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Jeong J, Ahn K, Yun K, Kim M, Choi Y, Han M, Mun S, Kim YT, Lee KE, Kim MY, Ahn Y, Han K. Exploring oral bacterial compositional network in two oral disease groups using a convergent approach of NGS-molecular diagnostics. Genes Genomics 2024; 46:881-898. [PMID: 38847972 DOI: 10.1007/s13258-024-01526-6] [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: 04/20/2024] [Accepted: 05/26/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND Since most of the commonly known oral diseases are explained in link with balance of microbial community, an accurate bacterial taxonomy profiling for determining bacterial compositional network is essential. However, compared to intestinal microbiome, research data pool related to oral microbiome is small, and general 16S rRNA screening method has a taxonomy misclassification issue in confirming complex bacterial composition at the species level. OBJECTIVE Present study aimed to explore bacterial compositional networks at the species level within saliva of 39 oral disease patients (Dental Caries group: n = 26 and Periodontitis group: n = 13) through comparison with public Korean-specific healthy oral microbiome data. METHODS Here, we applied comprehensive molecular diagnostics based on qRT-PCR and Sanger sequencing methods to complement the technical limitations of NGS-based 16S V3-V4 amplicon sequencing technology. RESULTS As a result of microbiome profiling at the genus level, relative frequencies of many nitrate-reducing bacteria within each oral disease group were found to be significantly low compared to the healthy group. In addition, the molecular diagnostics-based bacterial identification method allowed the determination of the correct taxonomy of screened primary colonizers (Streptococcus and Actinomyces unclassification clusters) for each oral disease. Finally, as with the results of microbiome profiling at the genus level, many core-species classified within the saliva of each oral disease group were also related to nitrate-reduction, and it was estimated that various pathogens associated with each disease formed a bacterial network with the core-species. CONCLUSION Our study introduced a novel approach that can compensate for the difficulty of identifying an accurate bacterial compositional network at the species level due to unclear taxonomy classification by using the convergent approach of NGS-molecular diagnostics. Ultimately, we suggest that our experimental approach and results could be potential reference materials for researchers who intend to prevent oral disease by determining the correlation between oral health and bacterial compositional network according to the changes in the relative frequency for nitrate-reducing species.
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Affiliation(s)
- Jinuk Jeong
- Department of Bioconvergence Engineering, Dankook University, Yongin, 16890, Republic of Korea
| | - Kung Ahn
- HuNbiome Co., Ltd, R&D Center, Gasan Digital 1-Ro, Geumcheon-Gu, Seoul, Korea
| | - Kyeongeui Yun
- HuNbiome Co., Ltd, R&D Center, Gasan Digital 1-Ro, Geumcheon-Gu, Seoul, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Minseo Kim
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yeseul Choi
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Miyang Han
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Seyoung Mun
- College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea
- Smart Animal Bio Institute, Dankook University, Cheonan, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, Republic of Korea
| | - Yeon-Tae Kim
- Department of Periodontology, Daejeon Dental Hospital, Institute of Wonkwang Dental Research, Wonkwang University College of Dentistry, Daejeon, Korea
| | - Kyung Eun Lee
- Department of Oral Medicine, Department of Anesthesiology, School of Dentistry, Jeonbuk National University, Jeonju, 54896, Korea
| | - Moon-Young Kim
- Department of Oral and Maxillofacial Surgery, College of Dentistry, Dankook University, Cheonan, 31116, Korea
| | - Yongju Ahn
- HuNbiome Co., Ltd, R&D Center, Gasan Digital 1-Ro, Geumcheon-Gu, Seoul, Korea.
| | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Yongin, 16890, Republic of Korea.
- HuNbiome Co., Ltd, R&D Center, Gasan Digital 1-Ro, Geumcheon-Gu, Seoul, Korea.
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea.
- College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea.
- Smart Animal Bio Institute, Dankook University, Cheonan, Republic of Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, Republic of Korea.
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Mato EG, Montaño-Barrientos BJ, Rivas-Mundiña B, Aneiros IV, López LS, Posse JL, Lamas LM. Anti-caries Streptococcus spp.: A potential preventive tool for special needs patients. SPECIAL CARE IN DENTISTRY 2024; 44:813-822. [PMID: 37674277 DOI: 10.1111/scd.12920] [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: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023]
Abstract
INTRODUCTION Probiotics are living microorganisms that act on the host-microbiome interface to restore the microbiota's physiological homeostasis. Numerous probiotics have been marketed with inhibitory activity against Streptococcus mutans and consequently with a potential anti-caries effect, mainly of the genera Lactobacillus and Bifidobacterium, whose main disadvantage is their limited ability to settle in the oral cavity. METHODS This narrative review describes the main Streptococcus spp. with probiotic anti-Streptococcus mutans activity, whose substantivity is greater than that of Lactobacillus spp. and consequently with anti-caries potentiality. We performed a literature review in the PubMed, Science Direct and Google Scholar databases of articles published in English (without time restriction) related to caries and probiotics. RESULTS The potential identified anti-caries probiotics included Streptococcus spp. A12, Streptococcus oralis (AJ3), Streptococcus oligofermentans, Streptococcus salivarius (K12, M18, JH, LAB813, 24SMB), Streptococcus spp. with arginolytic activity (S. sanguinis, S. gordonii, S. ratti, S. parasanguinis, S. intermedius, S. australis, and S. cristatus), Streptococcus rattus (JH145), Streptococcus dentisani and Streptococcus downii. CONCLUSIONS The possibility of using these Streptococcus spp. as probiotics that inhibit the growth of dental plaque and the development of carious lesions represents a potential tool of particular interest for individuals with physical or intellectual disabilities that impede the routine and effective application of mechanical dental plaque removal techniques.
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Affiliation(s)
- Eliane García Mato
- Medical-Surgical Dentistry Research Group (OMEQUI), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Bitalio J Montaño-Barrientos
- Clinical Microbiology, Hospital Álvaro Cunqueiro, University Hospital Complex of Vigo, Microbiology and Infectology Group, Galicia Sur Health Research Institute (IISGS), Vigo, Galicia, Spain
| | - Berta Rivas-Mundiña
- Medical-Surgical Dentistry Research Group (OMEQUI), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Iván Varela Aneiros
- Medical-Surgical Dentistry Research Group (OMEQUI), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Lucía Sande López
- Medical-Surgical Dentistry Research Group (OMEQUI), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Jacobo Limeres Posse
- Medical-Surgical Dentistry Research Group (OMEQUI), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Lucía Martínez Lamas
- Clinical Microbiology, Hospital Álvaro Cunqueiro, University Hospital Complex of Vigo, Microbiology and Infectology Group, Galicia Sur Health Research Institute (IISGS), Vigo, Galicia, Spain
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Yu D, Zhang J, Gao N, Huo Y, Li W, Wang T, Zhang X, Simayijiang H, Yan J. Rapid and visual detection of specific bacteria for saliva and vaginal fluid identification with the lateral flow dipstick strategy. Int J Legal Med 2023; 137:1853-1863. [PMID: 37358650 DOI: 10.1007/s00414-023-03051-9] [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: 02/06/2023] [Accepted: 06/19/2023] [Indexed: 06/27/2023]
Abstract
Identification of body fluids is critical for crime scene reconstruction, and a source of investigation source of investigative leads. In recent years, microbial DNA analysis using sequencing and quantitative real-time polymerase chain reaction have been used to identify body fluids. However, these techniques are time-consuming, expensive, and require complex workflows. In this study, a new method for simultaneous detection of Streptococcus salivarius and Lactobacillus crispatus using polymerase chain reaction (PCR) in combination with a lateral flow dipstick (LFD) was developed to identify saliva and vaginal fluid in forensic samples. LFD results can be observed with the naked eye within 3 min with a sensitivity of 0.001 ng/µL DNA. The PCR-LFD assay was successfully used to detect S. salivarius and L. crispatus in saliva and vaginal fluid respectively, and showed negative results in blood, semen, nasal fluid, and skin. Moreover, saliva and vaginal fluid were detectable even at an extremely high mixing ratio of sample DNA (1:999). Saliva and vaginal fluid were identified in various mock forensic samples. These results indicate that saliva and vaginal fluid can be effectively detected by identifying S. salivarius and L. crispatus, respectively. Furthermore, we have shown that DNA samples used to identify saliva and vaginal fluid can also provide a complete short tandem repeat (STR) profile when used as source material for forensic STR profiling. In summary, our results suggest that PCR-LFD is a promising assay for rapid, simple, reliable, and efficient identification of body fluids.
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Affiliation(s)
- Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Niu Gao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Wanting Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China.
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China.
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Campagnoli LIM, Varesi A, Barbieri A, Marchesi N, Pascale A. Targeting the Gut-Eye Axis: An Emerging Strategy to Face Ocular Diseases. Int J Mol Sci 2023; 24:13338. [PMID: 37686143 PMCID: PMC10488056 DOI: 10.3390/ijms241713338] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/20/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023] Open
Abstract
The human microbiota refers to a large variety of microorganisms (bacteria, viruses, and fungi) that live in different human body sites, including the gut, oral cavity, skin, and eyes. In particular, the presence of an ocular surface microbiota with a crucial role in maintaining ocular surface homeostasis by preventing colonization from pathogen species has been recently demonstrated. Moreover, recent studies underline a potential association between gut microbiota (GM) and ocular health. In this respect, some evidence supports the existence of a gut-eye axis involved in the pathogenesis of several ocular diseases, including age-related macular degeneration, uveitis, diabetic retinopathy, dry eye, and glaucoma. Therefore, understanding the link between the GM and these ocular disorders might be useful for the development of new therapeutic approaches, such as probiotics, prebiotics, symbiotics, or faecal microbiota transplantation through which the GM could be modulated, thus allowing better management of these diseases.
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Affiliation(s)
| | - Angelica Varesi
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy;
| | - Annalisa Barbieri
- Department of Drug Sciences, Unit of Pharmacology, University of Pavia, 27100 Pavia, Italy; (A.B.); (N.M.)
| | - Nicoletta Marchesi
- Department of Drug Sciences, Unit of Pharmacology, University of Pavia, 27100 Pavia, Italy; (A.B.); (N.M.)
| | - Alessia Pascale
- Department of Drug Sciences, Unit of Pharmacology, University of Pavia, 27100 Pavia, Italy; (A.B.); (N.M.)
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Ranjan A, Arora J, Chauhan A, Basniwal RK, Kumari A, Rajput VD, Prazdnova EV, Ghosh A, Mukerjee N, Mandzhieva SS, Sushkova S, Minkina T, Jindal T. Advances in characterization of probiotics and challenges in industrial application. Biotechnol Genet Eng Rev 2022:1-44. [PMID: 36200338 DOI: 10.1080/02648725.2022.2122287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.
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Affiliation(s)
- Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Jayati Arora
- Amity Institute of Environmental Sciences, Amity University, Noida, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
| | - Rupesh Kumar Basniwal
- Amity Institute of Advanced Research and Studies (M&D), Amity University, Noida, India
| | - Arpna Kumari
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Evgeniya V Prazdnova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Nobendu Mukerjee
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, New South Wales, Australia
| | - Saglara S Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology Safety and Management, Amity University, Noida, India
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Trukhan DI, Sulimov AF, Trukhan LY. Changes in the organs and tissues of the oral cavity in the new coronavirus infection (COVID-19): A review. CONSILIUM MEDICUM 2022. [DOI: 10.26442/20751753.2022.5.201755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2 infection can cause changes in the organs and tissues of the oral cavity, which is associated with a wide distribution of angiotensin-converting enzyme type 2 in the oral cavity, mainly epithelial cells of the oral mucosa, gums and fibroblasts of the periodontal ligament. Thus, the oral mucosa is susceptible to SARS-CoV-2 infection and may act as a gateway for the virus, as well as a reservoir for SARS-CoV-2. We searched the literature for the period from the beginning of the pandemic until May 30, 2022, devoted to the study of changes in the organs and tissues of the oral cavity with a new coronavirus infection (COVID-19) in the electronic search engines PubMed/MEDLINE and Scopus. A special place in the study of changes in the organs and tissues of the oral cavity with a new coronavirus infection (COVID-19) is occupied by periodontal pathology. A number of reviews and clinical studies conclude the importance of good oral hygiene and periodontal health as an important aspect of COVID-19 prevention and management. Oral probiotics can be considered as a promising direction for correcting changes in organs and tissues of the oral cavity in COVID-19.
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Sijtsma L, Suarez JE, Sundh I, Vlak J, Barizzone F, Hempen M, Correia S, Herman L. Update of the list of QPS-recommended microbiological agents intentionally added to food or feed as notified to EFSA 16: suitability of taxonomic units notified to EFSA until March 2022. EFSA J 2022; 20:e07408. [PMID: 35898292 PMCID: PMC9310698 DOI: 10.2903/j.efsa.2022.7408] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of microorganisms, intended for use in the food or feed chains, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge, safety concerns and occurrence of antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS TUs. Of the 50 microorganisms notified to EFSA in October 2021 to March 2022 (inclusive), 41 were not evaluated: 10 filamentous fungi, 1 Enterococcus faecium, 1 Clostridium butyricum, 3 Escherichia coli and 1 Streptomyces spp. because are excluded from QPS evaluation, and 25 TUs that have already a QPS status. Nine notifications, corresponding to seven TUs were evaluated: four of these, Streptococcus salivarius, Companilactobacillus formosensis, Pseudonocardia autotrophica and Papiliotrema terrestris, being evaluated for the first time. The other three, Microbacterium foliorum, Pseudomonas fluorescens and Ensifer adhaerens were re-assessed. None of these TUs were recommended for QPS status: Ensifer adhaerens, Microbacterium foliorum, Companilactobacillus formosensis and Papiliotrema terrestris due to a limited body of knowledge, Streptococcus salivarius due to its ability to cause bacteraemia and systemic infection that results in a variety of morbidities, Pseudonocardia autotrophica due to lack of body of knowledge and uncertainty on the safety of biologically active compounds which can be produced, and Pseudomonas fluorescens due to possible safety concerns.
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Kiselnikova LP, Toma EI. Changes in the main dental parameters of preschoolers with caries affected by long-term probiotic intake. Pediatr Dent 2022. [DOI: 10.33925/1683-3031-2022-22-2-97-102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Relevance. For several decades, they have added bacteria called probiotics to some foods for their positive effects on human health. In dental practice, probiotics may help fight caries and inflammatory periodontal diseases. Dentists are interested in probiotics because of the latter’s ability to adhere to and colonize various oral tissues.Purpose. To evaluate the clinical effectiveness of S. salivarius M18 probiotic in preschool children.Material and methods. The study formed 2 groups (45 children in each) of children aged 3 to 6 years with multiple dental caries who underwent dental treatment and 4-fold fluoride varnish application. The main group took 2 courses of S. salivarius M18 probiotic lozenges (the 1st course from February 16 to May 16, 2021, and the 2nd course from October 26, 2021, to January 26, 2022). The children of the comparison group did not use the probiotic. We evaluated the Hygiene Index by Fedorov-Volodkina, dmf(t) rate, ICDAS-II index, and PMA index in children of both groups at the baseline and after 3, 6 and 12 months. Additionally, both groups kept food diaries. The statistical data processing was performed variance analysis of using the Friedman test (significant differences were at p ≤ 0.05).Results. The year of observation in preschool children showed that two 3-month courses of an S. salivarius M18 probiotic intake led to a signifcant improvement in the hygiene index by 2.2 times, 2.3-fold stabilization of initial caries according to the ICDAS II index, caries decrease by 81%, gingivitis prevalence reduction (PMA index decrease by 72.9%).Conclusion. The study results confirm the effectiveness of S. salivarius M18 probiotic in preschoolers with caries as a means of dental status correction and stabilization.
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Affiliation(s)
| | - E. I. Toma
- A. I. Yevdokimov Moscow State University of Medicine and Dentistry
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