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Lee YS, Umam K, Kuo TF, Yang YL, Feng CS, Yang WC. Functional and mechanistic studies of a phytogenic formulation, Shrimp Best, in growth performance and vibriosis in whiteleg shrimp. Sci Rep 2024; 14:11584. [PMID: 38773245 PMCID: PMC11109214 DOI: 10.1038/s41598-024-62436-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
Climate change and disease threaten shrimp farming. Here, we studied the beneficial properties of a phytogenic formulation, Shrimp Best (SB), in whiteleg shrimp. Functional studies showed that SB dose-dependently increased shrimp body weight and decreased feed conversion ratio. We found that SB protected against Vibrio parahaemolyticus as evidenced by survival rate, bacterial load, and hepatopancreatic pathology in shrimp. Finally, we explored the likely mechanism by which SB affects growth performance and vibriosis in shrimp. The 16S rRNA sequencing data showed that SB increased 6 probiotic genera and decreased 6 genera of pathogenic bacteria in shrimp. Among these, SB increased the proportion of Lactobacillus johnsonii and decreased that of V. parahaemolyticus in shrimp guts. To dissect the relationship among SB, Lactobacillus and Vibrio, we investigated the in vitro regulation of Lactobacillus and Vibrio by SB. SB at ≥ 0.25 μg/mL promoted L. johnsonii growth. Additionally, L. johnsonii and its supernatant could inhibit V. parahaemolyticus. Furthermore, SB could up-regulate five anti-Vibrio metabolites of L. johnsonii, which caused bacterial membrane destruction. In parallel, we identified 3 fatty acids as active compounds from SB. Overall, this work demonstrated that SB improved growth performance and vibriosis protection in shrimp via the regulation of gut microbiota.
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Affiliation(s)
- Yi-San Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Khotibul Umam
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- National Chung Hsing University, Taichung, Taiwan
- Faculty of Life Science and Technology, Biotechnology, Sumbawa University of Technology, Sumbawa, Indonesia
| | - Tien-Fen Kuo
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ching-Shan Feng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Chin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan.
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.
- National Chung Hsing University, Taichung, Taiwan.
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.
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2
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Lebano I, Fracchetti F, Vigni ML, Mejia JF, Felis G, Lampis S. MALDI-TOF as a powerful tool for identifying and differentiating closely related microorganisms: the strange case of three reference strains of Paenibacillus polymyxa. Sci Rep 2024; 14:2585. [PMID: 38297004 PMCID: PMC10831075 DOI: 10.1038/s41598-023-50010-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/14/2023] [Indexed: 02/02/2024] Open
Abstract
Accurate identification and typing of microbes are crucial steps in gaining an awareness of the biological heterogeneity and reliability of microbial material within any proprietary or public collection. Paenibacillus polymyxa is a bacterial species of great agricultural and industrial importance due to its plant growth-promoting activities and production of several relevant secondary metabolites. In recent years, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an alternative rapid tool for identifying, typing, and differentiating closely related strains. In this study, we investigated the diversity of three P. polymyxa strains. The mass spectra of ATCC 842T, DSM 292, and DSM 365 were obtained, analysed, and compared to select discriminant peaks using ClinProTools software and generate classification models. MALDI-TOF MS analysis showed inconsistent results in identifying DSM 292 and DSM 365 as belonging to P. polimixa species, and comparative analysis of mass spectra revealed the presence of highly discriminatory biomarkers among the three strains. 16S rRNA sequencing and Average Nucleotide Identity (ANI) confirmed the discrepancies found in the proteomic analysis. The case study presented here suggests the enormous potential of the proteomic-based approach, combined with statistical tools, to predict and explore differences between closely related strains in large microbial datasets.
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Affiliation(s)
- Ilaria Lebano
- Syngenta Biologicals (Valagro SpA), 66041, Atessa, CH, Italy.
| | | | - Mario Li Vigni
- Syngenta Biologicals (Valagro SpA), 66041, Atessa, CH, Italy
| | | | - Giovanna Felis
- Department of Biotechnology and VUCC-DBT Verona University Culture Collection, University of Verona, 37154, Verona, VR, Italy
| | - Silvia Lampis
- Department of Biotechnology and VUCC-DBT Verona University Culture Collection, University of Verona, 37154, Verona, VR, Italy.
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3
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Zhang X, Zhang Y, Wang L, Li W, Hou L. Identification and control of gas-producing bacteria isolated from the swollen bagged soy sauce. Int J Food Microbiol 2023; 407:110396. [PMID: 37734207 DOI: 10.1016/j.ijfoodmicro.2023.110396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023]
Abstract
The swelling of soy sauce bags seriously affects product quality and causes food safety problems, which has become an urgent problem to solve in the condiment industry. Here, gas-producing bacteria in the swollen bagged soy sauce were isolated and identified to provide an effective control method for inhibiting their growth and solving the swelling of soy sauce bags. It was found that three gas-producing bacteria isolated from the swollen bagged soy sauce were confirmed as Bacillus amyloliquefaciens (G1), Bacillus sp. (G2) and Bacillus subtilis (P3) using 16S rDNA analysis. The strains' morphologies, growth rates, and physiological and biochemical characteristics were also compared. Further studies yielded the optimal growth time, temperature and pH for the three gas-producing bacteria (B. amyloliquefacien: 24 h, 37 °C, and pH 7; Bacillus sp.: 18 h, 30 °C, and pH 6.5-7.5; B. subtilis: 36 h, 30 °C, and pH 8). Bacillus sp. was more salt tolerant than the other two. Then the antibacterial effect of the combination was tested by the physicochemical index. The results showed that filtering through a 0.22 μm inorganic micro-filtration membrane, sterilizing at 121 °C for 2 min, and adding 1 g/kg potassium sorbate was effective methods to inhibit three gas-producing bacteria and control the swelling of soy sauce.
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Affiliation(s)
- Xiangdi Zhang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology. No. 29, 13th. Avenue, Tianjin Economic and Technological, Tianjin 300457, China
| | - Yuxiu Zhang
- Tianjin Agricultural Center of Eco-Environment Monitoring and Agro-Product Quality Testing, No. 50th Xihu Road, Nankai District, Tianjin 300193, China
| | - Lingling Wang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology. No. 29, 13th. Avenue, Tianjin Economic and Technological, Tianjin 300457, China
| | - Wanning Li
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology. No. 29, 13th. Avenue, Tianjin Economic and Technological, Tianjin 300457, China
| | - Lihua Hou
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology. No. 29, 13th. Avenue, Tianjin Economic and Technological, Tianjin 300457, China.
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4
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Janiszewska D, Złoch M, Pomastowski P, Szultka-Młyńska M. Implications of Sample Preparation Methods on the MALDI-TOF MS Identification of Spore-Forming Bacillus Species from Food Samples: A Closer Look at Bacillus licheniformis, Peribacillus simplex, Lysinibacillus fusiformis, Bacillus flexus, and Bacillus marisflavi. ACS OMEGA 2023; 8:34982-34994. [PMID: 37779958 PMCID: PMC10536843 DOI: 10.1021/acsomega.3c04354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023]
Abstract
This research underscores the criticality of tailored culture conditions and incubation periods for effective and accurate identification of spore-forming bacteria: Bacillus licheniformis, Peribacillus simplex, Lysinibacillus fusiformis, Bacillus flexus, and Bacillus marisflav, isolated from food samples, utilizing the MALDI-TOF MS technique. All isolated strains were confirmed as Gram-positive bacteria from diverse genera through 16S rDNA gene sequencing. To enhance the accuracy of the identification process, the study employed an optimization strategy involving a varied incubation time (ranging from 1 to 48 h) and two distinct sample preparation approaches-direct transfer facilitated by formic acid and protein extraction via ethanol. It was observed that matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) could successfully identify approximately 47% of the samples following a 24 h incubation period. The study emphasizes the critical role of sample preparation methods in enabling precise bacterial identification. Our findings reveal the necessity of tailoring the incubation time for each sample, as the optimum period for accurate identification fluctuated between 1 and 12 h. Further demonstrating the interplay between incubation time and spore quantity, our study used the Schaeffer-Fulton staining method to show that the lowest spore counts were detected between 5 and 8 h of incubation. This provides evidence that spore formation impacts bacterial identification. Our research thus deepens the understanding of spore-forming bacteria identification using MALDI-TOF MS and illuminates the various factors affecting the dependability and accuracy of this technique. Future research may explore additional variables, such as the effect of varying culture media, to further augment identification accuracy and gain a holistic understanding of spore-forming bacterial behavior in food samples. By enhancing our knowledge, these findings can substantially contribute to improving food safety and quality assurance strategies by enabling the more accurate and efficient identification of spore-forming bacteria in the food industry, thereby elevating the standards of food safety.
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Affiliation(s)
- Daria Janiszewska
- Department
of Environmental Chemistry and Bioanalytics, Gagarina 7, 87-100 Torun, Poland
| | - Michał Złoch
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
| | - Paweł Pomastowski
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
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Pinar-Méndez A, Galofré B, Blanch AR, García-Aljaro C. Culture and molecular methods as complementary tools for water quality management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157789. [PMID: 35931155 DOI: 10.1016/j.scitotenv.2022.157789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/30/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Bacterial communities in a full-scale drinking water treatment plant (DWTP) were characterized using matrix-assisted laser desorption/ionization time of flight mass-spectrometry (MALDI-TOF MS) to identify HPC isolates and the obtained results were compared to 16S rRNA (V4) metabarcoding data acquired in a previous study. Sixty-three samples were collected at nine stages of the potabilization process: river water and groundwater intake, decantation, sand filtration, ozonization, carbon filtration, reverse osmosis, the mixing chamber and post-chlorination drinking water. In total, 1807 bacterial colonies were isolated, 32 % of which were successfully identified to at least the genus level by MALDI-TOF MS using our previously developed Drinking Water Library. Trends in diversity were similar by both approaches, but differences were observed in the detection of taxa, especially at lower hierarchy levels. High bacterial diversity was observed in river and groundwater, where Proteobacteria predominated. The diversity decreased significantly after the chlorination step, where Bacillus sp. (Firmicutes) and an unknown genus of Obscuribacteraceae (Cyanobacteria) were the most prevalent genera according to MALDI-TOF MS and metabarcoding, respectively. The two approaches gave similar results for the decantation, sand filtration and mixing chamber steps, where the most abundant taxon was Flavobacterium. The combined use of these culture-based and culture-independent methods to characterize microbial populations may help to better understand the role of bacteria in water treatment and quality, which will be of value for DWTP management.
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Affiliation(s)
- Anna Pinar-Méndez
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain.
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, Barcelona, Spain
| | - Anicet R Blanch
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain
| | - Cristina García-Aljaro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), Barcelona, Spain.
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6
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The Application of MALDI-TOF MS for a Variability Study of Paenibacillus larvae. Vet Sci 2022; 9:vetsci9100521. [PMID: 36288134 PMCID: PMC9610059 DOI: 10.3390/vetsci9100521] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary An understanding of Paenibacillus larvae, the etiological agent of American foulbrood disease, species diversity is crucial for disease epidemiology investigations. Our data indicate that the protein fingerprinting-based MALDI-TOF method provides a much more thorough insight into P. larvae diversity compared to the DNA fingerprinting methods used at present. Abstract In recent decades, the significant deterioration of the health status of honey bees has been observed throughout the world. One of the most severe factors affecting the health of bee colonies worldwide is American foulbrood disease. This devastating disease, with no known cure, is caused by the Gram-positive spore-forming bacteria of Paenibacillus larvae species. At present, DNA-based methods are being used for P. larvae identification and typing. In our study, we compare two of the most advanced DNA-based technologies (rep-PCR and 16S rRNA analyses) with MALDI-TOF MS fingerprinting to evaluate P. larvae variability in Central Europe. While 16S rRNA analysis presents a very limited variation among the strains, MALDI-TOF MS is observed to be more efficient at differentiating P. larvae. Remarkably, no clear correlation is observed between whole-genome rep-PCR fingerprinting and MALDI-TOF MS-based typing. Our data indicate that MALDI-TOF protein profiling provides accurate and cost-effective methods for the rapid identification of P. larvae strains and provides novel perspectives on strain diversity compared to conventional DNA-based genotyping approaches. The current study provides a good foundation for future studies.
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7
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Liu TY, Chen CH, Yang YL, Tsai IJ, Ho YN, Chung CL. The brown root rot fungus Phellinus noxius affects microbial communities in different root-associated niches of Ficus trees. Environ Microbiol 2021; 24:276-297. [PMID: 34863027 DOI: 10.1111/1462-2920.15862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022]
Abstract
Brown root rot (BRR) caused by Phellinus noxius is a destructive tree disease in tropical and subtropical areas. To understand how BRR affects the composition of the plant rhizoplane-enriched microbiota, the microbiomes within five root-associated compartments (i.e., bulk soil, old/young root rhizosphere soil, old/young root tissue) of Ficus trees naturally infected by P. noxius were investigated. The level of P. noxius infection was determined by quantitative PCR. Illumina sequencing of the internal transcribed spacer and 16S rRNA revealed that P. noxius infection caused a significant reduction in fungal diversity in the bulk soil, the old root rhizosphere soil, and the old root tissue. Interestingly, Cosmospora was the only fungal genus positively correlated with P. noxius. The abundance and composition of dominant bacterial taxa such as Actinomadura, Bacillus, Rhodoplanes, and Streptomyces differed between BRR-diseased and healthy samples. Furthermore, 838 isolates belonging to 26 fungal and 35 bacterial genera were isolated and tested for interactions with P. noxius. Antagonistic activities were observed for isolates of Bacillus, Pseudomonas, Aspergillus, Penicillium, and Trichoderma. Cellophane overlay and cellulose/lignin utilization assays suggested that Cosmospora could tolerate the secretions of P. noxius and that the degradation of lignin by P. noxius may create suitable conditions for Cosmorpora growth.
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Affiliation(s)
- Tse-Yen Liu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City, 10617, Taiwan.,Division of Forest Protection, Taiwan Forestry Research Institute, Taipei City, 10066, Taiwan
| | - Chao-Han Chen
- Division of Forest Protection, Taiwan Forestry Research Institute, Taipei City, 10066, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei City, 11529, Taiwan
| | - Isheng J Tsai
- Biodiversity Research Center, Academia Sinica, Taipei City, 11529, Taiwan
| | - Ying-Ning Ho
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung City, 20224, Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City, 10617, Taiwan
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8
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Green nanotechnology for preserving and enriching yogurt with biologically available iron (II). INNOV FOOD SCI EMERG 2021. [DOI: 10.1016/j.ifset.2021.102645] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Low L, Fuentes-Utrilla P, Hodson J, O’Neil JD, Rossiter AE, Begum G, Suleiman K, Murray PI, Wallace GR, Loman NJ, Rauz S. Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis. PeerJ 2021; 9:e10778. [PMID: 33628638 PMCID: PMC7891086 DOI: 10.7717/peerj.10778] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Microbial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative. Nanopore sequencing technology is portable and capable of generating long sequencing reads in real-time. The aim of this study is to evaluate the potential of nanopore sequencing directly from clinical samples for the diagnosis of bacterial microbial keratitis. METHODS Using full-length 16S rRNA amplicon sequences from a defined mock microbial community, we evaluated and benchmarked our bioinformatics analysis pipeline for taxonomic assignment on three different 16S rRNA databases (NCBI 16S RefSeq, RDP and SILVA) with clustering at 97%, 99% and 100% similarities. Next, we optimised the sample collection using an ex vivo porcine model of microbial keratitis to compare DNA recovery rates of 12 different collection methods: 21-gauge needle, PTFE membrane (4 mm and 6 mm), Isohelix™ SK-2S, Sugi® Eyespear, Cotton, Rayon, Dryswab™, Hydraflock®, Albumin-coated, Purflock®, Purfoam and Polyester swabs. As a proof-of-concept study, we then used the sampling technique that provided the highest DNA recovery, along with the optimised bioinformatics pipeline, to prospectively collected samples from patients with suspected microbial keratitis. The resulting nanopore sequencing results were then compared to standard microbiology culture methods. RESULTS We found that applying alignment filtering to nanopore sequencing reads and aligning to the NCBI 16S RefSeq database at 100% similarity provided the most accurate bacterial taxa assignment. DNA concentration recovery rates differed significantly between the collection methods (p < 0.001), with the Sugi® Eyespear swab providing the highest mean rank of DNA concentration. Then, applying the optimised collection method and bioinformatics pipeline directly to samples from two patients with suspected microbial keratitis, sequencing results from Patient A were in agreement with culture results, whilst Patient B, with negative culture results and previous antibiotic use, showed agreement between nanopore and Illumina Miseq sequencing results. CONCLUSION We have optimised collection methods and demonstrated a novel workflow for identification of bacterial microbial keratitis using full-length 16S nanopore sequencing.
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Affiliation(s)
- Liying Low
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
| | - Pablo Fuentes-Utrilla
- MicrobesNG/School of Biosciences, University of Birmingham, Birmingham, West Midlands, UK
| | - James Hodson
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, West Midlands, UK
| | - John D. O’Neil
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
| | - Amanda E. Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, West Midlands, UK
| | - Ghazala Begum
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Birmingham, UK
| | - Kusy Suleiman
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
| | - Philip I. Murray
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
| | - Graham R. Wallace
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
| | - Nicholas J. Loman
- MicrobesNG/School of Biosciences, University of Birmingham, Birmingham, West Midlands, UK
| | - Saaeha Rauz
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
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Karpov DS, Osipova PG, Domashin AI, Polyakov NB, Solovyev AI, Zubasheva MV, Zhukhovitsky VG, Karpov VL, Poddubko SV, Novikova ND. Hyper-Resistance of the Bacillus licheniformis 24 Strain to Oxidative Stress Is Associated with Overexpression of Enzymatic Antioxidant System Genes. Mol Biol 2020. [DOI: 10.1134/s0026893320050040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Vidal LMR, Venas TM, Gonçalves ARP, Mattsson HK, Silva RVP, Nóbrega MS, Azevedo GPR, Garcia GD, Tschoeke DA, Vieira VV, Thompson FL, Thompson CC. Rapid screening of marine bacterial symbionts using MALDI-TOF MS. Arch Microbiol 2020; 202:2329-2336. [PMID: 32529508 DOI: 10.1007/s00203-020-01917-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 11/30/2022]
Abstract
Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) is a rapid, cost-effective and high-throughput method for bacteria characterization. However, most previous studies focused on clinical isolates. In this study, we evaluated the use of MALDI-TOF MS as a rapid screening tool for marine bacterial symbionts. A set of 255 isolates from different marine sources (corals, sponge, fish and seawater) was analyzed using cell lysates to obtain a rapid grouping. Cluster analysis of mass spectra and 16S rRNA showed 18 groups, including Vibrio, Bacillus, Pseudovibrio, Alteromonas and Ruegeria. MALDI-TOF distance similarity scores ≥ 60% and ≥ 70% correspond to ≥ 98.7% 16S rRNA gene sequence similarity and ≥ 95% pyrH gene sequence similarity, respectively. MALDI-TOF MS is a useful tool for Vibrio species groups' identification.
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Affiliation(s)
- Livia M R Vidal
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tainá M Venas
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Aline R P Gonçalves
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Hannah K Mattsson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Raphael V P Silva
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Maria S Nóbrega
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gustavo P R Azevedo
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gizele D Garcia
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Departamento de Ensino de Graduação, Campus UFRJ - Macaé Professor Aloisio Teixeira, Universidade Federal do Rio de Janeiro (UFRJ), Macaé, RJ, Brazil
| | - Diogo A Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Biomedical Engineer Program - COPPE (UFRJ), Rio de Janeiro, Brazil
| | - Verônica V Vieira
- Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane C Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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12
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Zhang XJ, Liu HC, Zhou YG, Wu XL, Nie Y, Li QR, Wang MZ, Zhao L, Cai M, Kang YQ. Pseudomonas Saliphila sp. nov., a Bacterium Isolated from Oil-Well Production Water in Qinghai Oilfield of China. Curr Microbiol 2020; 77:1924-1931. [DOI: 10.1007/s00284-020-01986-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/06/2020] [Indexed: 10/24/2022]
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13
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Datir SS, Yousf S, Sharma S, Kochle M, Ravikumar A, Chugh J. Cold storage reveals distinct metabolic perturbations in processing and non-processing cultivars of potato (Solanum tuberosum L.). Sci Rep 2020; 10:6268. [PMID: 32286457 PMCID: PMC7156394 DOI: 10.1038/s41598-020-63329-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 03/27/2020] [Indexed: 11/09/2022] Open
Abstract
Cold-induced sweetening (CIS) causes considerable losses to the potato processing industry wherein the selection of potato genotypes using biochemical information has found to be advantageous. Here, 1H NMR spectroscopy was performed to identify metabolic perturbations from tubers of five potato cultivars (Atlantic, Frito Lay-1533, Kufri Jyoti, Kufri Pukhraj, and PU1) differing in their CIS ability and processing characteristics at harvest and after cold storage (4 °C). Thirty-nine water-soluble metabolites were detected wherein significantly affected metabolites after cold storage were categorized into sugars, sugar alcohols, amino acids, and organic acids. Multivariate statistical analysis indicated significant differences in the metabolic profiles among the potato cultivars. Pathway enrichment analysis revealed that carbohydrates, amino acids, and organic acids are the key players in CIS. Interestingly, one of the processing cultivars, FL-1533, exhibited a unique combination of metabolites represented by low levels of glucose, fructose, and asparagine accompanied by high citrate levels. Conversely, non-processing cultivars (Kufri Pukhraj and Kufri Jyoti) showed elevated glucose, fructose, and malate levels. Our results indicate that metabolites such as glucose, fructose, sucrose, asparagine, glutamine, citrate, malate, proline, 4-aminobutyrate can be potentially utilized for the prediction, selection, and development of potato cultivars for long-term storage, nutritional, as well as processing attributes.
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Affiliation(s)
- Sagar S Datir
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India. .,Biology Department, Biosciences Complex, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
| | - Saleem Yousf
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Shilpy Sharma
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Mohit Kochle
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Ameeta Ravikumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Jeetender Chugh
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, 411008, India. .,Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
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López AC, Alippi AM. Feasibility of using RFLP of PCR-amplified 16S rRNA gene(s) for rapid differentiation of isolates of aerobic spore-forming bacteria from honey. J Microbiol Methods 2019; 165:105690. [PMID: 31425714 DOI: 10.1016/j.mimet.2019.105690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/15/2019] [Accepted: 08/15/2019] [Indexed: 11/24/2022]
Abstract
This study aimed to assess the feasibility of using RFLP of PCR-amplified 16S rRNA gene (s) by using universal primers 27f/1492r and a combination of three restriction enzymes, AluI, CfoI, and TaqI, for a low-cost, rapid screen for a primarily differentiation of isolates of the complex of aerobic spore-forming bacteria commonly found in honey samples. The described method produced unique and distinguishable patterns to differentiate among 80 isolates belonging to 26 different species of Bacillus, Brevibacillus, Lysinibacillus, Rummeliibacillus, and Paenibacillus reported in honey and other apiarian sources.
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Affiliation(s)
- Ana C López
- Unidad de Bacteriología, Centro de Investigaciones de Fitopatología, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, cc 31, calle 60 y 119, 1900 La Plata, Argentina
| | - Adriana M Alippi
- Unidad de Bacteriología, Centro de Investigaciones de Fitopatología, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, cc 31, calle 60 y 119, 1900 La Plata, Argentina.
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15
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Analysis of bacteria associated with honeys of different geographical and botanical origin using two different identification approaches: MALDI-TOF MS and 16S rDNA PCR technique. PLoS One 2019; 14:e0217078. [PMID: 31120945 PMCID: PMC6532876 DOI: 10.1371/journal.pone.0217078] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/05/2019] [Indexed: 12/14/2022] Open
Abstract
In the presented work identification of microorganisms isolated from various types of honeys was performed. Martix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing were applied to study environmental bacteria strains.With both approches, problematic spore-forming Bacillus spp, but also Staphylococcus spp., Lysinibacillus spp., Micrococcus spp. and Brevibacillus spp were identified. However, application of spectrometric technique allows for an unambiguous distinction between species/species groups e.g.B. subtilis or B. cereus groups. MALDI TOF MS and 16S rDNA sequencing allow for construction of phyloproteomic and phylogenetic trees of identified bacterial species. Furthermore, the correlation beetween physicochemical properties, geographical and botanical origin and the presence bacterial species in honey samples were investigated.
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16
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Celandroni F, Vecchione A, Cara A, Mazzantini D, Lupetti A, Ghelardi E. Identification of Bacillus species: Implication on the quality of probiotic formulations. PLoS One 2019; 14:e0217021. [PMID: 31107885 PMCID: PMC6527297 DOI: 10.1371/journal.pone.0217021] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/02/2019] [Indexed: 11/26/2022] Open
Abstract
Spores of several Bacillus species have long history of consumption and safe use as probiotics and a variety of formulations containing these organisms are available in the global market. Considering the difficulties in the identification of Bacillus species and the poor microbiological quality of many probiotic formulations, we used three up-to-date methodological approaches for analyzing the content of ten formulations marketed in Italy and labeled to contain Bacillus spores. We compared the performance of biochemical tests based on the BCL Vitek2 card and MALDI-TOF mass spectrometry, using 16S rDNA sequencing as the reference technique. The BCL card performed well in identifying all Bacillus probiotic strains as well as the Bruker’s MALDI Biotyper. Nevertheless, the MALDI score values were sometimes lower than those indicated by the manufacturer for correct species identification. Contaminant bacteria (Lysinibacillus fusiformis, Acinetobacter baumannii, Bacillus cereus, Brevibacillus choshinensis, Bacillus licheniformis, Bacillus badius) were detected in some formulations. Characterization of the B. cereus contaminant showed the potential pathogenicity of this strain. Microbial enumeration performed by the plate count method revealed that the number of viable cells contained in many of the analyzed products differed from the labeled amount. Overall, our data show that only two of the ten analyzed formulations qualitatively and quantitatively respect what is on the label. Since probiotic properties are most often strain specific, molecular typing of isolates of the two most common Bacillus species, B. clausii and B. coagulans, was also performed. In conclusion, the majority of the analyzed products do not comply with quality requirements, most likely leading to reduced/absent efficacy of the preparation and representing a potential infective risk for consumers.
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Affiliation(s)
- Francesco Celandroni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Alessandra Vecchione
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Alice Cara
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Diletta Mazzantini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Antonella Lupetti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Emilia Ghelardi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
- Research Center Nutraceuticals and Food for Health-Nutrafood, University of Pisa, Pisa, Italy
- * E-mail:
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17
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Pajor M, Worobo RW, Milewski S, Szweda P. The Antimicrobial Potential of Bacteria Isolated from Honey Samples Produced in the Apiaries Located in Pomeranian Voivodeship in Northern Poland. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:E2002. [PMID: 30223435 PMCID: PMC6163485 DOI: 10.3390/ijerph15092002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 12/16/2022]
Abstract
The principal objective of this study was to determine whether the honeys produced in apiaries located in Pomeranian Voivodeship (Northern Poland) contain bacteria producing metabolites with growth inhibition potential against important human and animal pathogens. The pathogens included Staphylococcus aurues, Staphyloccocus epidermidis, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, and Candida albicans. From 12 samples of honey, 163 strains of bacteria were isolated. Activity against reference staphylococci: S. aurues ATCC 25923; S. aureus ATCC 29213; S. epidermidis 12228 was observed in 33 (20.3%), 38 (23.3%), and 41 (25.1%) isolates, respectively. High inhibitory activity was also found against Listeria monocytogenes ATCC 7644 in 34 strains (20.9%). Activity against Candida albicans ATCC 10231 and especially Gram-negative bacteria: Pseudomonas aeruginosa ATCC 27857 and Escherichia coli ATCC 25922 was rarely observed. Production of metabolites exhibiting activity against the three pathogens mentioned above was confirmed for 13 (7.8%), 3 (1.8%), and 2 (1.2%) isolates, respectively. Forty-six isolates were selected for further analysis. Within this group, metabolites synthesized by 18 producing strains (39.13%) inhibited growth of only one of the reference strains of pathogenic microorganisms. However, 14 (30.44%), 8 (17.39%), and 6 (13.04%) strains produced agents active against three, two, and four pathogens, respectively. Sequencing of the 16S rRNA gene revealed that 80.4% of these 46 producing strains belong to the genus Bacillus. However, some producing strains belonging to the genus of Peanibacillus, Lysinibacillus, Microbacterium, and Staphylococcus were also identified. Furthermore, the analysis of the sequences of 16S rRNA, as well as RAPD-PCR, exhibited a significant diversity in the strains tested, even in the case of bacteria isolated from the same honey (and classified to the same genus, usually Bacillus spp.). This observation suggests environmental origin (nectar, water, or pollen) of the producing strains. The research carried out confirmed that honey produced in Northern Poland is a promising source of strains of bacteria producing metabolites with antimicrobial activity.
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Affiliation(s)
- Magdalena Pajor
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland.
| | - Randy W Worobo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | - Sławomir Milewski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland.
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland.
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