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Bjørge Thomassen GM, Krych L, Knøchel S, Mehli L. Bacterial community development and diversity during the first year of production in a new salmon processing plant. Food Microbiol 2023; 109:104138. [DOI: 10.1016/j.fm.2022.104138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/26/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022]
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2
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Borges ASG, Basu M, Brinks E, Bang C, Cho GS, Baines JF, Franke A, Franz CMAP. Fast Identification Method for Screening Bacteria from Faecal Samples Using Oxford Nanopore Technologies MinION Sequencing. Curr Microbiol 2023; 80:101. [PMID: 36759384 PMCID: PMC9911510 DOI: 10.1007/s00284-023-03201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023]
Abstract
Most bacterial identification methods require extensive culturing, strain purification and DNA extraction protocols. This leads to additional expenses and time lags when isolating specific bacteria from complex microbiological ecosystems. This study aimed to develop a fast and robust method for identification of lactobacilli, bifidobacteria and Bacteroides in human faecal samples. Bacteria from faecal samples were cultured anaerobically on selective media. Sonication-based DNA extraction was performed, followed by almost complete 16S rRNA gene polymerase chain reaction amplification and MinION sequencing with the Flongle adapter. Sequence analysis was performed using NanoCLUST, while RStudio was used for graphics. For 110 of the 125 colonies investigated, 100% of reads were attributed to a single species, while the remaining 15 colonies consisted of mixtures of up to three different species. The proposed bacterial identification method is advantageous for isolating particular bacteria for which there are no exclusively selective media, as it avoids lengthy colony purification and DNA purification methods, and yields a quick colony identification with high accuracy. Therefore, this method can be used for directly screening for pure cultures of target microorganisms and is suitable for the identification of bacteria in culturomics studies.
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Affiliation(s)
- Ana Sofia G. Borges
- grid.72925.3b0000 0001 1017 8329Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Meghna Basu
- grid.412468.d0000 0004 0646 2097Section of Evolutionary Medicine, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, UKSH, Campus Kiel, Michaelisstraße 5, 24105 Kiel, Germany ,grid.419520.b0000 0001 2222 4708Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Erik Brinks
- grid.72925.3b0000 0001 1017 8329Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Corinna Bang
- grid.9764.c0000 0001 2153 9986Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Straße 1, 24103, Kiel, Germany.
| | - John F. Baines
- grid.412468.d0000 0004 0646 2097Section of Evolutionary Medicine, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, UKSH, Campus Kiel, Michaelisstraße 5, 24105 Kiel, Germany ,grid.419520.b0000 0001 2222 4708Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Andre Franke
- grid.9764.c0000 0001 2153 9986Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Charles M. A. P. Franz
- grid.72925.3b0000 0001 1017 8329Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
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3
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Shin JI, Ha JH, Kim KM, Choi JG, Park SR, Park HE, Park JS, Byun JH, Jung M, Baik SC, Lee WK, Kang HL, Yoo JW, Shin MK. A novel repeat sequence-based PCR (rep-PCR) using specific repeat sequences of Mycobacterium intracellulare as a DNA fingerprinting. Front Microbiol 2023; 14:1161194. [PMID: 37089534 PMCID: PMC10117815 DOI: 10.3389/fmicb.2023.1161194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/17/2023] [Indexed: 04/25/2023] Open
Abstract
Repetitive sequence-based PCR (rep-PCR) is a potential epidemiological technique that can provide high-throughput genotype fingerprints of heterogeneous Mycobacterium strains rapidly. Previously published rep-PCR primers, which are based on nucleotide sequences of Gram-negative bacteria may have low specificity for mycobacteria. Moreover, it was difficult to ensure the continuity of the study after the commercial rep-PCR kit was discontinued. Here, we designed a novel rep-PCR for Mycobacterium intracellulare, a major cause of nontuberculous mycobacterial pulmonary disease with frequent recurrence. We screened the 7,645 repeat sequences for 200 fragments from the genome of M. intracellulare ATCC 13950 in silico, finally generating five primers with more than 90% identity for a total of 226 loci in the genome. The five primers could make different band patterns depending on the genome of three different M. intracellulare strains using an in silico test. The novel rep-PCR with the five primers was conducted using 34 bacterial samples of 7 species containing 25 M. intracellulare clinical isolates, compared with previous published rep-PCRs. This shows distinguished patterns depending on species and blotting assay for 6 species implied the sequence specificity of the five primers. The Designed rep-PCR had a 95-98% of similarity value in the reproducibility test and showed 7 groups of fingerprints in M. intracellulare strains. Designed rep-PCR had a correlation value of 0.814 with VNTR, reference epidemiological method. This study provides a promising genotype fingerprinting method for tracing the recurrence of heterogeneous M. intracellulare.
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Affiliation(s)
- Jeong-Ih Shin
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Jong-Hun Ha
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Kyu-Min Kim
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Jeong-Gyu Choi
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Seo-Rin Park
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Hyun-Eui Park
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Jin-Sik Park
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Jung-Hyun Byun
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Myunghwan Jung
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Seung-Chul Baik
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Woo-Kon Lee
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Hyung-Lyun Kang
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Jung-Wan Yoo
- Department of Internal Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Jung-Wan Yoo,
| | - Min-Kyoung Shin
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- *Correspondence: Min-Kyoung Shin,
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Draft Genome Sequences of Seven
Limosilactobacillus fermentum
Indigenously Isolated Probiotic Strains from the Artisanal Fermented Milk Product Dahi. Microbiol Resour Announc 2022; 11:e0074222. [PMID: 36214690 PMCID: PMC9670941 DOI: 10.1128/mra.00742-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Here, we report the draft genome sequences of seven strains of potentially probiotic Limosilactobacillus fermentum isolated from the traditional fermented milk product dahi. The estimated average genome size was 1,955,815 bp, with a median GC content of 52%. Genome annotation predicted an average of 1,871 protein-coding genes and 47 RNAs.
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Wang Y, Xu H, Dong Z, Wang Z, Yang Z, Yu X, Chang L. Micro/nano biomedical devices for point-of-care diagnosis of infectious respiratory diseases. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2022; 14:100116. [PMID: 35187465 PMCID: PMC8837495 DOI: 10.1016/j.medntd.2022.100116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/14/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022] Open
Abstract
Corona Virus Disease 2019 (COVID-19) has developed into a global pandemic in the last two years, causing significant impacts on our daily life in many countries. Rapid and accurate detection of COVID-19 is of great importance to both treatments and pandemic management. Till now, a variety of point-of-care testing (POCT) approaches devices, including nucleic acid-based test and immunological detection, have been developed and some of them has been rapidly ruled out for clinical diagnosis of COVID-19 due to the requirement of mass testing. In this review, we provide a summary and commentary on the methods and biomedical devices innovated or renovated for the quick and early diagnosis of COVID-19. In particular, some of micro and nano devices with miniaturized structures, showing outstanding analytical performances such as ultra-sensitivity, rapidness, accuracy and low cost, are discussed in this paper. We also provide our insights on the further implementation of biomedical devices using advanced micro and nano technologies to meet the demand of point-of-care diagnosis and home testing to facilitate pandemic management. In general, our paper provides a comprehensive overview of the latest advances on the POCT device for diagnosis of COVID-19, which may provide insightful knowledge for researcher to further develop novel diagnostic technologies for rapid and on-site detection of pathogens including SARS-CoV-2.
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Affiliation(s)
- Yang Wang
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Huiren Xu
- School of Biomedical Information and Engineering, Hainan Medical University, Haikou, 471100, China
| | - Zaizai Dong
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zhiying Wang
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, United Kingdom,Corresponding author
| | - Xinge Yu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China,Corresponding author.
| | - Lingqian Chang
- Key Laboratory for Biomechanics and Mechanobiology, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China,Corresponding author.
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Thomassen GMB, Krych L, Knøchel S, Mehli L. ON-rep-seq as a rapid and cost-effective alternative to whole-genome sequencing for species-level identification and strain-level discrimination of Listeria monocytogenes contamination in a salmon processing plant. Microbiologyopen 2021; 10:e1246. [PMID: 34964295 PMCID: PMC8591450 DOI: 10.1002/mbo3.1246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022] Open
Abstract
Identification, source tracking, and surveillance of food pathogens are crucial factors for the food-producing industry. Over the last decade, the techniques used for this have moved from conventional enrichment methods, through species-specific detection by PCR to sequencing-based methods, whole-genome sequencing (WGS) being the ultimate method. However, using WGS requires the right infrastructure, high computational power, and bioinformatics expertise. Therefore, there is a need for faster, more cost-effective, and more user-friendly methods. A newly developed method, ON-rep-seq, combines the classical rep-PCR method with nanopore sequencing, resulting in a highly discriminating set of sequences that can be used for species identification and also strain discrimination. This study is essentially a real industry case from a salmon processing plant. Twenty Listeria monocytogenes isolates were analyzed both by ON-rep-seq and WGS to identify and differentiate putative L. monocytogenes from a routine sampling of processing equipment and products, and finally, compare the strain-level discriminatory power of ON-rep-seq to different analyzing levels delivered from the WGS data. The analyses revealed that among the isolates tested there were three different strains. The isolates of the most frequently detected strain (n = 15) were all detected in the problematic area in the processing plant. The strain level discrimination done by ON-rep-seq was in full accordance with the interpretation of WGS data. Our findings also demonstrate that ON-rep-seq may serve as a primary screening method alternative to WGS for identification and strain-level differentiation for surveillance of potential pathogens in a food-producing environment.
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Affiliation(s)
| | - Lukasz Krych
- Department of Food ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Susanne Knøchel
- Department of Food ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Lisbeth Mehli
- Department of Biotechnology and Food ScienceNorwegian University of Science and Technology (NTNU)TrondheimNorway
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Kerkhof LJ. Is Oxford Nanopore sequencing ready for analyzing complex microbiomes? FEMS Microbiol Ecol 2021; 97:6098400. [PMID: 33444433 PMCID: PMC8068755 DOI: 10.1093/femsec/fiab001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
This minireview will discuss the improvements in Oxford Nanopore (Oxford; sequencing technology that make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65 to 96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.
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Affiliation(s)
- Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
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