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Dass M, Singh Y, Ghai M. A Review on Microbial Species for Forensic Body Fluid Identification in Healthy and Diseased Humans. Curr Microbiol 2023; 80:299. [PMID: 37491404 PMCID: PMC10368579 DOI: 10.1007/s00284-023-03413-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/08/2023] [Indexed: 07/27/2023]
Abstract
Microbial communities present in body fluids can assist in distinguishing between types of body fluids. Metagenomic studies have reported bacterial genera which are core to specific body fluids and are greatly influenced by geographical location and ethnicity. Bacteria in body fluids could also be due to bacterial infection; hence, it would be worthwhile taking into consideration bacterial species associated with diseases. The present review reports bacterial species characteristic of diseased and healthy body fluids across geographical locations, and bacteria described in forensic studies, with the aim of collating a set of bacteria to serve as the core species-specific markers for forensic body fluid identification. The most widely reported saliva-specific bacterial species are Streptococcus salivarius, Prevotella melaninogenica, Neisseria flavescens, with Fusobacterium nucleatum associated with increased diseased state. Lactobacillus crispatus and Lactobacillus iners are frequently dominant in the vaginal microbiome of healthy women. Atopobium vaginae, Prevotella bivia, and Gardnerella vaginalis are more prevalent in women with bacterial vaginosis. Semen and urine-specific bacteria at species level have not been reported, and menstrual blood bacteria are indistinguishable from vaginal fluid. Targeting more than one bacterial species is recommended for accurate body fluid identification. Although metagenomic sequencing provides information of a broad microbial profile, the specific bacterial species could be used to design biosensors for rapid body fluid identification. Validation of microbial typing methods and its application in identifying body fluids in a mixed sample would allow regular use of microbial profiling in a forensic workflow.
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Affiliation(s)
- Mishka Dass
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal, Westville Campus, Private Bag X 54001, Durban, KwaZulu-Natal South Africa
| | - Yashna Singh
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal, Westville Campus, Private Bag X 54001, Durban, KwaZulu-Natal South Africa
| | - Meenu Ghai
- Department of Genetics, School of Life Sciences, University of KwaZulu Natal, Westville Campus, Private Bag X 54001, Durban, KwaZulu-Natal South Africa
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2
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Li Y, Yang Z, Cai T, Jiang D, Luo J, Zhou Z. Untargeted metabolomics of saliva in caries-active and caries-free children in the mixed dentition. Front Cell Infect Microbiol 2023; 13:1104295. [PMID: 37082714 PMCID: PMC10110944 DOI: 10.3389/fcimb.2023.1104295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
ObjectiveTo compare the differences in salivary metabolites between caries-active and caries-free children in the mixed dentition, and explore their correlation with caries status.MethodsThe study involved 20 children (aged 8–9 years) in the mixed dentition, including 10 caries-active (aged 8.6 ± 0.49years) and 10 caries-free children(aged 8.5 ± 0.5years), with a male/female ratio of 1:1. The saliva samples were collected from all children. Metabolite extraction, LC-MS/MS-based untargeted metabolomics, qualitative and semi-quantitative analysis and bioinformatics analysis were performed to identify differential metabolites between the two sample groups. The differential metabolites identified were further analyzed in an attempt to find their correlations with caries status.ResultsIn the positive ion mode, a total of 1606 molecular features were detected in the samples of the two groups, 189 of which were differential metabolites when comparing the caries-active group with the caries-free group, including 104 up-regulated and 85 down-regulated metabolites. In the negative ion mode, a total of 532 molecular features were detected in the samples of two groups, 70 of which were differential metabolites when comparing the caries-active group with the caries-free group, including 37 up-regulated and 33 down-regulated metabolites. In the positive ion mode, two of the top 5 up-regulated differential metabolites were found in and annotated to specific metabolic pathways, whereas in the negative ion mode, only one of the top 5 up-regulated differential metabolites was found in and annotated to specific metabolic pathways. In both the positive and negative ion modes, the top 5 down-regulated differential metabolites were both annotated to the metabolic pathways. KEGG pathway enrichment analysis of differential metabolites showed that histamine and arachidonic acid identified in the positive ion mode, as well as succinate and L-histidine identified in the negative ion mode were enriched in the top 3 significantly altered pathways.ConclusionThe enriched differential metabolites including histamine, L-histidine and succinate were correlated with the presence of dental caries, but their role in the caries process needs to be further investigated.
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Affiliation(s)
- Yueheng Li
- Department of Preventive Dentistry, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Zhengyan Yang
- Department of Preventive Dentistry, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Ting Cai
- Department of Preventive Dentistry, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Dan Jiang
- Department of Preventive Dentistry, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Jun Luo
- Department of Preventive Dentistry, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
- *Correspondence: Jun Luo, ; Zhi Zhou,
| | - Zhi Zhou
- Department of Preventive Dentistry, Stomatological Hospital of Chongqing Medical University, Chongqing, China
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
- *Correspondence: Jun Luo, ; Zhi Zhou,
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3
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Złoch M, Rodzik A, Pauter K, Szultka-Młyńska M, Rogowska A, Kupczyk W, Pomastowski P, Buszewski B. Problems with identifying and distinguishing salivary streptococci: a multi-instrumental approach. Future Microbiol 2021; 15:1157-1171. [PMID: 32954849 DOI: 10.2217/fmb-2020-0036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aim: The purpose of this study was to create an alternative protocol for the DNA-based identification of salivary microbiota focused on the distinguishing of Streptococcus species. Materials & methods: Salivary bacteria were identified using 16S rDNA sequencing and proteins and lipids profiling using MALDI-TOF/MS as well as FTIR analysis. Results: Most of the isolates belonged to streptococci - mostly the salivarious group indistinguishable by the molecular technique. In turn, MALDI analysis allowed for their fast and reliable classification. Although FTIR spectroscopy demonstrated the correct species classification, the spectra interpretation was time consuming and complicated. Conclusion: MALDI-TOF/MS demonstrated the biggest effectiveness in the identification and discrimination between the salivary streptococci, which could be easily incorporated in the workflow of routine microbiological laboratories.
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Affiliation(s)
- Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland
| | - Agnieszka Rodzik
- Department of Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Katarzyna Pauter
- Department of Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Małgorzata Szultka-Młyńska
- Department of Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Agnieszka Rogowska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland.,Department of Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Wojciech Kupczyk
- Department of General, Gastroenterological & Oncological Surgery, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland
| | - Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland.,Department of Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
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4
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Pauter K, Szultka-Młyńska M, Buszewski B. Determination and Identification of Antibiotic Drugs and Bacterial Strains in Biological Samples. Molecules 2020; 25:E2556. [PMID: 32486359 PMCID: PMC7321139 DOI: 10.3390/molecules25112556] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/22/2022] Open
Abstract
Antibiotics were initially natural substances. However, nowadays, they also include synthetic drugs, which show their activity against bacteria, killing or inhibiting their growth and division. Thanks to these properties, many antibiotics have quickly found practical application in the fight against infectious diseases such as tuberculosis, syphilis, gastrointestinal infections, pneumonia, bronchitis, meningitis and septicemia. Antibiotic resistance is currently a detrimental problem; therefore, in addition to the improvement of antibiotic therapy, attention should also be paid to active metabolites in the body, which may play an important role in exacerbating the existing problem. Taking into account the clinical, cognitive and diagnostic purposes of drug monitoring, it is important to select an appropriate analytical method that meets all the requirements. The detection and identification of the microorganism responsible for the infection is also an essential factor in the implementation of appropriate antibiotic therapy. In recent years, clinical microbiology laboratories have experienced revolutionary changes in the way microorganisms are identified. The MALDI-TOF MS technique may be interesting, especially in some areas where a quick analysis is required, as is the case with clinical microbiology. This method is not targeted, which means that no prior knowledge of the infectious agent is required, since identification is based on a database match.
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Affiliation(s)
- Katarzyna Pauter
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarin 7, 87-100 Torun, Poland; (K.P.); (B.B.)
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
| | - Małgorzata Szultka-Młyńska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarin 7, 87-100 Torun, Poland; (K.P.); (B.B.)
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarin 7, 87-100 Torun, Poland; (K.P.); (B.B.)
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100 Torun, Poland
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5
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Srivastava A, Saha S, Sahu C. Early and accurate detection of bacterial isolates from dental plaque in subjects with primary, mixed, and permanent dentition by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technique. J Indian Soc Periodontol 2020; 24:104-108. [PMID: 32189836 PMCID: PMC7069104 DOI: 10.4103/jisp.jisp_303_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 11/18/2022] Open
Abstract
Background: Bacterial colonization of dentition in different age groups can impact prognosis in different dental diseases. Latest diagnostic technique such as matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF) is increasingly being used for accurate identification of bacteria. This study was undertaken to evaluate the MALDI-TOF MS technique to identify bacterial pathogens from dental plaques in subjects with primary, mixed, and permanent dentition. Materials and Methods: The study included 150 subjects of different age groups and were divided into three groups - Group A: Subjects with primary dentition (n = 50), Group B: Subjects with mixed dentition (n = 50), and Group C: Subjects with permanent dentition (n = 50). Subgingival dental plaque samples were collected from buccal and lingual surfaces of premolar and molar teeth. Clinical parameters such as gingival index were recorded. Samples were cultured in routine aerobic and anaerobic medium. Bacterial growths were assessed by semiquantitative methods. Bacterial isolates were confirmed by MALDI-TOF MS technique. Results: MALDI-TOF MS detected all the culture-grown bacteria. In primary dentition group, purple and yellow complex bacteria predominated. Streptococcus spp. was the predominant bacteria (51%) followed by Escherichia coli (19%) and Veillonella spp. (19%). In mixed dentition and permanent group also, Streptococcus spp. was predominant (46%) followed by Veillonella spp. (24%) and E. coli(19%). However, in both groups, orange complex bacteria (bridge complex) such as Prevotella nigrescens and red complex bacteria (Porphyromonas gingivalis, 3%) were seen. For majority of bacteria, the load increased with age. Conclusions: The bacterial isolates showed a distinct age-specific colonization. The use of advanced technique such as MALDI-TOF MS is helpful in the detection of periodontal pathogens, and the effective oral health programs can be implemented to minimize the risk of periodontal diseases.
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Affiliation(s)
- Amitabh Srivastava
- Department of Periodontology and Implantology, Sardar Patel Post Graduate Institute of Dental and Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Sonali Saha
- Department of Periodontology and Implantology, Sardar Patel Post Graduate Institute of Dental and Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Chinmoy Sahu
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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6
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Ly D, Mayrhofer S, Agung Yogeswara IB, Nguyen TH, Domig KJ. Identification, Classification and Screening for γ-Amino-butyric Acid Production in Lactic Acid Bacteria from Cambodian Fermented Foods. Biomolecules 2019; 9:E768. [PMID: 31766706 PMCID: PMC6995518 DOI: 10.3390/biom9120768] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 11/16/2022] Open
Abstract
Screening for various types of lactic acid bacteria (LAB) that form the biological agent γ-amino-butyric acid (GABA) is important to produce different kinds of GABA-containing fermented foods. So far, no GABA-producing LAB have been reported from Cambodian fermented foods. Most small-scale fermentations and even some industrial processes in this country still rely on indigenous LAB. The application of GABA-producing autochthonous starters would allow the production of Cambodian fermented foods with an additional nutritional value that meet the population's dietary habits and that are also more attractive for the international food market. Matrix-assisted laser desorption/ionizing time-of-flight mass spectrometry (MALDI-TOF MS) and partial 16S rDNA sequencing were used to identify 68 LAB isolates from Cambodian fermented foods. These isolates were classified and grouped with (GTG)5 rep-PCR, resulting in 50 strains. Subsequently, all strains were investigated for their ability to produce GABA by thin layer chromatography. GABA-positive strains were further analyzed by the GABase assay. Of the six GABA-positive LAB strains-one Lactobacillus futsaii, two Lactobacillus namurensis, and three Lactobacillus plantarum strains-two Lactobacillus plantarum strains produced high amounts of GABA (20.34 mM, 16.47 mM). These strains should be further investigated for their potential application as GABA-producing starter cultures in the food applications.
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Affiliation(s)
- Dalin Ly
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria; (S.M.); (I.B.A.Y.); (T.-H.N.); (K.J.D.)
- Department of Food Biotechnology, Faculty of Agro-Industry, Royal University of Agriculture, Dangkor District, P.O. Box: 2696, Phnom Penh 12400, Cambodia
| | - Sigrid Mayrhofer
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria; (S.M.); (I.B.A.Y.); (T.-H.N.); (K.J.D.)
| | - I. B. Agung Yogeswara
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria; (S.M.); (I.B.A.Y.); (T.-H.N.); (K.J.D.)
- Department of Nutrition, Universitas Dhyana Pura, Bali 80361, Indonesia
| | - Thu-Ha Nguyen
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria; (S.M.); (I.B.A.Y.); (T.-H.N.); (K.J.D.)
| | - Konrad J. Domig
- Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria; (S.M.); (I.B.A.Y.); (T.-H.N.); (K.J.D.)
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7
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Kazazić SP, Topić Popović N, Strunjak-Perović I, Babić S, Florio D, Fioravanti M, Bojanić K, Čož-Rakovac R. Matrix-assisted laser desorption/ionization time of flight mass spectrometry identification of Vibrio (Listonella) anguillarum isolated from sea bass and sea bream. PLoS One 2019; 14:e0225343. [PMID: 31738803 PMCID: PMC6860450 DOI: 10.1371/journal.pone.0225343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/01/2019] [Indexed: 11/18/2022] Open
Abstract
Vibrio (Listonella) anguillarum is a pathogenic bacterium causing septicaemia in a wide range of marine organisms and inducing severe mortalities, thus it is crucial to conduct its accurate and rapid identification. The aim of this study was to assess MALDI-TOF MS as a method of choice for identification of clinical V. anguillarum isolates from affected marine fish. Since the method accuracy might be influenced by the type of the medium used, as well as by the incubation conditions, we tested V. anguillarum isolates grown on standard media with and without the addition of NaCl, cultured at three incubation temperatures, and at three incubation periods. The best scores were retrieved for V. anguillarum strains grown on NaCl-supplemented tryptone soy agar (TSA) at 22°C and incubated for 48h (100% identification to species level; overall score 2.232), followed by incubation at 37°C and 48h (100% to species level; score 2.192). The strains grown on non-supplemented TSA gave the best readings when incubated at 22°C for 72h (100% identification to species level; overall score 2.182), followed by incubation at 15°C for 72h (100% to species level; score 2.160). Unreliable identifications and no-identifications were growing with the incubation duration at 37°C, on both media, amounting to 88.89% for 7d incubation on supplemented TSA, and 92.60% for 7d incubation on non-supplemented TSA. The age of the cultured strains and use of media significantly impacted the mass spectra, demonstrating that for reliable identification, MALDI-TOF MS protein fingerprinting with the on-target extraction should be performed on strains grown on a NaCl-supplemented medium at temperatures between 15 and 22°C, incubated for 48–72 hours.
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Affiliation(s)
- Snježana P Kazazić
- Laboratory for Mass Spectrometry and Functional Proteomics, Rudjer Bošković Institute, Zagreb, Croatia
| | - Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia.,Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia.,Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Sanja Babić
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia.,Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Daniela Florio
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Ozzano Emilia, Italy
| | - Marialetizia Fioravanti
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Ozzano Emilia, Italy
| | - Krunoslav Bojanić
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia.,Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Rudjer Bošković Institute, Zagreb, Croatia.,Centre of Excellence for Marine Bioprospecting-BioProCro, Rudjer Bošković Institute, Zagreb, Croatia
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Zhang Y, Zhang Q. Relationship between tetracycline antibiotic susceptibility and genotype in oral cavity Lactobacilli clinical isolates. Antimicrob Resist Infect Control 2019; 8:27. [PMID: 30740220 PMCID: PMC6360694 DOI: 10.1186/s13756-019-0483-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 01/30/2019] [Indexed: 11/16/2022] Open
Abstract
Background Antibiotic resistance, is often conferred by the presence of antibiotic resistance genes. This study aimed to investigate the relationship between tetracycline resistance (Tet-R) and genotype in 31 Lactobacillus isolates from caries-active patients. Methods The tetracycline susceptibility of Lactobacillus isolates was determined using the agar spot test and the genetic characteristics associated with tetracycline resistance using whole-genome sequencing (WGS). Results The minimum inhibitory concentration (MIC) values of most isolates were equal to or lower than the breakpoint MIC values. Four strains that were phenotypically more sensitive (L. fermentum B09, S23 and L. rhamonsus B17) or more resistant (L. plantarum B43) than other isolates to tetracycline were subjected to conduct whole-genome sequencing in order to detect the tetracycline resistance genes. The results revealed that the most common Tet-R genes in Lactobacillus strains were tetT, tetW, tetO and tetL. In addition, tetPB, tcr3 and otrA were detected for the first time. There were distinct Tet-R gene mutations in Lactobacillus isolates. Overall, the mean expression values of Tet-R-mutated genes in L. plantarum B43 were elevated, and the relative expression levels of tetT and tetW genes in L. rhamonsus B17 L. fermentum B09 and S23 were decreased relative to reference strains. Conclusion The results of this study indicate that Lactobacillus isolates from saliva of caries-active patients do not present considerable tetracycline resistance reservoirs. However, genetic compounds associated with tetracycline resistance were identified by whole-genome sequencing, providing meaningful insights into tetracycline resistance mechanisms.
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Affiliation(s)
- Yifei Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing, People’s Republic of China
| | - Qian Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing, People’s Republic of China
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9
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Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease. Sci Rep 2018; 8:16598. [PMID: 30413731 PMCID: PMC6226508 DOI: 10.1038/s41598-018-33773-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 09/21/2018] [Indexed: 01/09/2023] Open
Abstract
Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p < 0.001 & FDR = 0.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies.
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10
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Sensitivity of caries pathogens to antimicrobial peptides related to caries risk. Clin Oral Investig 2018; 22:2519-2525. [PMID: 29372443 DOI: 10.1007/s00784-018-2348-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 01/17/2018] [Indexed: 01/26/2023]
Abstract
OBJECTIVES Antimicrobial peptides (AMPs) represent important facets of the immune system controlling infectious diseases. However, pathogens show varying susceptibilities to AMPs. This study investigates the susceptibilities of strains of Streptococcus mutans (SM), Actinomyces naeslundii (AN), and Lactobacillus spp. (LB) towards AMPs and if there are correlations between the appearance of such high-risk strains and clinical caries status. MATERIAL AND METHODS Plaque samples were collected from patients along with clinical examinations. Bacterial strains were identified via selective media, matrix-assisted laser desorption/ionization analysis-time of flight (MALDI-TOF), and arbitrary-primed-PCR (AP-PCR). Each strain was tested for susceptibility to LL-37, HBD-2, HNP-1, and HNP-3 or phosphate-buffered saline as negative control in a biofilm model on hydroxylapatite discs. Survival rates and resulting risk classification for each strain were determined. Correlations were calculated between the number of high-risk strains (all/S. mutans) appearing in patients and their clinical caries status. RESULTS Forty-seven patients were included with mean DMFT values of 11.4 ± 8.7. A total of 8 different SM, 30 LB, and 47 AN strains were detected. One-way ANOVA indicated that type/concentration of AMPs had major influence on reductions of Lactobacilli and Actinomyces. Seventeen strains of AN, 2 of SM, and 6 of LB had low susceptibilities to AMPs. The number of such strains in patients showed significant positive correlations to the DMFT values (all p = 0.001; r = 0.452; S. mutans p < 0.0001, r = 0.558). CONCLUSION The occurrence of low susceptible strains to AMPs seems to correlate with the individual caries status. CLINICAL RELEVANCE The results may lead to new ways to identify individuals with increased caries risk.
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Nouri Gharajalar S, Firouzamandi M. Molecular Detection of Antibiotic Resistance Determinants in Lactobacillus Bacteria Isolated from Human Dental Plaques. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2017. [DOI: 10.29252/jommid.5.3.4.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Foschi C, Laghi L, Parolin C, Giordani B, Compri M, Cevenini R, Marangoni A, Vitali B. Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR. PLoS One 2017; 12:e0172483. [PMID: 28207855 PMCID: PMC5312945 DOI: 10.1371/journal.pone.0172483] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/06/2017] [Indexed: 02/07/2023] Open
Abstract
Lactobacilli represent a wide range of bacterial species with several implications for the human host. They play a crucial role in maintaining the ecological equilibrium of different biological niches and are essential for fermented food production and probiotic formulation. Despite the consensus about the ‘health-promoting’ significance of Lactobacillus genus, its genotypic and phenotypic characterization still poses several difficulties. The aim of this study was to assess the integration of different approaches, genotypic (16S rRNA gene sequencing), proteomic (MALDI-TOF MS) and metabolomic (1H-NMR), for the taxonomic and metabolic characterization of Lactobacillus species. For this purpose we analyzed 40 strains of various origin (intestinal, vaginal, food, probiotics), belonging to different species. The high discriminatory power of MALDI-TOF for species identification was underlined by the excellent agreement with the genotypic analysis. Indeed, MALDI-TOF allowed to correctly identify 39 out of 40 Lactobacillus strains at the species level, with an overall concordance of 97.5%. In the perspective to simplify the MALDI TOF sample preparation, especially for routine practice, we demonstrated the perfect agreement of the colony-picking from agar plates with the protein extraction protocol. 1H-NMR analysis, applied to both culture supernatants and bacterial lysates, identified a panel of metabolites whose variations in concentration were associated with the taxonomy, but also revealed a high intra-species variability that did not allow a species-level identification. Therefore, despite not suitable for mere taxonomic purposes, metabolomics can be useful to correlate particular biological activities with taxonomy and to understand the mechanisms related to the antimicrobial effect shown by some Lactobacillus species.
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Affiliation(s)
- Claudio Foschi
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | - Luca Laghi
- Centre of Foodomics, Department of Agro-Food Science and Technology, University of Bologna, Bologna, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Barbara Giordani
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Monica Compri
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | | | | | - Beatrice Vitali
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Mikelsaar M, Sepp E, Štšepetova J, Songisepp E, Mändar R. Biodiversity of Intestinal Lactic Acid Bacteria in the Healthy Population. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 932:1-64. [DOI: 10.1007/5584_2016_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Lee MR, Tsai CJ, Liang SK, Lin CK, Huang YT, Hsueh PR. Clinical characteristics of bacteraemia caused by Lactobacillus spp. and antimicrobial susceptibilities of the isolates at a medical centre in Taiwan, 2000–2014. Int J Antimicrob Agents 2015; 46:439-45. [DOI: 10.1016/j.ijantimicag.2015.06.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/20/2023]
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