/2021] [Indexed: 11/17/2022] Open
Abstract
Solubilized particulate organic matter (POM) rather than dissolved organic matter (DOM) has been speculated to be the major carbon and energy sources for heterotrophic prokaryotes in the ocean. However, the direct evidence is still lack. Here we characterized microbial transport proteins of POM collected from both euphotic (75 m, deep chlorophyll maximum DCM, and 100 m) and upper-twilight (200 m and 500 m) zones in three contrasting environments in the northwest Pacific Ocean using a metaproteomic approach. The proportion of transport proteins was relatively high at the bottom of the euphotic zone (200 m), indicating that this layer was the most active area of microbe-driven POM remineralization in the water column. In the upper-twilight zone, the predicted substrates of the identified transporters indicated that amino acids, carbohydrates, taurine, inorganic nutrients, urea, biopolymers, and cobalamin were essential substrates for the microbial community. SAR11, Rhodobacterales, Alteromonadales, and Enterobacteriales were the key contributors with the highest expression of transporters. Interestingly, both the taxonomy and function of the microbial communities varied among water layers and sites with different environments; however, the distribution of transporter types and their relevant organic substrates were similar among samples, suggesting that microbial communities took up similar compounds and were functionally redundant in organic matter utilization throughout the water column. The similar vertical distribution of transport proteins from the euphotic zone to the upper twilight zone among the contrasting environments indicated that solubilized POM rather than DOM was the preferable carbon and energy sources for the microbial communities.
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Affiliation(s)
- Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | | | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | | | - Lin Lin
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | | | | | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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99935
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Links MG, Dumonceaux TJ, McCarthy EL, Hemmingsen SM, Topp E, Town JR. CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems. Microorganisms 2021; 9:816. [PMID: 33924343 DOI: 10.3390/microorganisms9040816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.
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99936
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Anzalone A, Di Guardo M, Bella P, Ghadamgahi F, Dimaria G, Zago R, Cirvilleri G, Catara V. Bioprospecting of Beneficial Bacteria Traits Associated With Tomato Root in Greenhouse Environment Reveals That Sampling Sites Impact More Than the Root Compartment. Front Plant Sci 2021; 12:637582. [PMID: 33927735 PMCID: PMC8078776 DOI: 10.3389/fpls.2021.637582] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/10/2021] [Indexed: 05/06/2023]
Abstract
Tomato is subject to several diseases that affect both field- and greenhouse-grown crops. To select cost-effective potential biocontrol agents, we used laboratory throughput screening to identify bacterial strains with versatile characteristics suitable for multipurpose uses. The natural diversity of tomato root-associated bacterial communities was bioprospected under a real-world environment represented by an intensive tomato cultivation area characterized by extraseasonal productions in the greenhouse. Approximately 400 tomato root-associated bacterial isolates, in majority Gram-negative bacteria, were isolated from three compartments: the soil close to the root surface (rhizosphere, R), the root surface (rhizoplane, RP), and the root interior (endorhizosphere, E). A total of 33% of the isolates produced siderophores and were able to solubilize phosphates and grow on NA with 8% NaCl. A total of 30% of the root-associated bacteria showed antagonistic activity against all the tomato pathogens tested, i.e., Clavibacter michiganesis pv. michiganensis, Pseudomonas syringae pv. tomato, Pseudomonas corrugata and Xanthomonas euvesicatoria pv. perforans, and Fusarium oxysporum f. sp. lycopersici. We found that the sampling site rather than the root compartment of isolation influenced bacterial composition in terms of analyzed phenotype. This was demonstrated through a diversity analysis including general characteristics and PGPR traits, as well as biocontrol activity in vitro. Analysis of 16S rRNA gene (rDNA) sequencing of 77 culturable endophytic bacteria that shared multiple beneficial activity revealed a predominance of bacteria in Bacillales, Enterobacteriales, and Pseudomonadales. Their in vitro antagonistic activity showed that Bacillus species were significantly more active than the isolates in the other taxonomic group. In planta activity against phytopathogenic bacteria of a subset of Bacillus and Pseudomonas isolates was also assessed.
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Affiliation(s)
- Alice Anzalone
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Mario Di Guardo
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Farideh Ghadamgahi
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Giulio Dimaria
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | | | - Gabriella Cirvilleri
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
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99937
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Zou M, Ma PP, Liu WS, Liang X, Li XY, Li YZ, Liu BT. Prevalence and Antibiotic Resistance Characteristics of Extraintestinal Pathogenic Escherichia coli among Healthy Chickens from Farms and Live Poultry Markets in China. Animals (Basel) 2021; 11:ani11041112. [PMID: 33924454 PMCID: PMC8070349 DOI: 10.3390/ani11041112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/16/2023] Open
Abstract
Simple Summary Chicken meat has been proved to be a suspected source of extraintestinal pathogenic Escherichia coli (ExPEC), causing several diseases in humans, and bacteria in healthy chickens can contaminate chicken carcasses at the slaughter; however, reports about the prevalence and molecular characteristics of ExPEC in healthy chickens are still rare. In this study, among 926 E. coli isolates from healthy chickens in China, 22 (2.4%) were qualified as ExPEC and these ExPEC isolates were clonally unrelated. A total of six serogroups were identified in this study, with O78 being the most predominant type, and all the six serogroups had been frequently reported in human ExPEC isolates in many countries. All the 22 ExPEC isolates were multidrug-resistant and most isolates carried both blaCTX-M and fosA3 resistance genes. Notably, plasmid-borne colistin resistance gene mcr-1 was identified in six ExPEC isolates, among which two carried additional carbapenemase gene blaNDM, compromising both the efficacies of the two critically important drugs for humans, carbapenems and colistin. These results highlight that healthy chickens can serve as a potential reservoir for multidrug resistant ExPEC isolates, including mcr-1-containing ExPEC. Abstract Chicken products and chickens with colibacillosis are often reported to be a suspected source of extraintestinal pathogenic Escherichia coli (ExPEC) causing several diseases in humans. Such pathogens in healthy chickens can also contaminate chicken carcasses at the slaughter and then are transmitted to humans via food supply; however, reports about the ExPEC in healthy chickens are still rare. In this study, we determined the prevalence and characteristics of ExPEC isolates in healthy chickens in China. A total of 926 E. coli isolates from seven layer farms (371 isolates), one white-feather broiler farm (78 isolates) and 17 live poultry markets (477 isolates from yellow-feather broilers) in 10 cities in China, were isolated and analyzed for antibiotic resistance phenotypes and genotypes. The molecular detection of ExPEC among these healthy chicken E. coli isolates was performed by PCRs, and the serogroups and antibiotic resistance characteristics of ExPEC were also analyzed. Pulsed-field gel electrophoresis (PFGE) and Multilocus sequence typing (MLST) were used to analyze the genetic relatedness of these ExPEC isolates. We found that the resistance rate for each of the 15 antimicrobials tested among E. coli from white-feather broilers was significantly higher than that from brown-egg layers and that from yellow-feather broilers in live poultry markets (p < 0.05). A total of 22 of the 926 E. coli isolates (2.4%) from healthy chickens were qualified as ExPEC, and the detection rate (7.7%, 6/78) of ExPEC among white-feather broilers was significantly higher than that (1.6%, 6/371) from brown-egg layers and that (2.1%, 10/477) from yellow-feather broilers (p < 0.05). PFGE and MLST analysis indicated that clonal dissemination of these ExPEC isolates was unlikely. Serogroup O78 was the most predominant type among the six serogroups identified in this study, and all the six serogroups had been frequently reported in human ExPEC isolates in many countries. All the 22 ExPEC isolates were multidrug-resistant (MDR) and the resistance rates to ampicillin (100%) and sulfamethoxazole-trimethoprim (100%) were the highest, followed by tetracycline (95.5%) and doxycycline (90.9%). blaCTX-M was found in 15 of the 22 ExPEC isolates including 10 harboring additional fosfomycin resistance gene fosA3. Notably, plasmid-borne colistin resistance gene mcr-1 was identified in six ExPEC isolates in this study. Worryingly, two ExPEC isolates were found to carry both mcr-1 and blaNDM, compromising both the efficacies of carbapenems and colistin. The presence of ExPEC isolates in healthy chickens, especially those carrying mcr-1 and/or blaNDM, is alarming and will pose a threat to the health of consumers. To our knowledge, this is the first report of mcr-1-positive ExPEC isolates harboring blaNDM from healthy chickens.
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Affiliation(s)
- Ming Zou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (M.Z.); (P.-P.M.); (W.-S.L.); (X.L.)
| | - Ping-Ping Ma
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (M.Z.); (P.-P.M.); (W.-S.L.); (X.L.)
| | - Wen-Shuang Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (M.Z.); (P.-P.M.); (W.-S.L.); (X.L.)
| | - Xiao Liang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (M.Z.); (P.-P.M.); (W.-S.L.); (X.L.)
| | - Xu-Yong Li
- College of Agronomy, Liaocheng University, Liaocheng 252000, China;
| | - You-Zhi Li
- Shandong Veterinary Drug Quality Inspection Institute, Jinan 250022, China;
| | - Bao-Tao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (M.Z.); (P.-P.M.); (W.-S.L.); (X.L.)
- Correspondence: ; Tel.: +86-532-58957734
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99938
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Sintchenko V, Timms V, Sim E, Rockett R, Bachmann N, O'Sullivan M, Marais B. Microbial Genomics as a Catalyst for Targeted Antivirulence Therapeutics. Front Med (Lausanne) 2021; 8:641260. [PMID: 33928102 PMCID: PMC8076527 DOI: 10.3389/fmed.2021.641260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/17/2021] [Indexed: 01/06/2023] Open
Abstract
Virulence arresting drugs (VAD) are an expanding class of antimicrobial treatment that act to “disarm” rather than kill bacteria. Despite an increasing number of VAD being registered for clinical use, uptake is hampered by the lack of methods that can identify patients who are most likely to benefit from these new agents. The application of pathogen genomics can facilitate the rational utilization of advanced therapeutics for infectious diseases. The development of genomic assessment of VAD targets is essential to support the early stages of VAD diffusion into infectious disease management. Genomic identification and characterization of VAD targets in clinical isolates can augment antimicrobial stewardship and pharmacovigilance. Personalized genomics guided use of VAD will provide crucial policy guidance to regulating agencies, assist hospitals to optimize the use of these expensive medicines and create market opportunities for biotech companies and diagnostic laboratories.
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Affiliation(s)
- Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Verlaine Timms
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - Eby Sim
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Rebecca Rockett
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - Nathan Bachmann
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - Matthew O'Sullivan
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Ben Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Children's Hospital at Westmead, Westmead, NSW, Australia
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99939
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Sokolova AS, Putilova VP, Yarovaya OI, Zybkina AV, Mordvinova ED, Zaykovskaya AV, Shcherbakov DN, Orshanskaya IR, Sinegubova EO, Esaulkova IL, Borisevich SS, Bormotov NI, Shishkina LN, Zarubaev VV, Pyankov OV, Maksyutov RA, Salakhutdinov NF. Synthesis and Antiviral Activity of Camphene Derivatives against Different Types of Viruses. Molecules 2021; 26:2235. [PMID: 33924393 PMCID: PMC8070564 DOI: 10.3390/molecules26082235] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 12/25/2022] Open
Abstract
To date, the 'one bug-one drug' approach to antiviral drug development cannot effectively respond to the constant threat posed by an increasing diversity of viruses causing outbreaks of viral infections that turn out to be pathogenic for humans. Evidently, there is an urgent need for new strategies to develop efficient antiviral agents with broad-spectrum activities. In this paper, we identified camphene derivatives that showed broad antiviral activities in vitro against a panel of enveloped pathogenic viruses, including influenza virus A/PR/8/34 (H1N1), Ebola virus (EBOV), and the Hantaan virus. The lead-compound 2a, with pyrrolidine cycle in its structure, displayed antiviral activity against influenza virus (IC50 = 45.3 µM), Ebola pseudotype viruses (IC50 = 0.12 µM), and authentic EBOV (IC50 = 18.3 µM), as well as against pseudoviruses with Hantaan virus Gn-Gc glycoprotein (IC50 = 9.1 µM). The results of antiviral activity studies using pseudotype viruses and molecular modeling suggest that surface proteins of the viruses required for the fusion process between viral and cellular membranes are the likely target of compound 2a. The key structural fragments responsible for efficient binding are the bicyclic natural framework and the nitrogen atom. These data encourage us to conduct further investigations using bicyclic monoterpenoids as a scaffold for the rational design of membrane-fusion targeting inhibitors.
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Affiliation(s)
- Anastasiya S. Sokolova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent’ev av., 9, 630090 Novosibirsk, Russia; (V.P.P.); (O.I.Y.); (E.D.M.); (N.F.S.)
| | - Valentina P. Putilova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent’ev av., 9, 630090 Novosibirsk, Russia; (V.P.P.); (O.I.Y.); (E.D.M.); (N.F.S.)
| | - Olga I. Yarovaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent’ev av., 9, 630090 Novosibirsk, Russia; (V.P.P.); (O.I.Y.); (E.D.M.); (N.F.S.)
| | - Anastasiya V. Zybkina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Ekaterina D. Mordvinova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent’ev av., 9, 630090 Novosibirsk, Russia; (V.P.P.); (O.I.Y.); (E.D.M.); (N.F.S.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Dmitriy N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Iana R. Orshanskaya
- Pasteur Institute of Epidemiology and Microbiology, 14 Mira str., 197101 St. Petersburg, Russia; (I.R.O.); (E.O.S.); (I.L.E.); (V.V.Z.)
| | - Ekaterina O. Sinegubova
- Pasteur Institute of Epidemiology and Microbiology, 14 Mira str., 197101 St. Petersburg, Russia; (I.R.O.); (E.O.S.); (I.L.E.); (V.V.Z.)
| | - Iana L. Esaulkova
- Pasteur Institute of Epidemiology and Microbiology, 14 Mira str., 197101 St. Petersburg, Russia; (I.R.O.); (E.O.S.); (I.L.E.); (V.V.Z.)
| | - Sophia S. Borisevich
- Laboratory of Chemical Physics, Ufa Institute of Chemistry Ufa Federal Research Center, 71 Pr. Oktyabrya, 450078 Ufa, Russia;
| | - Nikolay I. Bormotov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Larisa N. Shishkina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Vladimir V. Zarubaev
- Pasteur Institute of Epidemiology and Microbiology, 14 Mira str., 197101 St. Petersburg, Russia; (I.R.O.); (E.O.S.); (I.L.E.); (V.V.Z.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Rinat A. Maksyutov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Nariman F. Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent’ev av., 9, 630090 Novosibirsk, Russia; (V.P.P.); (O.I.Y.); (E.D.M.); (N.F.S.)
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99940
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Fleury V, Zekeridou A, Lazarevic V, Gaïa N, Giannopoulou C, Genton L, Cancela J, Girard M, Goldstein R, Bally JF, Mombelli A, Schrenzel J, Burkhard PR. Oral Dysbiosis and Inflammation in Parkinson's Disease. J Parkinsons Dis 2021; 11:619-631. [PMID: 33646178 PMCID: PMC8150470 DOI: 10.3233/jpd-202459] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background: Oral microbiota has largely escaped attention in Parkinson’s disease (PD), despite its pivotal role in maintaining oral and systemic health. Objective: The aim of our study was to examine the composition of the oral microbiota and the degree of oral inflammation in PD. Methods: Twenty PD patients were compared to 20 healthy controls. Neurological, periodontal and dental examinations were performed as well as dental scaling and gingival crevicular fluid sampling for cytokines measurement (interleukine (IL)-1β, IL-6, IL-1 receptor antagonist (RA), interferon-γ and tumor necrosis factor (TNF)-α). Two months later, oral microbiota was sampled from saliva and subgingival dental plaque. A 16S rRNA gene amplicon sequencing was used to assess bacterial communities. Results: PD patients were in the early and mid-stage phases of their disease (Hoehn & Yahr 2–2.5). Dental and periodontal parameters did not differ between groups. The levels of IL-1β and IL-1RA were significantly increased in patients compared to controls with a trend for an increased level of TNF-α in patients. Both saliva and subgingival dental plaque microbiota differed between patients and controls. Streptococcus mutans, Kingella oralis, Actinomyces AFQC_s, Veillonella AFUJ_s, Scardovia, Lactobacillaceae, Negativicutes and Firmicutes were more abundant in patients, whereas Treponema KE332528_s, Lachnospiraceae AM420052_s, and phylum SR1 were less abundant. Conclusion: Our findings show that the oral microbiome is altered in early and mid-stage PD. Although PD patients had good dental and periodontal status, local inflammation was already present in the oral cavity. The relationship between oral dysbiosis, inflammation and the pathogenesis of PD requires further study.
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Affiliation(s)
- Vanessa Fleury
- Faculty of Medicine, University of Geneva, CMU, Geneva, Switzerland.,Division of Neurology, Geneva University Hospitals, Geneva, Switzerland
| | - Alkisti Zekeridou
- University Clinic of Dental Medicine, Division of Periodontology, University of Geneva, Geneva, Switzerland
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Nadia Gaïa
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Catherine Giannopoulou
- University Clinic of Dental Medicine, Division of Periodontology, University of Geneva, Geneva, Switzerland
| | - Laurence Genton
- Clinical Nutrition, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - José Cancela
- University Clinic of Dental Medicine, Division of Periodontology, University of Geneva, Geneva, Switzerland
| | - Myriam Girard
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Rachel Goldstein
- Division of Neurology, Geneva University Hospitals, Geneva, Switzerland
| | - Julien F Bally
- Division of Neurology, Geneva University Hospitals, Geneva, Switzerland
| | - Andrea Mombelli
- University Clinic of Dental Medicine, Division of Periodontology, University of Geneva, Geneva, Switzerland
| | - Jacques Schrenzel
- Faculty of Medicine, University of Geneva, CMU, Geneva, Switzerland.,Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Pierre R Burkhard
- Faculty of Medicine, University of Geneva, CMU, Geneva, Switzerland.,Division of Neurology, Geneva University Hospitals, Geneva, Switzerland
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99941
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Mizutani Y, Uesaka K, Ota A, Calassanzio M, Ratti C, Suzuki T, Fujimori F, Chiba S. De novo Sequencing of Novel Mycoviruses From Fusarium sambucinum: An Attempt on Direct RNA Sequencing of Viral dsRNAs. Front Microbiol 2021; 12:641484. [PMID: 33927702 PMCID: PMC8076516 DOI: 10.3389/fmicb.2021.641484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
An increasing number of viruses are continuously being found in a wide range of organisms, including fungi. Recent studies have revealed a wide viral diversity in microbes and a potential importance of these viruses in the natural environment. Although virus exploration has been accelerated by short-read, high-throughput sequencing (HTS), and viral de novo sequencing is still challenging because of several biological/molecular features such as micro-diversity and secondary structure of RNA genomes. This study conducted de novo sequencing of multiple double-stranded (ds) RNA (dsRNA) elements that were obtained from fungal viruses infecting two Fusarium sambucinum strains, FA1837 and FA2242, using conventional HTS and long-read direct RNA sequencing (DRS). De novo assembly of the read data from both technologies generated near-entire genomic sequence of the viruses, and the sequence homology search and phylogenetic analysis suggested that these represented novel species of the Hypoviridae, Totiviridae, and Mitoviridae families. However, the DRS-based consensus sequences contained numerous indel errors that differed from the HTS consensus sequences, and these errors hampered accurate open reading frame (ORF) prediction. Although with its present performance, the use of DRS is premature to determine viral genome sequences, the DRS-mediated sequencing shows great potential as a user-friendly platform for a one-shot, whole-genome sequencing of RNA viruses due to its long-reading ability and relative structure-tolerant nature.
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Affiliation(s)
- Yukiyoshi Mizutani
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Ayane Ota
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Matteo Calassanzio
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Fumihiro Fujimori
- Graduate School of Humanities and Life Sciences, Tokyo Kasei University, Itabashi, Japan
| | - Sotaro Chiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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99942
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Garcion C, Béven L, Foissac X. Comparison of Current Methods for Signal Peptide Prediction in Phytoplasmas. Front Microbiol 2021; 12:661524. [PMID: 33841387 PMCID: PMC8026896 DOI: 10.3389/fmicb.2021.661524] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
Although phytoplasma studies are still hampered by the lack of axenic cultivation methods, the availability of genome sequences allowed dramatic advances in the characterization of the virulence mechanisms deployed by phytoplasmas, and highlighted the detection of signal peptides as a crucial step to identify effectors secreted by phytoplasmas. However, various signal peptide prediction methods have been used to mine phytoplasma genomes, and no general evaluation of these methods is available so far for phytoplasma sequences. In this work, we compared the prediction performance of SignalP versions 3.0, 4.0, 4.1, 5.0 and Phobius on several sequence datasets originating from all deposited phytoplasma sequences. SignalP 4.1 with specific parameters showed the most exhaustive and consistent prediction ability. However, the configuration of SignalP 4.1 for increased sensitivity induced a much higher rate of false positives on transmembrane domains located at N-terminus. Moreover, sensitive signal peptide predictions could similarly be achieved by the transmembrane domain prediction ability of TMHMM and Phobius, due to the relatedness between signal peptides and transmembrane regions. Beyond the results presented herein, the datasets assembled in this study form a valuable benchmark to compare and evaluate signal peptide predictors in a field where experimental evidence of secretion is scarce. Additionally, this study illustrates the utility of comparative genomics to strengthen confidence in bioinformatic predictions.
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Affiliation(s)
- Christophe Garcion
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Villenave d'Ornon, France
| | - Laure Béven
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Villenave d'Ornon, France
| | - Xavier Foissac
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Villenave d'Ornon, France
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99943
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Chen Z, Shang JL, Hou S, Li T, Li Q, Yang YW, Hess WR, Qiu BS. Genomic and transcriptomic insights into the habitat adaptation of the diazotrophic paddy-field cyanobacterium Nostoc sphaeroides. Environ Microbiol 2021; 23:5802-5822. [PMID: 33848055 DOI: 10.1111/1462-2920.15521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 03/25/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Nitrogen-fixing cyanobacteria are common in paddy fields, one of the most productive wetland ecosystems. Here, we present the complete genome of Nostoc sphaeroides, a paddy-field diazotroph used for food and medicine for more than 1700 years and deciphered the transcriptional regulation during the developmental transition from hormogonia to vegetative filaments with heterocysts. The genome of N. sphaeroides consists of one circular chromosome (6.48 Mb), one of the largest ever reported megaplasmids (2.34 Mb), and seven plasmids. Multiple gene families involved in the adaption to high solar radiation and water fluctuation conditions were found expanded, while genes involved in anoxic adaptation and phosphonate utilization are located on the megaplasmid, suggesting its indispensable role in environmental adaptation. Distinct gene expression patterns were observed during the light-intensity-regulated transition from hormogonia to vegetative filaments, specifically, genes encoding proteins involved in photosynthetic light reaction, carbon fixation, nitrogen metabolism and heterocyst differentiation were significantly upregulated, whereas genes related to cell motility were down-regulated. Our results provide genomic and transcriptomic insights into the adaptation of a filamentous nitrogen-fixing cyanobacterium to the highly dynamic paddy-field habitat, suggesting N. sphaeroides as an excellent system to understand the transition from aquatic to terrestrial habitats and to support sustainable rice production.
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Affiliation(s)
- Zhen Chen
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China.,Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Jin-Long Shang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Shengwei Hou
- Department of Biological Sciences, University of Southern California, CA, Los Angeles, 90089, USA
| | - Tao Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, Hubei, 430072, China
| | - Qi Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, Hubei, 430072, China
| | - Yi-Wen Yang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Bao-Sheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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99944
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Abstract
Viral protein glycosylation represents a successful strategy employed by the parasite to take advantage of host-cell machinery for modification of its own proteins. The resulting glycans have unneglectable roles in viral infection and immune response. The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which presents on the surface of matured virion and mediates viral entry into the host, also undergoes extensive glycosylation to shield it from the human defense system. It is believed that the ongoing COVID-19 pandemic with more than 90,000,000 infections and 1,900,000 deaths is partly due to its successful glycosylation strategy. On the other hand, while glycan patches on S protein have been reported to shield the host immune response by masking "nonself" viral peptides with "self-glycans," the epitopes are also important in eliciting neutralizing antibodies. In this review, we will summarize the roles of S protein glycans in mediating virus-receptor interactions, and in antibody production, as well as indications for vaccine development.
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Affiliation(s)
| | | | - Hongliang Wang
- Department of Pathogen Biology and Immunology, Xi’an Jiaotong University Health Science Center, Xi’an, China
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99945
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Subramanian S, Gorday K, Marcus K, Orellana MR, Ren P, Luo XR, O'Donnell ME, Kuriyan J. Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction. eLife 2021; 10:e66181. [PMID: 33847559 PMCID: PMC8121543 DOI: 10.7554/elife.66181] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/03/2021] [Indexed: 02/06/2023] Open
Abstract
Clamp loaders are AAA+ ATPases that load sliding clamps onto DNA. We mapped the mutational sensitivity of the T4 bacteriophage sliding clamp and clamp loader by deep mutagenesis, and found that residues not involved in catalysis or binding display remarkable tolerance to mutation. An exception is a glutamine residue in the AAA+ module (Gln 118) that is not located at a catalytic or interfacial site. Gln 118 forms a hydrogen-bonded junction in a helical unit that we term the central coupler, because it connects the catalytic centers to DNA and the sliding clamp. A suppressor mutation indicates that hydrogen bonding in the junction is important, and molecular dynamics simulations reveal that it maintains rigidity in the central coupler. The glutamine-mediated junction is preserved in diverse AAA+ ATPases, suggesting that a connected network of hydrogen bonds that links ATP molecules is an essential aspect of allosteric communication in these proteins.
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Affiliation(s)
- Subu Subramanian
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Kent Gorday
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
| | - Kendra Marcus
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Matthew R Orellana
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Peter Ren
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Xiao Ran Luo
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Rockefeller UniversityNew YorkUnited States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
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99946
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Abstract
Motility is important for the survival and dispersal of many bacteria, and it often plays a role during infections. Regulation of bacterial motility by chemical stimuli is well studied, but recent work has added a new dimension to the problem of motility control. The bidirectional flagellar motor of the bacterium Escherichia coli recruits or releases torque-generating units (stator units) in response to changes in load. Here, we show that this mechanosensitive remodeling of the flagellar motor is independent of direction of rotation. Remodeling rate constants in clockwise rotating motors and in counterclockwise rotating motors, measured previously, fall on the same curve if plotted against torque. Increased torque decreases the off rate of stator units from the motor, thereby increasing the number of active stator units at steady state. A simple mathematical model based on observed dynamics provides quantitative insight into the underlying molecular interactions. The torque-dependent remodeling mechanism represents a robust strategy to quickly regulate output (torque) in response to changes in demand (load).
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Affiliation(s)
- Navish Wadhwa
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138;
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142
| | - Yuhai Tu
- T. J. Watson Research Center, IBM, Yorktown Heights, NY 10598
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142
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99947
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Ni Q, Zhang C, Li D, Xu H, Yao Y, Zhang M, Fan X, Zeng B, Yang D, Xie M. Effects of Dietary Alteration on the Gut Microbiome and Metabolome of the Rescued Bengal Slow Loris. Front Microbiol 2021; 12:650991. [PMID: 33841376 PMCID: PMC8024692 DOI: 10.3389/fmicb.2021.650991] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/02/2021] [Indexed: 11/25/2022] Open
Abstract
Bengal slow lorises (Nycticebus bengalensis) are threatened by illegal trade. Subsequently, numerous wild-born individuals are rescued and transferred to rescue centers. Metabonomic analysis of intestinal microbiomes has increasingly played a vital role in evaluating the effects of dietary alteration on the captive status of endangered non-human primates. A synthetic analysis was done to test the differences in gut microbes and fecal metabolites between two dietary groups of Bengal slow lorises across 8 weeks. Dietary interventions led to intra-group convergence and inter-group variation in the composition of intestinal flora, metabolites, and short-chain fatty acids (SCFAs). The control diet, consisting of gums and honey, significantly increased the abundance of some potential probiotics, such as Bifidobacterium and Roseburia, and the concentration of some anti-disease related metabolites. The decrease in some amino acid metabolites in the original group fed without gums was attributed to poor body condition. Some distinct SCFAs found in the control group indicated the dietary alteration herein was fat-restricted but fiber deficient. Cognizant of this, plant exudates and fiber-enriched food supplies should be considered an optimal approach for dietary improvement of the confiscated and captive Bengal slow lorises.
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Affiliation(s)
- Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chen Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Yaan, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaolan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Deying Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Yaan, China
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99948
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Abstract
The molecular mechanisms that help to place the division septum in bacteria is of fundamental importance to ensure cell proliferation and maintenance of cell shape and size. The Min protein system, found in many rod-shaped bacteria, is thought to play a major role in division site selection. Division site selection is a vital process to ensure generation of viable offspring. In many rod-shaped bacteria, a dynamic protein system, termed the Min system, acts as a central regulator of division site placement. The Min system is best studied in Escherichia coli, where it shows a remarkable oscillation from pole to pole with a time-averaged density minimum at midcell. Several components of the Min system are conserved in the Gram-positive model organism Bacillus subtilis. However, in B. subtilis, it is commonly believed that the system forms a stationary bipolar gradient from the cell poles to midcell. Here, we show that the Min system of B. subtilis localizes dynamically to active sites of division, often organized in clusters. We provide physical modeling using measured diffusion constants that describe the observed enrichment of the Min system at the septum. Mathematical modeling suggests that the observed localization pattern of Min proteins corresponds to a dynamic equilibrium state. Our data provide evidence for the importance of ongoing septation for the Min dynamics, consistent with a major role of the Min system in controlling active division sites but not cell pole areas.
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99949
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Nishida A, Miyamoto J, Shimizu H, Kimura I. Gut microbial short-chain fatty acids-mediated olfactory receptor 78 stimulation promotes anorexigenic gut hormone peptide YY secretion in mice. Biochem Biophys Res Commun 2021; 557:48-54. [PMID: 33862459 DOI: 10.1016/j.bbrc.2021.03.167] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 03/30/2021] [Indexed: 02/09/2023]
Abstract
Olfactory receptor 78 (Olfr78), which is also known as a receptor for short-chain fatty acids (SCFAs) produced via gut microbial fermentation from indigestible polysaccharides such as dietary fibers, is expressed in the enteroendocrine cells of the colon. However, the role of Olfr78 in gut hormone secretion remains unknown. Here, we aimed to investigate the function and mechanism of action of Olfr78 in vivo and in vitro. Toward this, we assessed the expression of Olfr78 in several tissues, affinity of Olfr78 to various monocarboxylates, and the secretion of anorexigenic gut hormone peptide YY (PYY) via Olfr78 using various molecular and biochemical techniques. Olfr78 was abundantly expressed in the colon and mouse enteroendocrine cell line STC-1 and showed specific affinity to SCFAs such as acetate and propionate, but not butyrate, in a monocarboxylate ligand screening assay using a heterologous expression system. Acetate promoted PYY secretion in STC-1 cells via Olfr78-protein kinase A signaling, whereas the effects were abolished by Olfr78 RNA interference. Colonic SCFAs production via oral administration of fructo-oligosaccharide significantly increased plasma PYY levels, whereas this effect was abolished in Olfr78-deficient and germ-free mice. These results suggested that the SCFA receptor Olfr78 is important for anti-obesity and anorexigenic effects of the gut microbiota and dietary fibers.
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Affiliation(s)
- Akari Nishida
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan
| | - Junki Miyamoto
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Hidenori Shimizu
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, 100-0004, Japan; Noster Inc., Kamiueno, Muko, Kyoto, 617-0006, Japan
| | - Ikuo Kimura
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-shi, Tokyo 183-8509, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, 100-0004, Japan; Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan.
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Cui WJ, Zhang B, Zhao R, Liu LX, Jiao J, Zhang Z, Tian CF. Lineage-Specific Rewiring of Core Pathways Predating Innovation of Legume Nodules Shapes Symbiotic Efficiency. mSystems 2021; 6:e01299-20. [PMID: 33850043 DOI: 10.1128/mSystems.01299-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The interkingdom coevolution innovated the rhizobium-legume symbiosis. The application of this nitrogen-fixing system in sustainable agriculture is usually impeded by incompatible interactions between partners. However, the progressive evolution of rhizobium-legume compatibility remains elusive. In this work, deletions of rhcV encoding a structural component of the type three secretion system allow related Sinorhizobium strains to nodulate a previously incompatible soybean cultivar (Glycine max). These rhcV mutants show low to medium to high symbiotic efficiency on the same cultivated soybean while being indistinguishable on wild soybean plants (Glycine soja). The dual pantranscriptomics reveals nodule-specific activation of core symbiosis genes of Sinorhizobium and Glycine genes associated with genome duplication events along the chronogram. Unexpectedly, symbiotic efficiency is in line with lineage-dependent transcriptional profiles of core pathways which predate the diversification of Fabaceae and Sinorhizobium. This is supported by further physiological and biochemical experiments. Particularly, low-efficiency nodules show disordered antioxidant activity and low-energy status, which restrict nitrogen fixation activity. Collectively, the ancient core pathways play a crucial role in optimizing the function of later-evolved mutualistic arsenals in the rhizobium-legume coevolution. IMPORTANCE Significant roles of complex extracellular microbiota in environmental adaptation of eukaryotes in ever-changing circumstances have been revealed. Given the intracellular infection ability, facultative endosymbionts can be considered pioneers within complex extracellular microbiota and are ideal organisms for understanding the early stage of interkingdom adaptation. This work reveals that the later innovation of key symbiotic arsenals and the lineage-specific network rewiring in ancient core pathways, predating the divergence of legumes and rhizobia, underline the progressive evolution of rhizobium-legume compatibility. This insight not only is significant for improving the application benefits of rhizobial inoculants in sustainable agriculture but also advances our general understanding of the interkingdom coevolution which is theoretically explored by all host-microbiota interactions.
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