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Al Ofairi BA, Saeed MK, Al-Qubaty M, Abdulkareem AM, Al-Jahrani MA. Diagnostic value of IgG antibody and stool antigen tests for chronic Helicobacter pylori infections in Ibb Governorate, Yemen. Sci Rep 2024; 14:7536. [PMID: 38553516 PMCID: PMC10980813 DOI: 10.1038/s41598-024-58165-w] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/26/2024] [Indexed: 04/02/2024] Open
Abstract
The stool antigen test (SAT) and the serum Helicobacter pylori (H. pylori) IgG antibody assays exhibit significant utility in the clinical diagnosis of H. pylori infection and in distinguishing between acute and chronic infections. The main objective of the current study was to identify the diagnostic value of serum H. pylori IgG antibody and SAT in the detection of H. pylori infections among chronic H. pylori-infected patients residing in Ibb Governorate, Yemen. 200 patients with H. pylori infection, confirmed through positive results in the serum immunochromatographic antibody test, were selected for H. pylori infection confirmation using serum H. pylori IgG antibodies and SAT across diverse hospitals, gastroenterology, and Hepatology clinics in Ibb Governorate. After the selection of patients, blood and stool specimens were obtained from all participants and underwent analysis via the Statistical Package for the Social Sciences (SPSS). The prevalence of H. pylori infection demonstrated variability based on the confirmatory tests, with rates of 54% for SAT and 78.5% for serum H. pylori IgG antibody, contrasting with a 100% prevalence observed in the screening serum immunochromatographic antibody test. Clinically, the study categorized H. pylori infections into four stages, whereby a significant proportion of patients (40.5%) exhibited positivity for both serum H. pylori IgG antibody and SAT, indicative of active chronic infections. The majority of positive cases only manifested serum H. pylori IgG antibody presence (chronic infections) at 38%, whereas 13.5% exclusively tested positive for SAT, corresponding to acute infections. Moreover, 88% of patients did not have either serum H. pylori IgG antibody or SAT (absence of infections) during confirmatory tests. Noteworthy is the study's approach employing multiple tests for H. pylori infection detection, focusing predominantly on chronic infections-prevailing types caused by H. pylori. The results revealed a significant association between serum levels of H. pylori IgG antibody and SAT results with the presence of diverse gastrointestinal symptoms among patients, which increased with long H. pylori infection durations.
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Affiliation(s)
- Bashir A Al Ofairi
- Section of Microbiology, Departement of Biological Sciences, Faculty of Science, Sana'a University, Sana'a, Yemen.
- Departement of Medical Laboratory, Faculty of Medical Sciences, Queen Arwa University, Sana'a, Yemen.
| | - Marwan K Saeed
- Section of Microbiology, Departement of Biological Sciences, Faculty of Science, Sana'a University, Sana'a, Yemen.
- Department of Medical Laboratories, University of Science and Technology, Ibb, Yemen.
| | | | - Ahmed M Abdulkareem
- Section of Microbiology, Departement of Biological Sciences, Faculty of Science, Sana'a University, Sana'a, Yemen
| | - Majed A Al-Jahrani
- Section of Microbiology, Departement of Biological Sciences, Faculty of Science, Sana'a University, Sana'a, Yemen
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Buenestado-Serrano S, Martínez-Lirola M, Herranz-Martín M, Esteban J, Broncano-Lavado A, Molero-Salinas A, Sanz-Pérez A, Blázquez J, Ruedas-López A, Toro C, López-Roa P, Domingo D, Zamarrón E, Ruiz Serrano MJ, Muñoz P, Pérez-Lago L, García de Viedma D. Microevolution, reinfection and highly complex genomic diversity in patients with sequential isolates of Mycobacterium abscessus. Nat Commun 2024; 15:2717. [PMID: 38548737 PMCID: PMC10979023 DOI: 10.1038/s41467-024-46552-w] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/01/2024] [Indexed: 04/01/2024] Open
Abstract
Mycobacterium abscessus is an opportunistic, extensively drug-resistant non-tuberculous mycobacterium. Few genomic studies consider its diversity in persistent infections. Our aim was to characterize microevolution/reinfection events in persistent infections. Fifty-three sequential isolates from 14 patients were sequenced to determine SNV-based distances, assign resistance mutations and characterize plasmids. Genomic analysis revealed 12 persistent cases (0-13 differential SNVs), one reinfection (15,956 SNVs) and one very complex case (23 sequential isolates over 192 months), in which a first period of persistence (58 months) involving the same genotype 1 was followed by identification of a genotype 2 (76 SNVs) in 6 additional alternating isolates; additionally, ten transient genotypes (88-243 SNVs) were found. A macrolide resistance mutation was identified from the second isolate. Despite high diversity, the genotypes shared a common phylogenetic ancestor and some coexisted in the same specimens. Genomic analysis is required to access the true intra-patient complexity behind persistent infections involving M. abscessus.
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Affiliation(s)
- Sergio Buenestado-Serrano
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Doctor Esquerdo, 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C/Doctor Esquerdo, 46, 28007, Madrid, Spain
- Escuela de Doctorado, Universidad de Alcalá, Plaza de San Diego, s/n, 28801, Alcalá de Henares, Madrid, Spain
| | | | - Marta Herranz-Martín
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Doctor Esquerdo, 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C/Doctor Esquerdo, 46, 28007, Madrid, Spain
| | - Jaime Esteban
- Servicio de Microbiología, Instituto de Investigación Sanitaria Fundación Jiménez Díaz-UAM, Hospital Universitario La Fundación Jiménez Díaz, Av. de los Reyes Católicos, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas - CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio Broncano-Lavado
- Servicio de Microbiología, Instituto de Investigación Sanitaria Fundación Jiménez Díaz-UAM, Hospital Universitario La Fundación Jiménez Díaz, Av. de los Reyes Católicos, 28040, Madrid, Spain
| | - Andrea Molero-Salinas
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Doctor Esquerdo, 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C/Doctor Esquerdo, 46, 28007, Madrid, Spain
| | - Amadeo Sanz-Pérez
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Doctor Esquerdo, 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C/Doctor Esquerdo, 46, 28007, Madrid, Spain
| | - Jesús Blázquez
- Department of Microbial Biotechnology, National Center for Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), C/ Darwin, 3, Campus de la Universidad Autónoma-Cantoblanco, 28049, Madrid, Spain
| | - Alba Ruedas-López
- Microbiología y Enfermedades Infecciosas, Hospital Universitario 12 de Octubre, Av. de Córdoba, s/n, 28041, Madrid, Spain
| | - Carlos Toro
- Servicio de Microbiología y Parasitología, Hospital Universitario La Paz - IdiPAZ, Madrid, Spain
| | - Paula López-Roa
- Microbiología y Enfermedades Infecciosas, Hospital Universitario 12 de Octubre, Av. de Córdoba, s/n, 28041, Madrid, Spain
| | - Diego Domingo
- Servicio de Microbiología, Instituto de Investigación Sanitaria, Hospital Universitario La Princesa, Calle de Diego de León, 62, 28006, Madrid, Spain
| | - Ester Zamarrón
- Servicio de Neumología, Hospital Universitario La Paz -IdiPAZ, Madrid, Spain
| | - María Jesús Ruiz Serrano
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Doctor Esquerdo, 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C/Doctor Esquerdo, 46, 28007, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias - CIBERES, Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Doctor Esquerdo, 46, 28007, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C/Doctor Esquerdo, 46, 28007, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias - CIBERES, Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Av. Séneca, 2, 28040, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Doctor Esquerdo, 46, 28007, Madrid, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C/Doctor Esquerdo, 46, 28007, Madrid, Spain.
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, C/Doctor Esquerdo, 46, 28007, Madrid, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), C/Doctor Esquerdo, 46, 28007, Madrid, Spain.
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias - CIBERES, Instituto de Salud Carlos III, Madrid, Spain.
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Stratigaki M, Armirotti A, Ottonello G, Manente S, Traviglia A. Fungal and bacterial species richness in biodeteriorated seventeenth century Venetian manuscripts. Sci Rep 2024; 14:7003. [PMID: 38523163 PMCID: PMC10961312 DOI: 10.1038/s41598-024-57228-2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/15/2024] [Indexed: 03/26/2024] Open
Abstract
Historical paper documents are susceptible to complex degradation processes, including biodeterioration, which can progressively compromise their aesthetic and structural integrity. This study analyses seventeenth century handwritten historical letters stored at the Correr Museum Library in Venice, Italy, exhibiting pronounced signs of biodeterioration. The techniques used encompassed traditional colony isolation on agar plates and proteomics analyses, employing nanoscale liquid chromatography coupled with high-resolution mass spectrometry (nano-LC-MS). Fluorescence microscopy was used for the first time in the historical paper biodeterioration context to supplement the conventional stereoscopic, optical, and scanning electron microscopic imaging techniques. This method enables the visualisation of microorganisms beyond and beneath the paper's surface through their natural intrinsic autofluorescence in a non-invasive and non-destructive way. The results demonstrate a diverse, complex, and abundant microbiota composed of coexisting fungal and bacterial species (Ascomycota, Mucoromycota, Basidiomycota, Proteobacteria, and Actinobacteria), along with mite carcasses, insects, parasites, and possibly protists. Furthermore, this study reveals certain species that were not previously documented in the biodeterioration of historical paper, including human pathogens, such as Histoplasma capsulatum, Brucella, Candida albicans, and species of Aspergillus (A. flavus, A. fumigatus, A. oryzae, A. terreus, A. niger) known to cause infections or produce mycotoxins, posing substantial risk to both artefacts and humans.
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Affiliation(s)
- Maria Stratigaki
- Center for Cultural Heritage Technology (CCHT), Istituto Italiano di Tecnologia, Via Torino 155, 30172, Venice, Italy.
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Giuliana Ottonello
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Sabrina Manente
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy
| | - Arianna Traviglia
- Center for Cultural Heritage Technology (CCHT), Istituto Italiano di Tecnologia, Via Torino 155, 30172, Venice, Italy
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Morimura A, Taniguchi M, Takei H, Sakamoto O, Naono N, Akeda Y, Onozuka D, Yoshimura J, Tomono K, Kutsuna S, Hamaguchi S. Using novel micropore technology combined with artificial intelligence to differentiate Staphylococcus aureus and Staphylococcus epidermidis. Sci Rep 2024; 14:6994. [PMID: 38523156 PMCID: PMC10961322 DOI: 10.1038/s41598-024-55773-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
Methods for identifying bacterial pathogens are broadly categorised into conventional culture-based microbiology, nucleic acid-based tests, and mass spectrometry. The conventional method requires several days to isolate and identify bacteria. Nucleic acid-based tests and mass spectrometry are relatively rapid and reliable, but they require trained technicians. Moreover, mass spectrometry requires expensive equipment. The development of a novel, inexpensive, and simple technique for identifying bacterial pathogens is needed. Through combining micropore technology and assembly machine learning, we developed a novel classifier whose receiver operating characteristic (ROC) curve showed an area under the ROC curve of 0.94, which rapidly differentiated between Staphylococcus aureus and Staphylococcus epidermidis in this proof-of-concept study. Morphologically similar bacteria belonging to an identical genus can be distinguished using our method, which requires no specific training, and may facilitate the diagnosis and treatment of patients with bacterial infections in remote areas and in developing countries.
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Affiliation(s)
- Ayumi Morimura
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Hiroyasu Takei
- Aipore Inc., 26-1 Sakuraoka-cho, Shibuya-ku, Tokyo, 150-8512, Japan
| | - Osamu Sakamoto
- Aipore Inc., 26-1 Sakuraoka-cho, Shibuya-ku, Tokyo, 150-8512, Japan
| | - Norihiko Naono
- Aipore Inc., 26-1 Sakuraoka-cho, Shibuya-ku, Tokyo, 150-8512, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Daisuke Onozuka
- Department of Oral Microbe Control, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jumpei Yoshimura
- Department of Traumatology and Acute Critical Medicine, Graduate School of Medicine, Osaka University, 2-15 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazunori Tomono
- Osaka Institute of Public Health, 1-3-3 Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan
| | - Satoshi Kutsuna
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Oral Microbe Control, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Division of Infection Control and Prevention, Osaka University Hospital, 2-15 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shigeto Hamaguchi
- Division of Infection Control and Prevention, Osaka University Hospital, 2-15 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Transformative Analysis for Human Specimen, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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5
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Hinnu M, Putrinš M, Kogermann K, Kaldalu N, Tenson T. Fluorescent reporters give new insights into antibiotics-induced nonsense and frameshift mistranslation. Sci Rep 2024; 14:6883. [PMID: 38519558 PMCID: PMC10959953 DOI: 10.1038/s41598-024-57597-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/20/2024] [Indexed: 03/25/2024] Open
Abstract
We developed a reporter system based on simultaneous expression of two fluorescent proteins: GFP as a reporter of the capacity of protein synthesis and mutated mScarlet-I as a reporter of translational errors. Because of the unique stop codons or frameshift mutations introduced into the mScarlet-I gene, red fluorescence was produced only after a mistranslation event. These reporters allowed us to estimate mistranslation at a single cell level using either flow cytometry or fluorescence microscopy. We found that laboratory strains of Escherichia coli are more prone to mistranslation compared to the clinical isolates. As relevant for uropathogenic E. coli, growth in human urine elevated translational frameshifting compared to standard laboratory media, whereas different standard media had a small effect on translational fidelity. Antibiotic-induced mistranslation was studied by using amikacin (aminoglycoside family) and azithromycin (macrolide family). Bactericidal amikacin induced preferably stop-codon readthrough at a moderate level. Bacteriostatic azithromycin on the other hand induced both frameshifting and stop-codon readthrough at much higher level. Single cell analysis revealed that fluorescent reporter-protein signal can be lost due to leakage from a fraction of bacteria in the presence of antibiotics, demonstrating the complexity of the antimicrobial activity.
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Affiliation(s)
- Mariliis Hinnu
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia.
| | - Marta Putrinš
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
- Institute of Pharmacy, University of Tartu, 50411, Tartu, Estonia
| | - Karin Kogermann
- Institute of Pharmacy, University of Tartu, 50411, Tartu, Estonia
| | - Niilo Kaldalu
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
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Thakali O, Mercier É, Eid W, Wellman M, Brasset-Gorny J, Overton AK, Knapp JJ, Manuel D, Charles TC, Goodridge L, Arts EJ, Poon AFY, Brown RS, Graber TE, Delatolla R, DeGroot CT. Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation. Sci Rep 2024; 14:3728. [PMID: 38355869 PMCID: PMC10866965 DOI: 10.1038/s41598-024-54319-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 02/11/2024] [Indexed: 02/16/2024] Open
Abstract
Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity of RT-qPCR has been achieved, in part, by monitoring two or more genomic loci of SARS-CoV-2. In Ontario, Canada, the provincial Wastewater Surveillance Initiative reports the average copies of the CDC N1 and N2 loci normalized to the fecal biomarker pepper mild mottle virus. In November 2021, the emergence of the Omicron variant of concern, harboring a C28311T mutation within the CDC N1 probe region, challenged the accuracy of the consensus between the RT-qPCR measurements of the N1 and N2 loci of SARS-CoV-2. In this study, we developed and applied a novel real-time dual loci quality assurance and control framework based on the relative difference between the loci measurements to the City of Ottawa dataset to identify a loss of sensitivity of the N1 assay in the period from July 10, 2022 to January 31, 2023. Further analysis via sequencing and allele-specific RT-qPCR revealed a high proportion of mutations C28312T and A28330G during the study period, both in the City of Ottawa and across the province. It is hypothesized that nucleotide mutations in the probe region, especially A28330G, led to inefficient annealing, resulting in reduction in sensitivity and accuracy of the N1 assay. This study highlights the importance of implementing quality assurance and control criteria to continually evaluate, in near real-time, the accuracy of the signal produced in wastewater surveillance applications that rely on detection of pathogens whose genomes undergo high rates of mutation.
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Affiliation(s)
- Ocean Thakali
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Élisabeth Mercier
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Walaa Eid
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Martin Wellman
- The Ottawa Hospital Research Institute, 1053 Carling Ave, Ottawa, ON, K1Y 4E9, Canada
| | - Julia Brasset-Gorny
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Alyssa K Overton
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Jennifer J Knapp
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Douglas Manuel
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
- Department of Family Medicine, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON, K1N 6N5, Canada
- School of Epidemiology and Public Health, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON, K1N 6N5, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Lawrence Goodridge
- Department of Food Science, Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Art F Y Poon
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - R Stephen Brown
- School of Environmental Studies and Department of Chemistry, Queen's University, Kingston, ON, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher T DeGroot
- Department of Mechanical and Materials Engineering, Western University, London, ON, N6A 5B9, Canada.
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7
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Gao S, Zhao X, Leng Y, Xia Z. Dietary supplementation with inulin improves burn-induced skeletal muscle atrophy by regulating gut microbiota disorders. Sci Rep 2024; 14:2328. [PMID: 38282163 PMCID: PMC10822858 DOI: 10.1038/s41598-024-52066-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 01/12/2024] [Indexed: 01/30/2024] Open
Abstract
Inulin, as a prebiotic, could modulate the gut microbiota. Burn injury leads to gut microbiota disorders and skeletal muscle catabolism. Therefore, whether inulin can improve burn-induced muscle atrophy by regulating microbiota disorders remains unknown. This study aimed to clarify that inulin intake alleviates gut microbiota disorders and skeletal muscle atrophy in burned rats. Rats were divided into the sham group, burn group, prebiotic inulin intervention group, and pseudo-aseptic validation group. A 30% total body surface area (TBSA) third-degree burn wound on dorsal skin was evaluated in all groups except the sham group. Animals in the intervention group received 7 g/L inulin. Animals in the validation group received antibiotic cocktail and inulin treatment. In our study inulin intervention could significantly alleviate the burn-induced skeletal muscle mass decrease and skeletal myoblast cell apoptosis. Inulin intake increased the abundances of Firmicutes and Actinobacteria but decreased the abundance of Proteobacteria. The biosynthesis of amino acids was the most meaningful metabolic pathway distinguishing the inulin intervention group from the burn group, and further mechanistic studies have shown that inulin can promote the phosphorylation of the myogenesis-related proteins PI3K, AKT and P70S6K and activate PI3K/AKT signaling for protein synthesis. In conclusion, inulin alleviated burn induced muscle atrophy through PI3K/AKT signaling and regulated gut microbiota dysbiosis.
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Affiliation(s)
- Shan Gao
- Department of Anaesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaoshuai Zhao
- Department of Anaesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yan Leng
- Department of Anaesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhongyuan Xia
- Department of Anaesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
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8
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Thomas J, Mughal F, Roper KJ, Kotsiri A, Albalawi W, Alshehri A, Reddy YBS, Mukherjee S, Pollakis G, Paxton WA, Hoptroff M. Development of a pseudo-typed virus particle based method to determine the efficacy of virucidal agents. Sci Rep 2024; 14:2174. [PMID: 38273020 PMCID: PMC10810821 DOI: 10.1038/s41598-024-52177-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
The ongoing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic has highlighted the threat that viral outbreaks pose to global health. A key tool in the arsenal to prevent and control viral disease outbreaks is disinfection of equipment and surfaces with formulations that contain virucidal agents (VA). However, assessment of the efficacy of virus inactivation often requires live virus assays or surrogate viruses such as Modified Vaccinia Virus Ankara (MVA), which can be expensive, time consuming and technically challenging. Therefore, we have developed a pseudo-typed virus (PV) based approach to assess the inactivation of enveloped viruses with a fast and quantitative output that can be adapted to emerging viruses. Additionally, we have developed a method to completely remove the cytotoxicity of virucidal agents while retaining the required sensitivity to measure PV infectivity. Our results indicated that the removal of cytotoxicity was an essential step to accurately measure virus inactivation. Further, we demonstrated that there was no difference in susceptibility to virus inactivation between PVs that express the envelopes of HIV-1, SARS-CoV-2, and Influenza A/Indonesia. Therefore, we have developed an effective and safe alternative to live virus assays that enables the rapid assessment of virucidal activity for the development and optimization of virucidal reagents.
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Affiliation(s)
- Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK.
| | - Farah Mughal
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
| | - Kelly J Roper
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
| | - Aurelia Kotsiri
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
| | - Wejdan Albalawi
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
| | - Abdullateef Alshehri
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK
| | - Yugandhar B S Reddy
- Unilever Research & Development Centre, 64 Main Road, Whitefield, Bangalore, Karnataka, 560066, India
| | - Sayandip Mukherjee
- Unilever Research & Development Centre, 64 Main Road, Whitefield, Bangalore, Karnataka, 560066, India
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK.
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology (CIMI), Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, L69 7BE, UK.
| | - Michael Hoptroff
- Unilever Research & Development, Port Sunlight, Bebington, Wirral, CH63 3JW, UK.
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9
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Wang X, Ling R, Peng Y, Qiu W, Chen D. RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA ac 4C modification. Int J Oral Sci 2024; 16:6. [PMID: 38246918 PMCID: PMC10800354 DOI: 10.1038/s41368-023-00276-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Existing studies have underscored the pivotal role of N-acetyltransferase 10 (NAT10) in various cancers. However, the outcomes of protein-protein interactions between NAT10 and its protein partners in head and neck squamous cell carcinoma (HNSCC) remain unexplored. In this study, we identified a significant upregulation of RNA-binding protein with serine-rich domain 1 (RNPS1) in HNSCC, where RNPS1 inhibits the ubiquitination degradation of NAT10 by E3 ubiquitin ligase, zinc finger SWIM domain-containing protein 6 (ZSWIM6), through direct protein interaction, thereby promoting high NAT10 expression in HNSCC. This upregulated NAT10 stability mediates the enhancement of specific tRNA ac4C modifications, subsequently boosting the translation process of genes involved in pathways such as IL-6 signaling, IL-8 signaling, and PTEN signaling that play roles in regulating HNSCC malignant progression, ultimately influencing the survival and prognosis of HNSCC patients. Additionally, we pioneered the development of TRMC-seq, leading to the discovery of novel tRNA-ac4C modification sites, thereby providing a potent sequencing tool for tRNA-ac4C research. Our findings expand the repertoire of tRNA ac4C modifications and identify a role of tRNA ac4C in the regulation of mRNA translation in HNSCC.
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Affiliation(s)
- Xiaochen Wang
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rongsong Ling
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yurong Peng
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weiqiong Qiu
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Demeng Chen
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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10
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Srilohasin P, Warit S, Prammananan T, Smithtikarn S, Kanitpun R, Kaewparuehaschai M, Noradechanon K, Meesawat S, Thakaew N, Sakulwittayasuk N, Kemthong T, Palaga T, Malaivijitnond S, Chaiprasert A. Advancing tuberculosis diagnosis and management in cynomolgus macaques using Xpert MTB/RIF ultra assay. Sci Rep 2024; 14:1518. [PMID: 38233591 PMCID: PMC10794203 DOI: 10.1038/s41598-024-51824-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
The detection and management of Mycobacterium tuberculosis complex (MTBC) infection, the causative agent of tuberculosis (TB), in macaques, including cynomolgus macaques (Macaca fascicularis), are of significant concern in research and regions where macaques coexist with humans or other animals. This study explored the utility of the Xpert MTB/RIF Ultra assay, a widely adopted molecular diagnostic tool to diagnose tuberculosis (TB) in humans, to detect DNA from the Mycobacterium tuberculosis complex in clinical samples obtained from cynomolgus macaques. This investigation involved a comprehensive comparative analysis, integrating established conventional diagnostic methodologies, assessing oropharyngeal-tracheal wash (PW) and buccal swab (BS) specimen types, and follow-up assessments at 3-month, 6-month, and 12-month intervals. Our results demonstrated that the Xpert MTB/RIF Ultra assay was able to detect MTBC in 12 of 316 clinical samples obtained from cynomolgus macaques, presenting a potential advantage over bacterial culture and chest radiographs. The Xpert MTB/RIF Ultra assay exhibited exceptional sensitivity (100%) at the animal level, successfully detecting all macaques positive for M. tuberculosis as confirmed by traditional culture methods. The use of PW samples revealed that 5 positive samples from 99 (5.1%) were recommended for testing, compared to 0 samples from 99 buccal swab (BS) samples (0.0%). In particular, the definitive diagnosis of TB was confirmed in three deceased macaques by MTB culture, which detected the presence of the bacterium in tissue autopsy. Our findings demonstrate that the implementation of the Xpert MTB/RIF Ultra assay, along with prompt isolation measures, effectively reduced active TB cases among cynomolgus macaques over a 12-month period. These findings highlight the advance of the Xpert MTB/RIF Ultra assay in TB diagnosis and its crucial role in preventing potential outbreaks in cynomolgus macaques. With its rapidity, high sensitivity, and specificity, the Xpert MTB/RIF Ultra assay can be highly suitable for use in reference laboratories to confirm TB disease and effectively interrupt TB transmission.
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Affiliation(s)
- Prapaporn Srilohasin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
| | - Saradee Warit
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Thailand
| | - Therdsak Prammananan
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Thailand
| | - Saijai Smithtikarn
- Division of Tuberculosis, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Reka Kanitpun
- National Institute of Animal Health, Bangkok, Thailand
| | | | - Kirana Noradechanon
- Department of National Parks, Wildlife and Plant Conservation, Chachoengsao, Thailand
| | - Suthirote Meesawat
- National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
| | - Nattakan Thakaew
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
| | | | - Taratorn Kemthong
- National Primate Research Center of Thailand-Chulalongkorn University, Saraburi, Thailand
| | - Tanapat Palaga
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Angkana Chaiprasert
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand.
- Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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11
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Abdellati S, Laumen JGE, de Block T, De Baetselier I, Van Den Bossche D, Van Dijck C, Manoharan-Basil SS, Kenyon C. Gonococcal resistance to zoliflodacin could emerge via transformation from commensal Neisseria species. An in-vitro transformation study. Sci Rep 2024; 14:1179. [PMID: 38216602 PMCID: PMC10786824 DOI: 10.1038/s41598-023-49943-z] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
One of the most promising new treatments for gonorrhoea currently in phase 3 clinical trials is zoliflodacin. Studies have found very little resistance to zoliflodacin in currently circulating N. gonorrhoeae strains, and in-vitro experiments demonstrated that it is difficult to induce resistance. However, zoliflodacin resistance may emerge in commensal Neisseria spp., which could then be transferred to N. gonorrhoeae via transformation. In this study, we investigated this commensal-resistance-pathway hypothesis for zoliflodacin. To induce zoliflodacin resistance, ten wild-type susceptible isolates belonging to 5 Neisseria species were serially passaged for up to 48 h on gonococcal agar plates containing increasing zoliflodacin concentrations. Within 7 to 10 days, all strains except N. lactamica, exhibited MICs of ≥ 4 µg/mL, resulting in MIC increase ranging from 8- to 64-fold. The last passaged strains and their baseline were sequenced. We detected mutations previously reported to cause zoliflodacin resistance in GyrB (D429N and S467N), novel mutations in the quinolone resistance determining region (QRDR) (M464R and T472P) and mutations outside the QRDR at amino acid positions 28 and 29 associated with low level resistance (MIC 2 µg/mL). Genomic DNA from the laboratory evolved zoliflodacin-resistant strains was transformed into the respective baseline wild-type strain, resulting in MICs of ≥ 8 µg/mL in most cases. WGS of transformants with decreased zoliflodacin susceptibility revealed presence of the same zoliflodacin resistance determinants as observed in the donor strains. Two inter-species transformation experiments were conducted to investigate whether zoliflodacin resistance determinants of commensal Neisseria spp. could be acquired by N. gonorrhoeae. N. gonorrhoeae strain WHO P was exposed to (i) pooled genomic DNA from the two resistant N. mucosa strains and (ii) a gyrB amplicon of the resistant N. subflava strain 45/1_8. Transformants of both experiments exhibited an MIC of 2 µg/mL and whole genome analysis revealed uptake of the mutations detected in the donor strains. This is the first in-vitro study to report that zoliflodacin resistance can be induced in commensal Neisseria spp. and subsequently transformed into N. gonorrhoeae.
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Affiliation(s)
- Saïd Abdellati
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jolein Gyonne Elise Laumen
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Laboratory of Medical Microbiology, University of Antwerp, Wilrijk, Belgium
| | - Tessa de Block
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Irith De Baetselier
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dorien Van Den Bossche
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christophe Van Dijck
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Laboratory of Medical Microbiology, University of Antwerp, Wilrijk, Belgium
| | | | - Chris Kenyon
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, South Africa
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12
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Lin Y, Liang X, Li Z, Gong T, Ren B, Li Y, Peng X. Omics for deciphering oral microecology. Int J Oral Sci 2024; 16:2. [PMID: 38195684 PMCID: PMC10776764 DOI: 10.1038/s41368-023-00264-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/03/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
The human oral microbiome harbors one of the most diverse microbial communities in the human body, playing critical roles in oral and systemic health. Recent technological innovations are propelling the characterization and manipulation of oral microbiota. High-throughput sequencing enables comprehensive taxonomic and functional profiling of oral microbiomes. New long-read platforms improve genome assembly from complex samples. Single-cell genomics provides insights into uncultured taxa. Advanced imaging modalities including fluorescence, mass spectrometry, and Raman spectroscopy have enabled the visualization of the spatial organization and interactions of oral microbes with increasing resolution. Fluorescence techniques link phylogenetic identity with localization. Mass spectrometry imaging reveals metabolic niches and activities while Raman spectroscopy generates rapid biomolecular fingerprints for classification. Culturomics facilitates the isolation and cultivation of novel fastidious oral taxa using high-throughput approaches. Ongoing integration of these technologies holds the promise of transforming our understanding of oral microbiome assembly, gene expression, metabolites, microenvironments, virulence mechanisms, and microbe-host interfaces in the context of health and disease. However, significant knowledge gaps persist regarding community origins, developmental trajectories, homeostasis versus dysbiosis triggers, functional biomarkers, and strategies to deliberately reshape the oral microbiome for therapeutic benefit. The convergence of sequencing, imaging, cultureomics, synthetic systems, and biomimetic models will provide unprecedented insights into the oral microbiome and offer opportunities to predict, prevent, diagnose, and treat associated oral diseases.
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Affiliation(s)
- Yongwang Lin
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaoyue Liang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhengyi Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Biao Ren
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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13
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Burnie J, Fernandes C, Chaphekar D, Wei D, Ahmed S, Persaud AT, Khader N, Cicala C, Arthos J, Tang VA, Guzzo C. Identification of CD38, CD97, and CD278 on the HIV surface using a novel flow virometry screening assay. Sci Rep 2023; 13:23025. [PMID: 38155248 PMCID: PMC10754950 DOI: 10.1038/s41598-023-50365-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023] Open
Abstract
While numerous cellular proteins in the HIV envelope are known to alter virus infection, methodology to rapidly phenotype the virion surface in a high throughput, single virion manner is lacking. Thus, many human proteins may exist on the virion surface that remain undescribed. Herein, we developed a novel flow virometry screening assay to discover new proteins on the surface of HIV particles. By screening a CD4+ T cell line and its progeny virions, along with four HIV isolates produced in primary cells, we discovered 59 new candidate proteins in the HIV envelope that were consistently detected across diverse HIV isolates. Among these discoveries, CD38, CD97, and CD278 were consistently present at high levels on virions when using orthogonal techniques to corroborate flow virometry results. This study yields new discoveries about virus biology and demonstrates the utility and feasibility of a novel flow virometry assay to phenotype individual virions.
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Affiliation(s)
- Jonathan Burnie
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada
| | - Claire Fernandes
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada
| | - Deepa Chaphekar
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada
| | - Danlan Wei
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shubeen Ahmed
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada
| | - Arvin Tejnarine Persaud
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada
| | - Nawrah Khader
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vera A Tang
- Flow Cytometry and Virometry Core Facility, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada
| | - Christina Guzzo
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, Canada.
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada.
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14
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Ngom SI, Maski S, Rached B, Chouati T, Oliveira Correia L, Juste C, Meylheuc T, Henrissat B, El Fahime E, Amar M, Béra-Maillet C. Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes. Sci Rep 2023; 13:22785. [PMID: 38129471 PMCID: PMC10740013 DOI: 10.1038/s41598-023-49724-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Bacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius, re-identified as Bacillus paralicheniformis and Bacillus licheniformis, using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis. Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.
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Affiliation(s)
- Serigne Inssa Ngom
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Soufiane Maski
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Département de Biologie, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Bahia Rached
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Laboratoire de Chimie-Physique et Biotechnologies des Biomolécules et Matériaux/Equipe Microbiologie Biomolécules et Biotechnologies, Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Taha Chouati
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Lydie Oliveira Correia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, PAPPSO, 78350, Jouy-en-Josas, France
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Thierry Meylheuc
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, MIMA2, 78350, Jouy en Josas, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Elmostafa El Fahime
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Mohamed Amar
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
| | - Christel Béra-Maillet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco.
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15
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Tian J, Deng W, Zhang Z, Xu J, Yang G, Zhao G, Yang S, Jiang W, Gu Y. Discovery and remodeling of Vibrio natriegens as a microbial platform for efficient formic acid biorefinery. Nat Commun 2023; 14:7758. [PMID: 38012202 PMCID: PMC10682008 DOI: 10.1038/s41467-023-43631-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
Formic acid (FA) has emerged as a promising one-carbon feedstock for biorefinery. However, developing efficient microbial hosts for economically competitive FA utilization remains a grand challenge. Here, we discover that the bacterium Vibrio natriegens has exceptional FA tolerance and metabolic capacity natively. This bacterium is remodeled by rewiring the serine cycle and the TCA cycle, resulting in a non-native closed loop (S-TCA) which as a powerful metabolic sink, in combination with laboratory evolution, enables rapid emergence of synthetic strains with significantly improved FA-utilizing ability. Further introduction of a foreign indigoidine-forming pathway into the synthetic V. natriegens strain leads to the production of 29.0 g · L-1 indigoidine and consumption of 165.3 g · L-1 formate within 72 h, achieving a formate consumption rate of 2.3 g · L-1 · h-1. This work provides an important microbial chassis as well as design rules to develop industrially viable microorganisms for FA biorefinery.
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Affiliation(s)
- Jinzhong Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- Xianghu Laboratory, Hangzhou, 311231, China.
| | - Wangshuying Deng
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziwen Zhang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Xu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311215, China
| | | | - Guoping Zhao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sheng Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weihong Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yang Gu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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16
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Li S, Zhao Y, Wu S, Zhang X, Yang B, Tian L, Han X. Regulation of species metabolism in synthetic community systems by environmental pH oscillations. Nat Commun 2023; 14:7507. [PMID: 37980410 PMCID: PMC10657449 DOI: 10.1038/s41467-023-43398-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
Constructing a synthetic community system helps scientist understand the complex interactions among species in a community and its environment. Herein, a two-species community is constructed with species A (artificial cells encapsulating pH-responsive molecules and sucrose) and species B (Saccharomyces cerevisiae), which causes the environment to exhibit pH oscillation behaviour due to the generation and dissipation of CO2. In addition, a three-species community is constructed with species A' (artificial cells containing sucrose and G6P), species B, and species C (artificial cells containing NAD+ and G6PDH). The solution pH oscillation regulates the periodical release of G6P from species A'; G6P then enters species C to promote the metabolic reaction that converts NAD+ to NADH. The location of species A' and B determines the metabolism behaviour in species C in the spatially coded three-species communities with CA'B, CBA', and A'CB patterns. The proposed synthetic community system provides a foundation to construct a more complicated microecosystem.
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Affiliation(s)
- Shubin Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Yingming Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Shuqi Wu
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xiangxiang Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Boyu Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Liangfei Tian
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China.
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17
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Moufti MA, Hamad M, Al Shawa A, Mardini A, Ghebeh S. Efficacy and design requirements of UV light cabinets for disinfection of exchangeable non-sterilizable "dental objects". Sci Rep 2023; 13:19755. [PMID: 37957167 PMCID: PMC10643671 DOI: 10.1038/s41598-023-45481-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
Non-sterilizable items such as prosthodontics items constitute a high risk of transmitting dangerous pathogens, including Coronavirus, between patients and healthcare personnel. Although UV rays are recognized for their germicidal efficacy, large and expensive UV devices previously hindered their adoption in dental offices. During the COVID-19 pandemic, small UV devices became available for domestic use, albeit with varying designs and effectiveness. Our study assesses the disinfection capacity of a UV light cabinet for four dental materials and discusses crucial design features for effective performance. Specimens of each material (silicone impressions, stone cast, acrylic denture base, and indelible pencils) were contaminated with Escherichia coli Bl21, and randomly divided into three study groups: UV device (UVG), impressions disinfection solution (SG), and control (CG). The experiment was repeated thrice, and disinfection efficacy assessed by colony forming units (CFU) count. A 2.5-min UV exposure achieved full disinfection for all materials. Significantly different results were found between groups (p < 0.05, one-way ANOVA, Tukey HSD), except for indelible pencils, where UVG and SG were both highly effective. UV cabinets surpass SG's disinfection efficacy. Compact UV devices can offer affordable, portable, and efficient disinfection for non-sterilizable dental objects, with careful consideration of wavelength, exposure, intensity, and safety.
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Affiliation(s)
- M A Moufti
- College of Dental Medicine, University of Sharjah, P.O.Box 27272, Sharjah, UAE.
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE.
| | - M Hamad
- College of Health Sciences, University of Sharjah, Sharjah, UAE
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
| | - A Al Shawa
- College of Dental Medicine, University of Sharjah, P.O.Box 27272, Sharjah, UAE
| | - A Mardini
- College of Dental Medicine, University of Sharjah, P.O.Box 27272, Sharjah, UAE
| | - S Ghebeh
- College of Dental Medicine, University of Sharjah, P.O.Box 27272, Sharjah, UAE
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18
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Muts RM, den Boer MA, Bardoel BW, Aerts PC, de Haas CJC, Heck AJR, Rooijakkers SHM, Heesterbeek DAC. Artificial surface labelling of Escherichia coli with StrepTagII antigen to study how monoclonal antibodies drive complement-mediated killing. Sci Rep 2023; 13:18836. [PMID: 37914798 PMCID: PMC10620216 DOI: 10.1038/s41598-023-46026-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
Antibodies play a key role in the immune defence against Gram-negative bacteria. After binding to bacterial surface antigens, IgG and IgM can activate the complement system and trigger formation of lytic membrane attack complex (MAC) pores. Molecular studies to compare functional activity of antibodies on bacteria are hampered by the limited availability of well-defined antibodies against bacterial surface antigens. Therefore, we genetically engineered E. coli by expressing the StrepTagII antigen into outer membrane protein X (OmpX) and validated that these engineered bacteria were recognised by anti-StrepTagII antibodies. We then combined this antigen-antibody system with a purified complement assay to avoid interference of serum components and directly compare MAC-mediated bacterial killing via IgG1 and pentameric IgM. While both IgG1 and IgM could induce MAC-mediated killing, we show that IgM has an increased capacity to induce complement-mediated killing of E. coli compared to IgG1. While Fc mutations that enhance IgG clustering after target binding could not improve MAC formation, mutations that cause formation of pre-assembled IgG hexamers enhanced the complement activating capacity of IgG1. Altogether, we here present a system to study antibody-dependent complement activation on E. coli and show IgM's enhanced capacity over IgG to induce complement-mediated lysis of E. coli.
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Affiliation(s)
- Remy M Muts
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomic Center, 3584 CH, Utrecht, The Netherlands
| | - Bart W Bardoel
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Piet C Aerts
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Carla J C de Haas
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomic Center, 3584 CH, Utrecht, The Netherlands
| | - Suzan H M Rooijakkers
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Dani A C Heesterbeek
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands.
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19
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König A, Sadova N, Dornmayr M, Schwarzinger B, Neuhauser C, Stadlbauer V, Wallner M, Woischitzschläger J, Müller A, Tona R, Kofel D, Weghuber J. Combined acid hydrolysis and fermentation improves bioactivity of citrus flavonoids in vitro and in vivo. Commun Biol 2023; 6:1083. [PMID: 37880345 PMCID: PMC10600125 DOI: 10.1038/s42003-023-05424-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023] Open
Abstract
Many bioactive plant compounds, known as phytochemicals, have the potential to improve health. Unfortunately, the bioavailability and bioactivity of phytochemicals such as polyphenolic flavonoids are reduced due to conjugation with sugar moieties. Here, we combine acid hydrolysis and tailored fermentation by lactic acid bacteria (Lactiplantibacillus plantarum) to convert the biologically less active flavonoid glycosides hesperidin and naringin into the more active aglycones hesperetin and naringenin. Using a comprehensive approach, we identify the most effective hydrolysis and fermentation conditions to increase the concentration of the aglycones in citrus extracts. The higher cellular transport and bioactivity of the biotransformed citrus extract are also demonstrated in vitro and in vivo. Superior antioxidant, anti-inflammatory and cell migration activities in vitro, as well as intestinal barrier protecting and antioxidant activities in Drosophila melanogaster are identified. In conclusion, the presented biotransformation approach improves the bioactivity of flavonoids, clearly traced back to the increase in aglycone content.
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Affiliation(s)
- Alice König
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels, 4600, Austria
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, Tulln, 3430, Austria
| | - Nadiia Sadova
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels, 4600, Austria
| | - Marion Dornmayr
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels, 4600, Austria
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, Tulln, 3430, Austria
| | - Bettina Schwarzinger
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels, 4600, Austria
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, Tulln, 3430, Austria
| | - Cathrina Neuhauser
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels, 4600, Austria
| | - Verena Stadlbauer
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels, 4600, Austria
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, Tulln, 3430, Austria
| | - Melanie Wallner
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels, 4600, Austria
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, Tulln, 3430, Austria
| | - Jakob Woischitzschläger
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels, 4600, Austria
| | - Andreas Müller
- TriPlant AG, Industriestrasse 17, Buetzberg, 4922, Switzerland
| | - Rolf Tona
- TriPlant AG, Industriestrasse 17, Buetzberg, 4922, Switzerland
| | - Daniel Kofel
- TriPlant AG, Industriestrasse 17, Buetzberg, 4922, Switzerland
| | - Julian Weghuber
- Center of Excellence Food Technology and Nutrition, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, Wels, 4600, Austria.
- FFoQSI GmbH-Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Technopark 1D, Tulln, 3430, Austria.
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20
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Moliszewska E, Maculewicz D, Stępniewska H. Characterization of three-nucleate Rhizoctonia AG-E based on their morphology and phylogeny. Sci Rep 2023; 13:17328. [PMID: 37833315 PMCID: PMC10575891 DOI: 10.1038/s41598-023-44448-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
The genus Rhizoctonia has been classified into two main groups according to the number of nuclei. Binucleate Rhizoctonia strains have two nuclei in each cell, whereas multinucleate Rhizoctonia fungi were observed to have a variable number of nuclei ranging from 4 to 16 in each cell. In the study, twelve Polish isolates were tested. According to ITS1-5,8S-ITS2 rDNA sequences, the isolates were classified in the AG-E. Their affiliation to AG was confirmed by anastomosis reactions with tester isolates. The number of nuclei was counted with DAPI staining under a fluorescent microscope, and the diameter of the hyphae was also measured. Not all AG-E isolates had the same number of nuclei in their cells: one group among these fungi produced cells with a diverse number of nuclei, usually 3; however, this number ranged from 2 to 4, making the average number of nuclei close to 3. It can be assumed that all isolates with three nuclei belong to this group, which may greatly facilitate the preliminary identification of trinucleate isolates of Rhizoctonia spp. belonging to AG-E. Based on these characters, we call these isolates AG-E-3n isolates. The thiamine requirement is not helpful in classifying and describing the AG-E strains.
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Affiliation(s)
- Ewa Moliszewska
- Faculty of Natural Sciences and Technology, Institute of Environmental Engineering and Biotechnology, University of Opole, Opole, Poland.
| | - Dagna Maculewicz
- Faculty of Health Sciences, Institute of Health Sciences, University of Opole, Opole, Poland
| | - Hanna Stępniewska
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Kraków, Poland
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21
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Li X, Heinemann M. Quantifying intracellular glucose levels when yeast is grown in glucose media. Sci Rep 2023; 13:17066. [PMID: 37816759 PMCID: PMC10564791 DOI: 10.1038/s41598-023-43602-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/26/2023] [Indexed: 10/12/2023] Open
Abstract
In Saccharomyces cerevisiae, intracellular glucose levels impact glucose transport and regulate carbon metabolism via various glucose sensors. To investigate mechanisms of glucose sensing, it is essential to know the intracellular glucose concentrations. Measuring intracellular glucose concentrations, however, is challenging when cells are grown on glucose, as glucose in the water phase around cells or stuck to the cell surface can be carried over during cell sampling and in the following attributed to intracellular glucose, resulting in an overestimation of intracellular glucose concentrations. Using lactose as a carryover marker in the growth medium, we found that glucose carryover originates from both the water phase and from sticking to the cell surface. Using a hexokinase null strain to estimate the glucose carryover from the cell surface, we found that glucose stuck on the cell surface only contributes a minor fraction of the carryover. To correct the glucose carryover, we revisited L-glucose as a carryover marker. Here, we found that L-glucose slowly enters cells. Thus, we added L-glucose to yeast cultures growing on uniformly 13C-labeled D-glucose only shortly before sampling. Using GC-MS to distinguish between the two differently labeled sugars and subtracting the carryover effect, we determined the intracellular glucose concentrations among two yeast strains with distinct kinetics of glucose transport to be at 0.89 mM in the wild-type strain and around 0.24 mM in a mutant with compromised glucose uptake. Together, our study provides insight into the origin of the glucose carryover effect and suggests that L-glucose added to the culture shortly before sampling is a possible method that yet has limitations with regard to measurement accuracy.
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Affiliation(s)
- Xiang Li
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Department of Life Science, Division of Systems and Synthetic Biology, Chalmers University of Technology, Kemigården 1, SE-412 96, Göteborg, Sweden
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
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22
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Huang Y, Sheth RU, Zhao S, Cohen LA, Dabaghi K, Moody T, Sun Y, Ricaurte D, Richardson M, Velez-Cortes F, Blazejewski T, Kaufman A, Ronda C, Wang HH. High-throughput microbial culturomics using automation and machine learning. Nat Biotechnol 2023; 41:1424-1433. [PMID: 36805559 PMCID: PMC10567565 DOI: 10.1038/s41587-023-01674-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/11/2023] [Indexed: 02/22/2023]
Abstract
Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research, and traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive, difficult-to-scale and lack phenotype-genotype integration. Here we describe an open-source high-throughput robotic strain isolation platform for the rapid generation of isolates on demand. We develop a machine learning approach that leverages colony morphology and genomic data to maximize the diversity of microbes isolated and enable targeted picking of specific genera. Application of this platform on fecal samples from 20 humans yields personalized gut microbiome biobanks totaling 26,997 isolates that represented >80% of all abundant taxa. Spatial analysis on >100,000 visually captured colonies reveals cogrowth patterns between Ruminococcaceae, Bacteroidaceae, Coriobacteriaceae and Bifidobacteriaceae families that suggest important microbial interactions. Comparative analysis of 1,197 high-quality genomes from these biobanks shows interesting intra- and interpersonal strain evolution, selection and horizontal gene transfer. This culturomics framework should empower new research efforts to systematize the collection and quantitative analysis of imaging-based phenotypes with high-resolution genomics data for many emerging microbiome studies.
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Affiliation(s)
- Yiming Huang
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Ravi U Sheth
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Shijie Zhao
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Lucas A Cohen
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Kendall Dabaghi
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Thomas Moody
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Yiwei Sun
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Deirdre Ricaurte
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Miles Richardson
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | | | - Andrew Kaufman
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Carlotta Ronda
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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23
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Nakatsuji M, Sato N, Sakamoto S, Watanabe K, Teruuchi Y, Takeuchi M, Inui T, Ishihara H. Non-electrostatic interactions associated with aggregate formation between polyallylamine and Escherichia coli. Sci Rep 2023; 13:14793. [PMID: 37684326 PMCID: PMC10491771 DOI: 10.1038/s41598-023-42120-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/05/2023] [Indexed: 09/10/2023] Open
Abstract
Bacterial aggregation by mixing with polymers is applied as pretreatment to identify pathogens in patients with infectious diseases. However, the detailed interaction between polymers and bacteria has yet to be fully understood. Here, we investigate the interaction between polyallylamine and Escherichia coli by isothermal titration calorimetry. Aggregation was observed at pH 10 and the binding was driven by favorable enthalpic gain such as the electrostatic interaction. Neither aggregation nor the apparent heat of binding was observed at pH 4.0, despite the strong positive charge of polyallylamine. These results suggest that intermolecular repulsive forces of the abundant positive charge of polyallylamine cause an increased loss of conformational entropy by binding. Non-electrostatic interaction plays a critical role for aggregation.
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Affiliation(s)
- Masatoshi Nakatsuji
- Research and Development Headquarters, Nitto Boseki Co., Ltd., 2-4-1 Kojimachi, Chiyoda-ku, Tokyo, 102-8489, Japan
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Natsuki Sato
- Research and Development Headquarters, Nitto Boseki Co., Ltd., 2-4-1 Kojimachi, Chiyoda-ku, Tokyo, 102-8489, Japan
| | - Shiho Sakamoto
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Koji Watanabe
- Specialty Chemicals Division, Nittobo Medical Co., Ltd., 1 Shiojima, Fukuhara, Fukuyama, Koriyama, Fukushima, 963-8061, Japan
| | - Yoko Teruuchi
- Specialty Chemicals Division, Nittobo Medical Co., Ltd., 1 Shiojima, Fukuhara, Fukuyama, Koriyama, Fukushima, 963-8061, Japan
| | - Minoru Takeuchi
- Research and Development Headquarters, Nitto Boseki Co., Ltd., 2-4-1 Kojimachi, Chiyoda-ku, Tokyo, 102-8489, Japan
| | - Takashi Inui
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan.
- Laboratory of Biological Macromolecules, Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan.
| | - Hideki Ishihara
- Research and Development Headquarters, Nitto Boseki Co., Ltd., 2-4-1 Kojimachi, Chiyoda-ku, Tokyo, 102-8489, Japan.
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24
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Li D, Dong H, Cao X, Wang W, Li C. Enhancing photosynthetic CO 2 fixation by assembling metal-organic frameworks on Chlorella pyrenoidosa. Nat Commun 2023; 14:5337. [PMID: 37660048 PMCID: PMC10475011 DOI: 10.1038/s41467-023-40839-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 08/12/2023] [Indexed: 09/04/2023] Open
Abstract
The CO2 concentration at ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is crucial to improve photosynthetic efficiency for biomass yield. However, how to concentrate and transport atmospheric CO2 towards the Rubisco carboxylation is a big challenge. Herein, we report the self-assembly of metal-organic frameworks (MOFs) on the surface of the green alga Chlorella pyrenoidosa that can greatly enhance the photosynthetic carbon fixation. The chemical CO2 concentrating approach improves the apparent photo conversion efficiency to about 1.9 folds, which is up to 9.8% in ambient air from an intrinsic 5.1%. We find that the efficient carbon fixation lies in the conversion of the captured CO2 to the transportable HCO3- species at bio-organic interface. This work demonstrates a chemical approach of concentrating atmospheric CO2 for enhancing biomass yield of photosynthesis.
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Affiliation(s)
- Dingyi Li
- School of Materials Science and Engineering, National Institute for Advanced Materials, Nankai University, Tianjin, China
| | - Hong Dong
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian, China
| | - Xupeng Cao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wangyin Wang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian, China.
| | - Can Li
- School of Materials Science and Engineering, National Institute for Advanced Materials, Nankai University, Tianjin, China.
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian National Laboratory for Clean Energy, Dalian, China.
- University of Chinese Academy of Sciences, Beijing, China.
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25
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Xu Z, Wang Y, Sheng K, Rosenthal R, Liu N, Hua X, Zhang T, Chen J, Song M, Lv Y, Zhang S, Huang Y, Wang Z, Cao T, Shen Y, Jiang Y, Yu Y, Chen Y, Guo G, Yin P, Weitz DA, Wang Y. Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq. Nat Commun 2023; 14:5130. [PMID: 37612289 PMCID: PMC10447461 DOI: 10.1038/s41467-023-40137-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 07/10/2023] [Indexed: 08/25/2023] Open
Abstract
Bacteria colonize almost all parts of the human body and can differ significantly. However, the population level transcriptomics measurements can only describe the average bacteria population behaviors, ignoring the heterogeneity among bacteria. Here, we report a droplet-based high-throughput single-microbe RNA-seq assay (smRandom-seq), using random primers for in situ cDNA generation, droplets for single-microbe barcoding, and CRISPR-based rRNA depletion for mRNA enrichment. smRandom-seq showed a high species specificity (99%), a minor doublet rate (1.6%), a reduced rRNA percentage (32%), and a sensitive gene detection (a median of ~1000 genes per single E. coli). Furthermore, smRandom-seq successfully captured transcriptome changes of thousands of individual E. coli and discovered a few antibiotic resistant subpopulations displaying distinct gene expression patterns of SOS response and metabolic pathways in E. coli population upon antibiotic stress. smRandom-seq provides a high-throughput single-microbe transcriptome profiling tool that will facilitate future discoveries in microbial resistance, persistence, microbe-host interaction, and microbiome research.
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Affiliation(s)
- Ziye Xu
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Yuting Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Kuanwei Sheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Raoul Rosenthal
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA, USA
| | - Nan Liu
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tianyu Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Jiaye Chen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Mengdi Song
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Yuexiao Lv
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Shunji Zhang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Yingjuan Huang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Zhaolun Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Ting Cao
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA, USA
| | - Yifei Shen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Chen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoji Guo
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - David A Weitz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA, USA.
| | - Yongcheng Wang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
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26
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Liu T, Li Y, Koydemir HC, Zhang Y, Yang E, Eryilmaz M, Wang H, Li J, Bai B, Ma G, Ozcan A. Rapid and stain-free quantification of viral plaque via lens-free holography and deep learning. Nat Biomed Eng 2023; 7:1040-1052. [PMID: 37349390 PMCID: PMC10427422 DOI: 10.1038/s41551-023-01057-7] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 05/14/2023] [Indexed: 06/24/2023]
Abstract
A plaque assay-the gold-standard method for measuring the concentration of replication-competent lytic virions-requires staining and usually more than 48 h of runtime. Here we show that lens-free holographic imaging and deep learning can be combined to expedite and automate the assay. The compact imaging device captures phase information label-free at a rate of approximately 0.32 gigapixels per hour per well, covers an area of about 30 × 30 mm2 and a 10-fold larger dynamic range of virus concentration than standard assays, and quantifies the infected area and the number of plaque-forming units. For the vesicular stomatitis virus, the automated plaque assay detected the first cell-lysing events caused by viral replication as early as 5 h after incubation, and in less than 20 h it detected plaque-forming units at rates higher than 90% at 100% specificity. Furthermore, it reduced the incubation time of the herpes simplex virus type 1 by about 48 h and that of the encephalomyocarditis virus by about 20 h. The stain-free assay should be amenable for use in virology research, vaccine development and clinical diagnosis.
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Affiliation(s)
- Tairan Liu
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA
- Bioengineering Department, University of California, Los Angeles, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, USA
| | - Yuzhu Li
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA
- Bioengineering Department, University of California, Los Angeles, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, USA
| | - Hatice Ceylan Koydemir
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Center for Remote Health Technologies and Systems, Texas A&M University, College Station, TX, USA
| | - Yijie Zhang
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA
- Bioengineering Department, University of California, Los Angeles, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, USA
| | - Ethan Yang
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA
- Department of Mathematics, University of California, Los Angeles, CA, USA
| | - Merve Eryilmaz
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA
- Bioengineering Department, University of California, Los Angeles, USA
| | - Hongda Wang
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA
- Bioengineering Department, University of California, Los Angeles, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, USA
| | - Jingxi Li
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA
- Bioengineering Department, University of California, Los Angeles, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, USA
| | - Bijie Bai
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA
- Bioengineering Department, University of California, Los Angeles, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, USA
| | - Guangdong Ma
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA
- School of Physics, Xi'an Jiaotong University, Xi'an, China
| | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, USA.
- Bioengineering Department, University of California, Los Angeles, USA.
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, USA.
- Department of Surgery, University of California, Los Angeles, CA, USA.
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27
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Kotb E, Alabdalall AH, Alghamdi AI, Ababutain IM, Aldakeel SA, Al-Zuwaid SK, Algarudi BM, Algarudi SM, Ahmed AA, Albarrag AM. Screening for chitin degrading bacteria in the environment of Saudi Arabia and characterization of the most potent chitinase from Streptomyces variabilis Am1. Sci Rep 2023; 13:11723. [PMID: 37474592 PMCID: PMC10359409 DOI: 10.1038/s41598-023-38876-2] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/16/2023] [Indexed: 07/22/2023] Open
Abstract
Forty-six promising chitinolytic isolates were recovered during a screening for chitinolytic bacteria in the environment of Saudi Arabia. The top three isolates belonged to the genus Streptomyces. Streptomyces variabilis Am1 was able to excrete the highest amount of chitinases, reaching the maximum at 84 h with 0.5% yeast extract and nitrogen source and 2% galactose as a carbon source. Purification of chitinase by DEAE-Cellulose and Sephadex G75 improved the specific activity to 18.6-fold and the recovery to 23.8% and showed a mass at 56 kDa. The optimal catalysis of the purified chitinase was at 40 °C and pH 8 with high thermostability and pH stability as reflected by a midpoint temperature value of 66.6 °C and stability at pH 4-9. The protein reagents SDS, EDTA, and EGTA significantly inhibited the enzyme and the EDTA-chelated chitinase restored its activity after the addition of Fe2+ ions suggesting a metallo-chitinase type with ferric ions as cofactors. Chitinase exerted high antifungal activity against some phytopathogenic fungi. Interestingly, the tested Streptomyces were able to produce chitosan nanocubes along with chitosan from chitin degradation which may be an additional power in their antifungal activity in nature. This work also reveals the importance of unexplored environments as a pool of promising microorganisms with biotechnological applications.
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Affiliation(s)
- Essam Kotb
- Basic and Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia.
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia.
| | - Amira H Alabdalall
- Basic and Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Azzah I Alghamdi
- Basic and Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Ibtisam M Ababutain
- Basic and Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Sumayh A Aldakeel
- The National Center for Genomic Technology (NCGT), Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Genomic of Infectious Diseases Laboratory, Saudi Center for Disease Prevention and Control, Public Health Authority, Riyadh, Saudi Arabia
| | - Safa K Al-Zuwaid
- Basic and Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Batool M Algarudi
- Basic and Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Sakina M Algarudi
- Basic and Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University (IAU), P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Asmaa A Ahmed
- Department of Statistics, Faculty of Commerce, Al-Azhar University (Girls' Branch), P.O. Box 11751, Cairo, Egypt
| | - Ahmed M Albarrag
- Department of Pathology, School of Medicine, King Saud University, Riyadh, Saudi Arabia
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28
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Oftedal TF, Diep DB. Flow cytometric detection of vancomycin-resistant Enterococcus faecium in urine using fluorescently labelled enterocin K1. Sci Rep 2023; 13:10930. [PMID: 37414859 PMCID: PMC10325980 DOI: 10.1038/s41598-023-38114-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/03/2023] [Indexed: 07/08/2023] Open
Abstract
A urinary tract infection (UTI) occurs when bacteria enter and multiply in the urinary system. The infection is most often caused by enteric bacteria that normally live in the gut, which include Enterococcus faecium. Without antibiotic treatment, UTIs can progress to life-threatening septic shock. Early diagnosis and identification of the pathogen will reduce antibiotic use and improve patient outcomes. In this work, we develop and optimize a cost-effective and rapid (< 40 min) method for detecting E. faecium in urine. The method uses a fluorescently labelled bacteriocin enterocin K1 (FITC-EntK1) that binds specifically to E. faecium and is then detected using a conventional flow cytometer. Using this detection assay, urine containing E. faecium was identified by an increase in the fluorescent signals by 25-73-fold (median fluorescence intensity) compared to control samples containing Escherichia coli or Staphylococcus aureus. The method presented in this work is a proof of concept showing the potential of bacteriocins to act as specific probes for the detection of specific bacteria, such as pathogens, in biological samples.
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Affiliation(s)
- Thomas F Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Dzung B Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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29
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Ohta A, Nishi K, Hirota K, Matsuo Y. Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution. Sci Rep 2023; 13:9785. [PMID: 37328565 PMCID: PMC10275880 DOI: 10.1038/s41598-023-37016-0] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023] Open
Abstract
The study of microbiota has been revolutionized by the development of DNA metabarcoding. This sequence-based approach enables the direct detection of microorganisms without the need for culture and isolation, which significantly reduces analysis time and offers more comprehensive taxonomic profiles across broad phylogenetic lineages. While there has been an accumulating number of researches on bacteria, molecular phylogenetic analysis of fungi still remains challenging due to the lack of standardized tools and the incompleteness of reference databases limiting the accurate and precise identification of fungal taxa. Here, we present a DNA metabarcoding workflow for characterizing fungal microbiota with high taxonomic resolution. This method involves amplifying longer stretches of ribosomal RNA operons and sequencing them using nanopore long-read sequencing technology. The resulting reads were error-polished to generate consensus sequences with 99.5-100% accuracy, which were then aligned against reference genome assemblies. The efficacy of this method was explored using a polymicrobial mock community and patient-derived specimens, demonstrating the marked potential of long-read sequencing combined with consensus calling for accurate taxonomic classification. Our approach offers a powerful tool for the rapid identification of pathogenic fungi and has the promise to significantly improve our understanding of the role of fungi in health and disease.
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Affiliation(s)
- Atsufumi Ohta
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Kenichiro Nishi
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
- Department of Anesthesiology and Intensive Care, Osaka Red Cross Hospital, Osaka, Japan
| | - Kiichi Hirota
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Yoshiyuki Matsuo
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan.
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30
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Wu SC, Jan HM, Vallecillo-Zúniga ML, Rathgeber MF, Stowell CS, Murdock KL, Patel KR, Nakahara H, Stowell CJ, Nahm MH, Arthur CM, Cummings RD, Stowell SR. Whole microbe arrays accurately predict interactions and overall antimicrobial activity of galectin-8 toward distinct strains of Streptococcus pneumoniae. Sci Rep 2023; 13:5324. [PMID: 37005394 PMCID: PMC10067959 DOI: 10.1038/s41598-023-27964-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/10/2023] [Indexed: 04/04/2023] Open
Abstract
Microbial glycan microarrays (MGMs) populated with purified microbial glycans have been used to define the specificity of host immune factors toward microbes in a high throughput manner. However, a limitation of such arrays is that glycan presentation may not fully recapitulate the natural presentation that exists on microbes. This raises the possibility that interactions observed on the array, while often helpful in predicting actual interactions with intact microbes, may not always accurately ascertain the overall affinity of a host immune factor for a given microbe. Using galectin-8 (Gal-8) as a probe, we compared the specificity and overall affinity observed using a MGM populated with glycans harvested from various strains of Streptococcus pneumoniae to an intact microbe microarray (MMA). Our results demonstrate that while similarities in binding specificity between the MGM and MMA are apparent, Gal-8 binding toward the MMA more accurately predicted interactions with strains of S. pneumoniae, including the overall specificity of Gal-8 antimicrobial activity. Taken together, these results not only demonstrate that Gal-8 possesses antimicrobial activity against distinct strains of S. pneumoniae that utilize molecular mimicry, but that microarray platforms populated with intact microbes present an advantageous strategy when exploring host interactions with microbes.
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Affiliation(s)
- Shang-Chuen Wu
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Hau-Ming Jan
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Mary L Vallecillo-Zúniga
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Matthew F Rathgeber
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Caleb S Stowell
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Kaleb L Murdock
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Kashyap R Patel
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Hirotomo Nakahara
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Carter J Stowell
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Moon H Nahm
- Department of Medicine, University of Alabama at Birmingham, 1720 2nd Ave South Birmingham, Alabama, 35294, USA
| | - Connie M Arthur
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Richard D Cummings
- Harvard Glycomics Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Sean R Stowell
- Joint Program in Transfusion Medicine, Department of Pathology, Brigham and Women's Hospital, National Center for Functional Glycomics, 630E New Research Building, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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31
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Cao Z, Zuo W, Wang L, Chen J, Qu Z, Jin F, Dai L. Spatial profiling of microbial communities by sequential FISH with error-robust encoding. Nat Commun 2023; 14:1477. [PMID: 36932092 PMCID: PMC10023729 DOI: 10.1038/s41467-023-37188-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Spatial analysis of microbiomes at single cell resolution with high multiplexity and accuracy has remained challenging. Here we present spatial profiling of a microbiome using sequential error-robust fluorescence in situ hybridization (SEER-FISH), a highly multiplexed and accurate imaging method that allows mapping of microbial communities at micron-scale. We show that multiplexity of RNA profiling in microbiomes can be increased significantly by sequential rounds of probe hybridization and dissociation. Combined with error-correction strategies, we demonstrate that SEER-FISH enables accurate taxonomic identification in complex microbial communities. Using microbial communities composed of diverse bacterial taxa isolated from plant rhizospheres, we apply SEER-FISH to quantify the abundance of each taxon and map microbial biogeography on roots. At micron-scale, we identify clustering of microbial cells from multiple species on the rhizoplane. Under treatment of plant metabolites, we find spatial re-organization of microbial colonization along the root and alterations in spatial association among microbial taxa. Taken together, SEER-FISH provides a useful method for profiling the spatial ecology of complex microbial communities in situ.
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Affiliation(s)
- Zhaohui Cao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lanxiang Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Junyu Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zepeng Qu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fan Jin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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32
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Sun H, Luan G, Ma Y, Lou W, Chen R, Feng D, Zhang S, Sun J, Lu X. Engineered hypermutation adapts cyanobacterial photosynthesis to combined high light and high temperature stress. Nat Commun 2023; 14:1238. [PMID: 36871084 PMCID: PMC9985602 DOI: 10.1038/s41467-023-36964-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Photosynthesis can be impaired by combined high light and high temperature (HLHT) stress. Obtaining HLHT tolerant photoautotrophs is laborious and time-consuming, and in most cases the underlying molecular mechanisms remain unclear. Here, we increase the mutation rates of cyanobacterium Synechococcus elongatus PCC 7942 by three orders of magnitude through combinatory perturbations of the genetic fidelity machinery and cultivation environment. Utilizing the hypermutation system, we isolate Synechococcus mutants with improved HLHT tolerance and identify genome mutations contributing to the adaptation process. A specific mutation located in the upstream non-coding region of the gene encoding a shikimate kinase results in enhanced expression of this gene. Overexpression of the shikimate kinase encoding gene in both Synechococcus and Synechocystis leads to improved HLHT tolerance. Transcriptome analysis indicates that the mutation remodels the photosynthetic chain and metabolism network in Synechococcus. Thus, mutations identified by the hypermutation system are useful for engineering cyanobacteria with improved HLHT tolerance.
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Affiliation(s)
- Huili Sun
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Guodong Luan
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China.
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China.
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China.
- Dalian National Laboratory for Clean Energy, 116023, Dalian, Liaoning, China.
| | - Yifan Ma
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- College of Life Science and Technology, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Wenjing Lou
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
| | - Rongze Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dandan Feng
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
| | - Shanshan Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jiahui Sun
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xuefeng Lu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China.
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China.
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China.
- Dalian National Laboratory for Clean Energy, 116023, Dalian, Liaoning, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, Shandong, China.
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33
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Feng S, Guo L, Wang H, Yang S, Liu H. Bacterial PncA improves diet-induced NAFLD in mice by enabling the transition from nicotinamide to nicotinic acid. Commun Biol 2023; 6:235. [PMID: 36864222 PMCID: PMC9981684 DOI: 10.1038/s42003-023-04613-8] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is crucial for energy metabolism, oxidative stress, DNA damage repair, longevity regulation, and several signaling processes. To date, several NAD+ synthesis pathways have been found in microbiota and mammals, but the potential relationship between gut microbiota and their hosts in regulating NAD+ homeostasis remains largely unknown. Here, we showed that an analog of the first-line tuberculosis drug pyrazinamide, which is converted by nicotinamidase/pyrazinamidase (PncA) to its active form, affected NAD+ level in the intestines and liver of mice and disrupted the homeostasis of gut microbiota. Furthermore, by overexpressing modified PncA of Escherichia coli, NAD+ levels in mouse liver were significantly increased, and diet-induced non-alcoholic fatty liver disease (NAFLD) was ameliorated in mice. Overall, the PncA gene in microbiota plays an important role in regulating NAD+ synthesis in the host, thereby providing a potential target for modulating host NAD+ level.
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Affiliation(s)
- Shengyu Feng
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, 200123, Shanghai, China
| | - Liuling Guo
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, 200123, Shanghai, China
| | - Hao Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, 200123, Shanghai, China
| | - Shanshan Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, 200123, Shanghai, China
| | - Hailiang Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, 200123, Shanghai, China.
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, 832003, Shihezi, China.
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Średnicka P, Roszko MŁ, Popowski D, Kowalczyk M, Wójcicki M, Emanowicz P, Szczepańska M, Kotyrba D, Juszczuk-Kubiak E. Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach. Sci Rep 2023; 13:3026. [PMID: 36810418 DOI: 10.1038/s41598-023-29637-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/08/2023] [Indexed: 02/23/2023] Open
Abstract
Gut microbiota (GM) plays many key functions and helps maintain the host's health. Consequently, the development of GM cultivation under in vitro stimulating physiological conditions has gained extreme interest in different fields. In this study, we evaluated the impact of four culture media: Gut Microbiota Medium (GMM), Schaedler Broth (SM), Fermentation Medium (FM), and Carbohydrate Free Basal Medium (CFBM) on preserving the biodiversity and metabolic activity of human GM in batch in vitro cultures using PMA treatment coupled with 16S rDNA sequencing (PMA-seq) and LC-HR-MS/MS untargeted metabolomics supplemented with GC-MS SCFA profiling. Before the experiments, we determined the possibility of using the pooled faecal samples (MIX) from healthy donors (n = 15) as inoculum to reduce the number of variables and ensure the reproducibility of in vitro cultivation tests. Results showed the suitability of pooling faecal samples for in vitro cultivation study. Non-cultured MIX inoculum was characterized by higher α-diversity (Shannon effective count, and Effective microbial richness) compared to inocula from individual donors. After 24 h of cultivation, a significant effect of culture media composition on GM taxonomic and metabolomic profiles was observed. The SM and GMM had the highest α-diversity (Shannon effective count). The highest number of core ASVs (125) shared with non-cultured MIX inoculum and total SCFAs production was observed in the SM. These results might contribute to the development of standardized protocols for human GM in vitro cultivation by preventing methodological bias in the data.
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Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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Affiliation(s)
- Sage Albright
- Department of Biology, University of Oregon, Eugene, USA
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, USA. .,Institute of Ecology and Evolution, University of Oregon, Eugene, USA.
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36
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Campbell IW, Hullahalli K, Turner JR, Waldor MK. Quantitative dose-response analysis untangles host bottlenecks to enteric infection. Nat Commun 2023; 14:456. [PMID: 36709326 DOI: 10.1038/s41467-023-36162-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/17/2023] [Indexed: 01/30/2023] Open
Abstract
Host bottlenecks prevent many infections before the onset of disease by eliminating invading pathogens. By monitoring the diversity of a barcoded population of the diarrhea causing bacterium Citrobacter rodentium during colonization of its natural host, mice, we determine the number of cells that found the infection by establishing a replicative niche. In female mice the size of the pathogen's founding population scales with dose and is controlled by a severe yet slow-acting bottleneck. Reducing stomach acid or changing host genotype modestly relaxes the bottleneck without breaking the fractional relationship between dose and founders. In contrast, disrupting the microbiota causes the founding population to no longer scale with the size of the inoculum and allows the pathogen to infect at almost any dose, indicating that the microbiota creates the dominant bottleneck. Further, in the absence of competition with the microbiota, the diversity of the pathogen population slowly contracts as the population is overtaken by bacteria having lost the critical virulence island, the locus of enterocyte effacement (LEE). Collectively, our findings reveal that the mechanisms of protection by colonization bottlenecks are reflected in and can be generally defined by the impact of dose on the pathogen's founding population.
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37
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Sugimoto S, Kinjo Y. Instantaneous Clearing of Biofilm (iCBiofilm): an optical approach to revisit bacterial and fungal biofilm imaging. Commun Biol 2023; 6:38. [PMID: 36690667 PMCID: PMC9870912 DOI: 10.1038/s42003-022-04396-4] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 12/21/2022] [Indexed: 01/24/2023] Open
Abstract
Whole-biofilm imaging at single-cell resolution is necessary for system-level analysis of cellular heterogeneity, identification of key matrix component functions and response to immune cells and antimicrobials. To this end, we developed a whole-biofilm clearing and imaging method, termed instantaneous clearing of biofilm (iCBiofilm). iCBiofilm is a simple, rapid, and efficient method involving the immersion of biofilm samples in a refractive index-matching medium, enabling instant whole-biofilm imaging with confocal laser scanning microscopy. We also developed non-fixing iCBiofilm, enabling live and dynamic imaging of biofilm development and actions of antimicrobials. iCBiofilm is applicable for multicolor imaging of fluorescent proteins, immunostained matrix components, and fluorescence labeled cells in biofilms with a thickness of several hundred micrometers. iCBiofilm is scalable from bacterial to fungal biofilms and can be used to observe biofilm-neutrophil interactions. iCBiofilm therefore represents an important advance for examining the dynamics and functions of biofilms and revisiting bacterial and fungal biofilm formation.
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Affiliation(s)
- Shinya Sugimoto
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
| | - Yuki Kinjo
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
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38
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Jin S, Huang Y, Dong C, Bai Y, Pan H, Hu Z. Effects of different straw returning amounts and fertilizer conditions on bacteria of rice's different part in rare earth mining area. Sci Rep 2023; 13:412. [PMID: 36624178 DOI: 10.1038/s41598-023-27553-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Pot experiments were conducted to explore the effects of different rice straw returning soil on the community structure and function of bacteria in rice root, rhizosphere, leaf and phyllosphere under 7 conditions of rice straw combined with different fertilizers respectively. The results showed that: rice straw returning in different ways increased the content of soil pH and K, and reduced the accumulation of N, P and organic matter in soil, and different rice straw returning ways had different effects; rice straw returning reduced dry weight of rice grain, 2% of rice straw returning reduced rice grain greater than that of 1% rice straw returning; The reduction of NP combined fertilization is greater than that of NK combined fertilization and NPK combined fertilization. Except for the decrease of chao_1 index in rice root at maturity, rice straw returning significantly improved the abundance, diversity and evenness of bacteria in rice root, rhizosphere, leaf and phyllosphere. Rice straw returning increased the content of REEs in rice, and 2% of rice straw returning soil increased rare earth element (REE) content in rice grain greater than that of 1% rice straw returning soil. Different ways of rice straw returning soil reduced the abundance of Bacillus, while the abundance of Exiguobacterium in rice leaves was hundreds of times higher than that of the control group, and the genus in leaves was dozens of times higher than that of the control group, 2% of rice straw returning soil increased the abundance of harmful bacteria and pathogens of Acidovorax, Clostridium sensu stricto, Citrobacter, Curtobacterium, and 1% of rice straw returning soil promoted the abundance of nitrogen fixing bacteria, plant growth-promoting bacteria, stress resistant bacteria such as Lactobacillus, Azospira, Acinetobacter, Bradyrhizobium and Acidocella; Environmental factors such as available P, organic matter, total nitrogen, nitrate nitrogen, rare earth element content in rice roots, available K and soil moisture are important factors affecting the community structure of bacteria in rice roots, rhizosphere, leaf and phyllosphere at tillering stage of the rice. pH, REE content in rice roots, shoots, organic matter, total nitrogen, nitrate nitrogen and soil moisture content are the main environmental factors affecting the community structure of bacteria in rice roots, rhizosphere, leaf and phyllosphere at maturity stage of rice. 2% rice straw returning soil promoted the formation of harmful bacteria, which may be an important reason for its significant reduction in the dry weight of rice grains.
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Magagnoli S, Alberoni D, Baffoni L, Martini A, Marini F, Di Gioia D, Mazzon M, Marzadori C, Campanelli G, Burgio G. The ground beetle Pseudoophonus rufipes gut microbiome is influenced by the farm management system. Sci Rep 2022; 12:22638. [PMID: 36587034 PMCID: PMC9805440 DOI: 10.1038/s41598-022-25408-7] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/29/2022] [Indexed: 01/01/2023] Open
Abstract
Intensive conventional farm management, characterized by high agrochemicals input, could alter the composition of microbial communities with potential negative effects on both functional traits and the ecosystem services provided. In this study, we investigated the gut microbial composition of a high ecological relevance carabid Pseudoophonus rufipes, sampled in two fields subjected to conventional and organic management practices. Carabids' gut microbiota was analyzed via qPCR and NGS. Profound differences between the microbial composition of organic and conventional samples were detected: the abundance of Tenericutes and Proteobacteria was significant higher in organic and conventional samples, respectively. Spiroplasmataceae and Bifidobacteriaceae families were significantly more abundant in samples from organic management, while Enterococcaceae, Morganellaceae and Yersiniaceae were more abundant in samples from conventional management. The diverse gut microbial composition of insects between the two management systems is related to the pressure of environmental stressors and it may representing an important bioindication of ecological functions and services provided by a carabid species.
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Affiliation(s)
- Serena Magagnoli
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Daniele Alberoni
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Loredana Baffoni
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Antonio Martini
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Francesca Marini
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Diana Di Gioia
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Martina Mazzon
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Claudio Marzadori
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Gabriele Campanelli
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia – Centro di ricerca Orticoltura e Florovivaismo (CREA -OF) - Sede di Monsampolo del Tronto, via Salaria 1, 63077 Monsampolo del Tronto, Italy
| | - Giovanni Burgio
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
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40
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Zeng Q, She L, Yuan H, Luo Y, Wang R, Mao W, Wang W, She Y, Wang C, Shi M, Cao T, Gan R, Li Y, Zhou J, Qian W, Hu S, Wang Y, Zheng X, Li K, Bai L, Pan X, Xi Z. A standalone incompatible insect technique enables mosquito suppression in the urban subtropics. Commun Biol 2022; 5:1419. [PMID: 36575240 PMCID: PMC9793375 DOI: 10.1038/s42003-022-04332-6] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/01/2022] [Indexed: 12/28/2022] Open
Abstract
The strong suppression of Aedes albopictus on two Guangzhou islands in China has been successfully achieved by releasing males with an artificial triple-Wolbachia infection. However, it requires the use of radiation to sterilize residual females to prevent population replacement. To develop a highly effective tool for dengue control, we tested a standalone incompatible insect technique (IIT) to control A. albopictus in the urban area of Changsha, an inland city where dengue recently emerged. Male mosquitoes were produced in a mass rearing facility in Guangzhou and transported over 670 km under low temperature to the release site. After a once-per-week release with high numbers of males (phase I) and a subsequent twice-per-week release with low numbers of males (phase II), the average numbers of hatched eggs and female adults collected weekly per trap were reduced by 97% and 85%, respectively. The population suppression caused a 94% decrease in mosquito biting at the release site compared to the control site. Remarkably, this strong suppression was achieved using only 28% of the number of males released in a previous trial. Despite the lack of irradiation to sterilize residual females, no triple-infected mosquitoes were detected in the field post release based on the monitoring of adult and larval A. albopictus populations for two years, indicating that population replacement was prevented. Our results support the feasibility of implementing a standalone IIT for dengue control in urban areas.
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Affiliation(s)
- Qin Zeng
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Lingzhi She
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Hao Yuan
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Yuying Luo
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Renke Wang
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Wei Mao
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Weifeng Wang
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Yueting She
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Chaojun Wang
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Mengyi Shi
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Ting Cao
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Renxian Gan
- Guangzhou Wolbaki Biotech Co., Ltd, Guangzhou, Guangdong PR China
| | - Yongjun Li
- Guangzhou Wolbaki Biotech Co., Ltd, Guangzhou, Guangdong PR China ,grid.258164.c0000 0004 1790 3548Present Address: Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou, PR China
| | - Jiayi Zhou
- Guangzhou Wolbaki Biotech Co., Ltd, Guangzhou, Guangdong PR China
| | - Wei Qian
- Guangzhou Wolbaki Biotech Co., Ltd, Guangzhou, Guangdong PR China
| | - Shixiong Hu
- grid.508374.dHunan Provincial Center for Disease Control and Prevention, Changsha, Hunan PR China
| | - Yong Wang
- grid.216417.70000 0001 0379 7164Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, Hunan PR China
| | - Xiaoying Zheng
- grid.12981.330000 0001 2360 039XSun Yat-sen University—Michigan State University Joint Center of Vector Control for Tropical Diseases, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong PR China
| | - Kuibiao Li
- grid.508371.80000 0004 1774 3337Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong PR China
| | - Lianyang Bai
- grid.410598.10000 0004 4911 9766Hunan Academy of Agricultural Sciences, Changsha, Hunan PR China
| | - Xiaoling Pan
- grid.411427.50000 0001 0089 3695The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Medical Laboratory Science, Hunan Normal University School of Medicine, Changsha, Hunan PR China ,grid.411427.50000 0001 0089 3695The Key Laboratory of Protein Chemistry and Developmental Biology of Fish of Ministry of Education, Hunan Normal University, Changsha, Hunan PR China
| | - Zhiyong Xi
- Guangzhou Wolbaki Biotech Co., Ltd, Guangzhou, Guangdong PR China ,grid.17088.360000 0001 2150 1785Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
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Ma W, Liu M, Zhang Z, Xu Y, Huang P, Guo D, Sun X, Huang H. Efficient co-production of EPA and DHA by Schizochytrium sp. via regulation of the polyketide synthase pathway. Commun Biol 2022; 5:1356. [PMID: 36494568 PMCID: PMC9734096 DOI: 10.1038/s42003-022-04334-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Presently, the supply of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) traditionally produced by marine fisheries will be insufficient to meet their market demand in food industry. Thus a sustainable alternative source is urgently required. Schizochytrium sp. is an ideal producer of DHA; however, its ability to co-produce DHA and EPA has not yet been proved. Herein, we first described a cobalamin-independent methionine synthase-like (MetE-like) complex, which contains independent acyltransferase and 3-ketoacyl synthase domains, independent of the traditional polyketide synthase (PKS) system. When the MetE-like complex was activated, the EPA content was increased from 1.26% to 7.63%, which is 6.06-folds higher than that in the inactivated condition. Through lipidomics, we find that EPA is more inclined to be stored as triglyceride. Finally, the EPA production was enhanced from 4.19 to 29.83 (mg/g cell dry weight) using mixed carbon sources, and the final yield reached 2.25 g/L EPA and 9.59 g/L DHA, which means that Schizochytrium sp. has great market potential for co-production of EPA and DHA.
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Affiliation(s)
- Wang Ma
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, China ,grid.260474.30000 0001 0089 5711College of Life Sciences, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, China
| | - Mengzhen Liu
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, China
| | - Zixu Zhang
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, China
| | - Yingshuang Xu
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, China
| | - Pengwei Huang
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, China ,grid.260474.30000 0001 0089 5711College of Life Sciences, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, China
| | - Dongsheng Guo
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, China
| | - Xiaoman Sun
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, China
| | - He Huang
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, China ,grid.412022.70000 0000 9389 5210College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, China
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42
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Liu M, Qin X, Wu X. Study on the technology of brewing red raspberry wine by using new immobilized yeast technology. Sci Rep 2022; 12:21344. [PMID: 36494418 PMCID: PMC9734102 DOI: 10.1038/s41598-022-25410-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
The aim of the present study was to establish a new process for brewing red raspberry wine with immobilized yeast and improve the value of red raspberry. Using the spore filaments of P. chrysogenum as a carrier to co-culture with yeast to obtain immobilized yeast. And the preparation method of immobilized yeast was optimized by single-factor experiment and orthogonal experiments. And the red raspberry wine was brewed in these conditions. The result shows that the optimal preparation conditions for the immobilized yeast of P. chrysogenum were 5 g/L gluconic acid, 5 g/L yeast extract, and the addition amount of P. chrysogenum spores 1 × 105 cfu/ml. Compared with free yeast, the immobilized yeast of P. chrysogenum has better fermenting ability, can better keep the anthocyanins and polyphenols and other active ingredients of red raspberry. The quality of the wine was improved due to increase in aroma components such as alcohols and esters. The immobilized yeast of P. chrysogenum maintained good fermentation performance after three consecutive fermentations.
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Affiliation(s)
- Miao Liu
- grid.411643.50000 0004 1761 0411School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia China
| | - Xiaoyu Qin
- grid.411643.50000 0004 1761 0411School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia China
| | - Xiaotong Wu
- grid.411643.50000 0004 1761 0411School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia China
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King E, Maxel S, Zhang Y, Kenney KC, Cui Y, Luu E, Siegel JB, Weiss GA, Luo R, Li H. Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. Nat Commun 2022; 13:7282. [PMID: 36435948 PMCID: PMC9701214 DOI: 10.1038/s41467-022-35021-x] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 11/15/2022] [Indexed: 11/28/2022] Open
Abstract
Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN+) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN+-based reducing power. This is based on an orthogonal, NMN+-dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN+. With a throughput of >106 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme's global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme's access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.
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Affiliation(s)
- Edward King
- grid.266093.80000 0001 0668 7243Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697 USA
| | - Sarah Maxel
- grid.266093.80000 0001 0668 7243Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA 92697 USA
| | - Yulai Zhang
- grid.266093.80000 0001 0668 7243Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA 92697 USA
| | - Karissa C. Kenney
- grid.266093.80000 0001 0668 7243Department of Chemistry, University of California Irvine, Irvine, CA 92697 USA
| | - Youtian Cui
- grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA 95616 USA
| | - Emma Luu
- grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA 95616 USA
| | - Justin B. Siegel
- grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA 95616 USA ,grid.27860.3b0000 0004 1936 9684Department of Chemistry, Molecular Medicine University of California, Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Department of Biochemistry and Molecular Medicine University of California, Davis, Davis, CA USA
| | - Gregory A. Weiss
- grid.266093.80000 0001 0668 7243Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697 USA ,grid.266093.80000 0001 0668 7243Department of Chemistry, University of California Irvine, Irvine, CA 92697 USA ,grid.266093.80000 0001 0668 7243Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697 USA
| | - Ray Luo
- grid.266093.80000 0001 0668 7243Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697 USA ,grid.266093.80000 0001 0668 7243Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA 92697 USA ,grid.266093.80000 0001 0668 7243Department Materials Science and Engineering, University of California Irvine, Irvine, CA 92697 USA ,grid.266093.80000 0001 0668 7243Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
| | - Han Li
- grid.266093.80000 0001 0668 7243Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA 92697 USA ,grid.266093.80000 0001 0668 7243Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 USA
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Sousa JMG, Louvado A, Coelho FJRC, Oliveira V, Oliveira H, Cleary DFR, Gomes NCM. In vitro study of the modulatory effects of heat-killed bacterial biomass on aquaculture bacterioplankton communities. Sci Rep 2022; 12:19699. [PMID: 36385260 PMCID: PMC9669034 DOI: 10.1038/s41598-022-23439-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
Recent studies have shown that the addition of non-viable microbial biomass or their components (postbiotics) to fish feed can modulate the gut microbiome and positively influence fish health in aquaculture systems. However, no information was hitherto available on the use of non-viable microbial biomass to manipulate aquaculture bacterioplankton communities. To fill this gap, here we used an in vitro model to assess the effects of heat-killed biomasses of an antagonistic strain Pseudoalteromonas rubra SubTr2 and a non-antagonist strain Escherichia coli DH5α on bacterioplankton communities of a recirculating aquaculture system (RAS). Our results showed that these biomasses can have generalist and species-specific effects on aquaculture bacterioplankton structure and function. In addition, they enriched the abundance of bacterial predators, reduced bacterial load and potentially influenced nutrient cycling and pathogen development in aquaculture water. Despite its preliminary nature, for the first time, this study showed that heat-killed microbial biomass has potential application as an in situ modulator of bacterioplankton in aquaculture systems.
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Affiliation(s)
- J. M. G. Sousa
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - A. Louvado
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - F. J. R. C. Coelho
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - V. Oliveira
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - H. Oliveira
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - D. F. R. Cleary
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - N. C. M. Gomes
- grid.7311.40000000123236065CESAM-Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
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Burg L, Crewe G, DiMeo J, Guo X, Li CG, Mayol M, Tempesta A, Lauzier W, Markham R, Crissy K, Barry C, Walsh B, Kirby JE, Straus D. Rapid pathogen identification and phenotypic antimicrobial susceptibility directly from urine specimens. Sci Rep 2022; 12:18315. [PMID: 36380053 PMCID: PMC9666529 DOI: 10.1038/s41598-022-22792-y] [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: 07/22/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Implementing effective antimicrobial therapy close to the onset of infection lowers morbidity and mortality and attenuates the spread of antimicrobial resistance. Current antimicrobial susceptibility testing (AST) methods, however, require several days to determine optimal therapies. We present technology and an automated platform that identify (ID) Urinary Tract Infection pathogens in 45 min and provide phenotypic AST results in less than 5 h from urine specimens without colony isolation. The ID and AST tests count cells fluorescently labeled with specific rRNA probes using non-magnified digital imaging. The ID test detected five pathogens at ≤ 7,000 CFU/mL and had a linear range of ~ 4 orders of magnitude. For contrived specimens, AST tests gave 93.1% categorical agreement with 1.3% Very Major Errors (VME), 0.3% Major Errors (ME), and 6.3% minor Errors (mE) compared to the broth microdilution (BMD) reference method. For clinical specimens, the ID test had 98.6% agreement and the AST test had 92.3% categorical agreement with 4.2% mE, 3.4% ME and 4.0% VME compared to BMD. Data presented demonstrates that direct-from-specimen AST tests can accurately determine antimicrobial susceptibility/resistance for each pathogen in a specimen containing two pathogens. The method is robust to urine matrix effects and off-target commensal and contaminating bacteria.
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Affiliation(s)
- Larry Burg
- First Light Diagnostics, 2 Omni Way, Chelmsford, MA, 01824, USA.
| | - Gretel Crewe
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - James DiMeo
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - Xin Guo
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - Carmen G. Li
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - Melissa Mayol
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - Andrew Tempesta
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - William Lauzier
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - Rachelle Markham
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - Katarzyna Crissy
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - Colleen Barry
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - Bruce Walsh
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
| | - James E. Kirby
- grid.239395.70000 0000 9011 8547Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215 USA
| | - Don Straus
- grid.434094.eFirst Light Diagnostics, 2 Omni Way, Chelmsford, MA 01824 USA
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Studivan MS, Baptist M, Molina V, Riley S, First M, Soderberg N, Rubin E, Rossin A, Holstein DM, Enochs IC. Transmission of stony coral tissue loss disease (SCTLD) in simulated ballast water confirms the potential for ship-born spread. Sci Rep 2022; 12:19248. [PMID: 36357458 DOI: 10.1038/s41598-022-21868-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/04/2022] [Indexed: 11/12/2022] Open
Abstract
Stony coral tissue loss disease (SCTLD) remains an unprecedented epizootic disease, representing a substantial threat to the persistence and health of coral reef ecosystems in the Tropical Western Atlantic since its first observation near Miami, Florida in 2014. In addition to transport between adjacent reefs indicative of waterborne pathogen(s) dispersing on ocean currents, it has spread throughout the Caribbean to geographically- and oceanographically-isolated reefs, in a manner suggestive of ship and ballast water transmission. Here we evaluate the potential for waterborne transmission of SCTLD including via simulated ballast water, and test the efficacy of commonly-used UV radiation treatment of ballast water. Two species of reef-building corals (Orbicella faveolata and Pseudodiploria strigosa) were subjected to (1) disease-exposed or UV-treated disease-exposed water, and (2) a ballast hold time series of disease-exposed water in two carefully-controlled experiments to evaluate transmission. Our experiments demonstrated transmission of SCTLD through water, rather than direct contact between diseased and healthy corals. While UV treatment of disease-exposed water led to a 50% reduction in the number of corals exhibiting disease signs in both species, the statistical risk of transmission and volume of water needed to elicit SCTLD lesions remained similar to untreated disease-exposed water. The ballast hold time (24 h vs. 120 h) did not have a significant effect on the onset of visible disease signs for either species, though there appeared to be some evidence of a concentration effect for P. strigosa as lesions were only observed after the 120 h ballast hold time. Results from both experiments suggest that the SCTLD pathogens can persist in both untreated and UV-treated ballast water and remain pathogenic. Ballast water may indeed pose a threat to the continued spread and persistence of SCTLD, warranting further investigation of additional ballast water treatments and pathogen detection methods.
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Kao HJ, Balasubramaniam A, Chen CC, Huang CM. Extracellular electrons transferred from honey probiotic Bacillus circulans inhibits inflammatory acne vulgaris. Sci Rep 2022; 12:19217. [PMID: 36357775 DOI: 10.1038/s41598-022-23848-9] [Citation(s) in RCA: 2] [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: 07/08/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
Bacillus circulans (B. circulans) is widely used as an electrogenic bacterium in microbial fuel cell (MFC) technology. This study evaluated whether B. circulans can ferment glucose to generate electricity and mitigate the effects of human skin pathogens. The electricity production of B. circulans was examined by measuring the voltage difference and verified using a ferrozine assay in vitro. To investigate the fermentation effects of B. circulans on inhibition of human skin pathogens, Cutibacterium acnes (C. acnes) was injected intradermally into mice ears to induce an inflammatory response. The results revealed that the glucose-B. circulans co-culture enhanced electricity production and significantly supressed C. acnes growth. The addition of roseoflavin to inhibit flavin production considerably reduced the electrical energy generated by B. circulans through metabolism and, in vivo test, recovered C. acnes count and macrophage inflammatory protein 2 (MIP-2) levels. This suggests that B. circulans can generate electrons that affect the growth of C. acnes through flavin-mediated electron transfer and alleviate the resultant inflammatory response. Our findings demonstrate that probiotics separated from natural substances and antimicrobial methods of generating electrical energy through carbon source fermentation can help in the treatment of bacterial infections.
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Nowak-Lange M, Niedziałkowska K, Bernat P, Lisowska K. In vitro study of the ecotoxicological risk of methylisothiazolinone and chloroxylenol towards soil bacteria. Sci Rep 2022; 12:19068. [PMID: 36352006 DOI: 10.1038/s41598-022-22981-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022] Open
Abstract
Methylisothiazolinone (MIT) and chloroxylenol (PCMX) are popular disinfectants often used in personal care products (PCPs). The unregulated discharge of these micropollutants into the environment, as well as the use of sewage sludge as fertilizer and reclaimed water in agriculture, poses a serious threat to ecosystems. However, research into their ecotoxicity towards nontarget organisms is very limited. In the present study, for the first time, the ecotoxicity of biocides to Pseudomonas putida, Pseudomonas moorei, Sphingomonas mali, and Bacillus subtilis was examined. The toxicity of MIT and PCMX was evaluated using the microdilution method, and their influence on the viability of bacterial cells was investigated by the AlamarBlue® test. The ability of the tested bacteria to form biofilms was examined by a microtiter plate assay. Intracellular reactive oxygen species (ROS) production was measured with CM-H2DCFDA. The effect of MIT and PCMX on phytohormone indole-3-acetic acid (IAA) production was determined by spectrophotometry and LC‒MS/MS techniques. The permeability of bacterial cell membranes was studied using the SYTOX Green assay. Changes in the phospholipid profile were analysed using LC‒MS/MS. The minimal inhibitory concentrations (MICs) values ranged from 3.907 to 15.625 mg L-1 for MIT and 62.5 to 250 mg L-1 for PCMX, indicating that MIT was more toxic. With increasing concentrations of MIT and PCMX, the cell viability, biofilm formation ability and phytohormone synthesis were maximally inhibited. Moreover, the growth of bacterial cell membrane permeability and a significantly increased content of ROS were observed, indicating that the exposure caused serious oxidative stress and homeostasis disorders. Additionally, modifications in the phospholipid profile were observed in response to the presence of sublethal concentrations of the chemicals. These results prove that the environmental threat posed by MIT and PCMX must be carefully monitored, especially as their use in PCPs is still growing.
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Lv Y, Wang L, Liu X, Chen B, Zhang M. Degradation kinetics of aromatic VOCs polluted wastewater by functional bacteria at laboratory scale. Sci Rep 2022; 12:19053. [PMID: 36351963 PMCID: PMC9646702 DOI: 10.1038/s41598-022-21356-4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/26/2022] [Indexed: 11/11/2022] Open
Abstract
Reaction kinetics in biodegradation process is the basis and key of bioremediation technology, which can be used to predict the interaction between microorganisms and environmental states in the system. In this study, the kinetic model (Monod, Moser, Tessier and Cotonis) and kinetic parameters of aerobic biodegradation of functional bacteria in simulated wastewater polluted by aromatic volatile organic compounds (VOCs) were determined by shaking flask experiment. Monod, Moser, Tessier and Contois models were used to fit the experimental data and determine the kinetic parameters based on nonlinear regression analysis. Experimental results demonstrated that the removal rate of aromatic VOCs at 72 h was between 34.78 and 99.75% depending on the initial concentration of aromatic VOCs. The specific growth rate μ and degradation rate q increased with the increase of substrate concentration. The model of Monod, Moser and Tessier could be used to simulate microbial growth and substrate degradation in simulated aromatic VOCs polluted wastewater. Then the model and corresponding kinetic parameters were used to predict the limit concentration of biodegradation and provide theoretical support for the subsequent dynamic simulation and field engineering.
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Affiliation(s)
- Ying Lv
- grid.459522.d0000 0000 9491 9421National Engineering Research Center for Environment-Friendly Metallurgy in Producing Premium Non-Ferrous Metals, GRINM Group Co., Ltd., Beijing, 101407 China ,grid.69775.3a0000 0004 0369 0705School of Metallurgical and Ecological Engineering, University of Science and Technology Beijing, Beijing, 100083 China ,grid.459522.d0000 0000 9491 9421GRINM Resources and Environment Tech. Co., Ltd., Beijing, 101407 China ,grid.459522.d0000 0000 9491 9421General Research Institute for Nonferrous Metals, Beijing, 100088 China
| | - Liangshi Wang
- grid.459522.d0000 0000 9491 9421National Engineering Research Center for Environment-Friendly Metallurgy in Producing Premium Non-Ferrous Metals, GRINM Group Co., Ltd., Beijing, 101407 China ,grid.459522.d0000 0000 9491 9421GRINM Resources and Environment Tech. Co., Ltd., Beijing, 101407 China ,grid.459522.d0000 0000 9491 9421General Research Institute for Nonferrous Metals, Beijing, 100088 China
| | - Xingyu Liu
- grid.459522.d0000 0000 9491 9421General Research Institute for Nonferrous Metals, Beijing, 100088 China ,grid.162107.30000 0001 2156 409XCollege of Water Resources and Environment, China University of Geosciences, Beijing, 100083 China
| | - Bowei Chen
- grid.459522.d0000 0000 9491 9421National Engineering Research Center for Environment-Friendly Metallurgy in Producing Premium Non-Ferrous Metals, GRINM Group Co., Ltd., Beijing, 101407 China ,grid.459522.d0000 0000 9491 9421GRINM Resources and Environment Tech. Co., Ltd., Beijing, 101407 China ,grid.459522.d0000 0000 9491 9421General Research Institute for Nonferrous Metals, Beijing, 100088 China
| | - Mingjiang Zhang
- grid.459522.d0000 0000 9491 9421National Engineering Research Center for Environment-Friendly Metallurgy in Producing Premium Non-Ferrous Metals, GRINM Group Co., Ltd., Beijing, 101407 China ,grid.459522.d0000 0000 9491 9421GRINM Resources and Environment Tech. Co., Ltd., Beijing, 101407 China ,grid.459522.d0000 0000 9491 9421General Research Institute for Nonferrous Metals, Beijing, 100088 China
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Abstract
This paper presents a generalisable method for the calibration of fluorescence readings on microplate readers, in order to convert arbitrary fluorescence units into absolute units. FPCountR relies on the generation of bespoke fluorescent protein (FP) calibrants, assays to determine protein concentration and activity, and a corresponding analytical workflow. We systematically characterise the assay protocols for accuracy, sensitivity and simplicity, and describe an 'ECmax' assay that outperforms the others and even enables accurate calibration without requiring the purification of FPs. To obtain cellular protein concentrations, we consider methods for the conversion of optical density to either cell counts or alternatively to cell volumes, as well as examining how cells can interfere with protein counting via fluorescence quenching, which we quantify and correct for the first time. Calibration across different instruments, disparate filter sets and mismatched gains is demonstrated to yield equivalent results. It also reveals that mCherry absorption at 600 nm does not confound cell density measurements unless expressed to over 100,000 proteins per cell. FPCountR is presented as pair of open access tools (protocol and R package) to enable the community to use this method, and ultimately to facilitate the quantitative characterisation of synthetic microbial circuits.
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Affiliation(s)
- Eszter Csibra
- grid.7445.20000 0001 2113 8111Department of Bioengineering, Imperial College Centre for Synthetic Biology (IC-CSynB), Imperial College London, London, SW7 2AY UK
| | - Guy-Bart Stan
- grid.7445.20000 0001 2113 8111Department of Bioengineering, Imperial College Centre for Synthetic Biology (IC-CSynB), Imperial College London, London, SW7 2AY UK
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