1
|
Pagnussatti MEL, de Barros Santos HS, Parolo CCF, Hilgert JB, Arthur RA. Oral microbiota: Taxonomic composition and functional profile in caries-free and in caries-affected individuals - A systematic review. Arch Oral Biol 2024; 168:106070. [PMID: 39226678 DOI: 10.1016/j.archoralbio.2024.106070] [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: 06/30/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024]
Abstract
OBJECTIVE To compare the oral microbiota among caries-free (CF) with caries-affected (CA) individuals, both at taxonomic and at functional levels. DESIGN This systematic review was conducted following PRISMA guidelines. A structured search was carried out in MEDLINE/PUBMED, Web of Science, EMBASE, LILACS, SciELO, Scopus and Google Scholar databases up to September, 2023. Observational studies, without any restriction on date of publication and using next-generation targeted or untargeted sequencing methods for identification of microbial communities were included. Qualitative synthesis was performed from all included studies. RESULTS 54 studies were included (43 cross-sectional; 11 cohort) comprising more than 3486 participants (at least 1666 CF and 1820 CA) whose saliva and/or dental plaque were used as clinical samples. Methodological quality was graded as "fair" for most of the studies. The abundance of 87 bacterial and 44 fungal genera were statistically different among CF and CA individuals. Atopobium spp., Capnocytophaga spp., Lactobacillus spp., Prevotella spp., Scardovia spp., Selenomonas spp. among others were frequently reported as being more abundant in CA individuals. Several functional patterns, such as lipids, carbohydrate, starch, sucrose, amino sugar metabolisms, among others, were identified as being specifically related to CF or to CA conditions. CONCLUSION In spite of the variability among the included studies and of the predominance of qualitative synthesis, groups of microorganisms as well as specific functional profiles coded by the assessed microbiota are differently abundant among caries-affected and caries-free individuals. These results need to be interpreted with caution considering the limitations inherent to each assessed primary study.
Collapse
Affiliation(s)
- Maria Eduarda Lisbôa Pagnussatti
- Preventive and Community Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2492, Porto Alegre 90035-003, Brazil.
| | - Heitor Sales de Barros Santos
- Preventive and Community Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2492, Porto Alegre 90035-003, Brazil.
| | - Clarissa Cavalcanti Fatturi Parolo
- Preventive and Community Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2492, Porto Alegre 90035-003, Brazil.
| | - Juliana Balbinot Hilgert
- Preventive and Community Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2492, Porto Alegre 90035-003, Brazil; National Council for Research and Development (CNPq).
| | - Rodrigo Alex Arthur
- Preventive and Community Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Ramiro Barcelos, 2492, Porto Alegre 90035-003, Brazil.
| |
Collapse
|
2
|
Bao K, Silbereisen A, Grossmann J, Nanni P, Gehrig P, Emingil G, Erguz M, Karapinar DY, Pekpinarli B, Belibasakis GN, Tsilingaridis G, Zaura E, Bostanci N. Protein Network Alterations in G-CSF Treated Severe Congenital Neutropenia Patients and Beneficial Effects of Oral Health Intervention. Proteomics Clin Appl 2024:e202400064. [PMID: 39096313 DOI: 10.1002/prca.202400064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 08/05/2024]
Abstract
PURPOSE Severe congenital neutropenia (SCN) is a raredisorder characterized by diminished neutrophil levels. Despite granulocytecolony-stimulating factor (G-CSF) treatment, SCN patients remain still prone tosevere infections, including periodontal disease-a significant oral healthrisk. This study investigates the host proteome and metaproteome in saliva andgingival crevicular fluid (GCF) of G-CSF-treated patients. EXPERIMENTAL DESIGN We used label-free quantitative proteomics on saliva and GCF samples from SCN patients before (n = 10, mean age: 10.7 ± 6.6 years) and after a 6-month oral hygiene intervention (n = 9,mean age: 11.6 ± 5.27 years), and from 12 healthy controls. RESULTS We quantified 894 proteins in saliva (648 human,246 bacterial) and 756 proteins in GCF (493 human, 263 bacterial). Predominant bacterial genera included Streptococcus, Veillonella, Selenomonas, Corynebacterium, Porphyromonas, and Prevotella. SCN patients showed reduced antimicrobial peptides (AMPs) and elevated complement proteins compared tohealthy controls. Oral hygiene intervention improved oral epithelial conditionsand reduced both AMPs and complement proteins. CONCLUSIONS AND CLINICAL RELEVANCE SCN patients have aunique proteomic profile with reduced AMPs and increased complement proteins, contributing to infection susceptibility. Oral hygiene intervention not onlyimproved oral health in SCN patients but also offers potential overall therapeuticbenefits.
Collapse
Affiliation(s)
- Kai Bao
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Angelika Silbereisen
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Jonas Grossmann
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB) Quartier Sorge-Batiment Amphipole, Lausanne, Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Peter Gehrig
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Gülnur Emingil
- Department of Periodontology, School of Dentistry, Ege University, İzmir, Turkey
| | - Merve Erguz
- Department of Periodontology, School of Dentistry, Ege University, İzmir, Turkey
| | | | - Burç Pekpinarli
- Department of Pediatrics, School of Dentistry, Ege University, İzmir, Turkey
| | - Georgios N Belibasakis
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Georgios Tsilingaridis
- Division of Pediatric Dentistry, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, Amsterdam, The Netherlands
| | - Nagihan Bostanci
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| |
Collapse
|
3
|
Kashyap B, Kullaa A. Salivary Metabolites Produced by Oral Microbes in Oral Diseases and Oral Squamous Cell Carcinoma: A Review. Metabolites 2024; 14:277. [PMID: 38786754 PMCID: PMC11122927 DOI: 10.3390/metabo14050277] [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: 03/06/2024] [Revised: 04/01/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
In recent years, salivary metabolome studies have provided new biological information and salivary biomarkers to diagnose different diseases at early stages. The saliva in the oral cavity is influenced by many factors that are reflected in the salivary metabolite profile. Oral microbes can alter the salivary metabolite profile and may express oral inflammation or oral diseases. The released microbial metabolites in the saliva represent the altered biochemical pathways in the oral cavity. This review highlights the oral microbial profile and microbial metabolites released in saliva and its use as a diagnostic biofluid for different oral diseases. The importance of salivary metabolites produced by oral microbes as risk factors for oral diseases and their possible relationship in oral carcinogenesis is discussed.
Collapse
Affiliation(s)
| | - Arja Kullaa
- Institute of Dentistry, University of Eastern Finland, 70211 Kuopio, Finland;
| |
Collapse
|
4
|
Alyousef YM, Piotrowski S, Alonaizan FA, Alsulaiman A, Alali AA, Almasood NN, Vatte C, Hamilton L, Gandla D, Lad H, Robinson FL, Cyrus C, Meng RC, Dowdell A, Piening B, Keating BJ, Al-Ali AK. Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries. BMC Oral Health 2023; 23:935. [PMID: 38012587 PMCID: PMC10683298 DOI: 10.1186/s12903-023-03448-3] [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: 12/08/2022] [Accepted: 09/24/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Oral microbiome sequencing has revealed key links between microbiome dysfunction and dental caries. However, these efforts have largely focused on Western populations, with few studies on the Middle Eastern communities. The current study aimed to identify the composition and abundance of the oral microbiota in saliva samples of children with different caries levels using machine learning approaches. METHODS Oral microbiota composition and abundance were identified in 250 Saudi participants with high dental caries and 150 with low dental caries using 16 S rRNA sequencing on a NextSeq 2000 SP flow cell (Illumina, CA) using 250 bp paired-end reads, and attempted to build a classifier using random forest models to assist in the early detection of caries. RESULTS The ADONIS test results indicate that there was no significant association between sex and Bray-Curtis dissimilarity (p ~ 0.93), but there was a significant association with dental caries status (p ~ 0.001). Using an alpha level of 0.05, five differentially abundant operational taxonomic units (OTUs) were identified between males and females as the main effect along with four differentially abundant OTUs between high and low dental caries. The mean metrics for the optimal hyperparameter combination using the model with only differentially abundant OTUs were: Accuracy (0.701); Matthew's correlation coefficient (0.0509); AUC (0.517) and F1 score (0.821) while the mean metrics for random forest model using all OTUs were:0.675; 0.054; 0.611 and 0.796 respectively. CONCLUSION The assessment of oral microbiota samples in a representative Saudi Arabian population for high and low metrics of dental caries yields signatures of abundances and diversity.
Collapse
Affiliation(s)
- Yousef M Alyousef
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Stanley Piotrowski
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Faisal A Alonaizan
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Ahmed Alsulaiman
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Ali A Alali
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Naif N Almasood
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Chittibabu Vatte
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, Cornish Road, Rakah, Dammam, 31441, Saudi Arabia
| | - Lauren Hamilton
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Divya Gandla
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Hetal Lad
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Fred L Robinson
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Cyril Cyrus
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, Cornish Road, Rakah, Dammam, 31441, Saudi Arabia
| | - Ryan C Meng
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Alexa Dowdell
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Brian Piening
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Brendan J Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Amein K Al-Ali
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, Cornish Road, Rakah, Dammam, 31441, Saudi Arabia.
| |
Collapse
|
5
|
Regueira-Iglesias A, Balsa-Castro C, Blanco-Pintos T, Tomás I. Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis. Mol Oral Microbiol 2023; 38:347-399. [PMID: 37804481 DOI: 10.1111/omi.12434] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them.
Collapse
Affiliation(s)
- Alba Regueira-Iglesias
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Carlos Balsa-Castro
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Triana Blanco-Pintos
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Inmaculada Tomás
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| |
Collapse
|
6
|
Chattopadhyay I, Lu W, Manikam R, Malarvili MB, Ambati RR, Gundamaraju R. Can metagenomics unravel the impact of oral bacteriome in human diseases? Biotechnol Genet Eng Rev 2022; 39:85-117. [PMID: 35861776 DOI: 10.1080/02648725.2022.2102877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Oral microbial ecosystems are vital in maintaining the health of the oral cavity and the entire body. Oral microbiota is associated with the progression of oral diseases such as dental caries, periodontal diseases, head and neck cancer, and several systemic diseases such as cardiovascular disease, rheumatoid arthritis, adverse pregnancy outcomes, diabetes, lung infection, colorectal cancer, and pancreatic cancer. Buccal mucosa, tongue dorsum, hard palate, saliva, palatine tonsils, throat, keratinized gingiva, supra-gingival plaque, subgingival plaque, dentures, and lips are microbial habitats of the oral cavity. Porphyromonas gingivalis may have a role in the development of periodontal diseases, oral cancer, diabetes, and atherosclerotic disease. Fusobacterium nucleatum showed a higher abundance in periodontal diseases, oral and colon cancer, adverse pregnancy outcomes, diabetes, and rheumatoid arthritis. The higher abundance of Prevotella intermedia is typical in periodontal diseases, rheumatoid arthritis, and adverse pregnancy outcome. S. salivarius displayed higher abundance in both dental caries and OSCC. Oral bacteria may influence systemic diseases through inflammation by releasing pro inflammatory cytokines. Identification of oral bacteria using culture-dependent approaches and next-generation sequencing-based metagenomic approaches is believed to significantly identify the therapeutic targets and non-invasive diagnostic indicators in different human diseases. Oral bacteria in saliva could be exploited as a non-invasive diagnostic indicator for the early detection of oral and systemic disorders. Other therapeutic approaches such as the use of probiotics, green tea polyphenol, cold atmospheric plasma (CAP) therapy, antimicrobial photodynamic therapy, and antimicrobial peptides are used to inhibit the growth of biofilm formation by oral bacteria.
Collapse
Affiliation(s)
| | - Wenying Lu
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Rishya Manikam
- Trauma and Emergency, University of Malaya, Kuala Lumpur, Malaysia
| | - M B Malarvili
- School of Biomedical and Health Science, Universiti Teknologi Malaysia, Skudai, Johor Bahru, Malaysia
| | - Ranga Rao Ambati
- Department of Biotechnology, Vignan`s Foundation for Science, Technology and Research (Deemed to be University), Guntur, Andhra Pradesh, India
| | - Rohit Gundamaraju
- ER stress and Mucosal immunology lab, School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| |
Collapse
|
7
|
Salivary microbiome differences in prepubertal children with and without adrenal androgen excess. Pediatr Res 2022; 91:1797-1803. [PMID: 34341500 PMCID: PMC8807752 DOI: 10.1038/s41390-021-01661-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/30/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Premature adrenarche is a condition of childhood adrenal androgen excess (AAE) in the absence of gonadotropin-dependent puberty, and has been linked to insulin resistance and progression to metabolic syndrome. Microbial dysbiosis is associated with progression of inflammatory states and chronic diseases. Here, we aimed to examine the salivary microbiomes of children with AAE and assess the relationship with adrenal androgens and metabolic parameters. METHODS In a prospective cross-sectional study of children with AAE and healthy controls, adrenal and metabolic parameters were characterized and salivary microbiome was profiled using V3-V4 16S rDNA gene amplicon sequencing. RESULTS There was increased α-diversity in AAE (5 M, 15 F) compared to controls (3 M, 8 F), with positive correlation of 11OHA4, 11KA4, testosterone, androstenedione, DHEA, and DHEAS. Subanalyses showed increased α-diversity in both overweight/obese AAE and normal weight AAE compared to normal weight controls. Genus Peptostreptococcus, Veillonella, and Streptococcus salivarius were increased in normal weight AAE. Genus Prevotella, Abiotrophia, and Neisseria were increased in overweight/obese AAE. CONCLUSION These pilot data demonstrate differences in salivary microbiome profiles of children with and without AAE. Further studies are needed to assess the causal relationships between adrenal androgens, metabolic dysfunction, and salivary microbiome composition. IMPACT This study is the first to report the salivary microbiome of prepubertal children with adrenal androgen excess (AAE). α-Diversity is increased in the salivary microbiome of children with AAE independent of weight status, and in this study cohort several serum androgens are positively associated with α-diversity. Several taxa that have been associated with periodontal disease and inflammation are found to be significantly increased in AAE.
Collapse
|
8
|
Xiao X, He S, He F, Wu X, Zheng Y. Metagenomic Analysis Reveals Neisseria bacilliformis Variation in the Early Childhood Caries Plaque Microbiome. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:2774772. [PMID: 34721624 PMCID: PMC8553469 DOI: 10.1155/2021/2774772] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/25/2021] [Indexed: 01/08/2023]
Abstract
The progression of early childhood caries (ECC) is caused by microbial colonized in dental plaque. However, the association framework both from 16s genus down to high resolution metagenomic strain level and from composition to genome function analysis on caries lacks. 16S rRNA sequence revealed the composition of 3-6 years dental caries (ECC, n = 29), and severe dental caries (SECC, n = 36) children are significantly different from caries-free controls (CF, n = 31). Especially, genus Neisseria is enriched in caries (P < 0.05). Metagenomics sequence of 3 ECCs, 3 SECCs, and 3 CFs reveals Neisseria bacilliformis ATCC BAA-1200 in genus Neisseria is also significantly enriched in caries (P < 0.05). Then, we recovered high-quality metagenomic assembly genomes (MAG), named bin 86, which have 99% identity with Neisseria bacilliformis ATCC BAA-1200 genome. Function analysis of Neisseria bacilliformis ATCC BAA-1200 genome shows its metabolism power of sugar and adhesion, colonization, acid production, and acid tolerance ability, which suggested Neisseria bacilliformis ATCC BAA-1200 may serve as a biomarker for childhood caries.
Collapse
Affiliation(s)
- Xiaofen Xiao
- Department of Stomatology, Shenzhen People's Hospital, Second Clinical Medical School of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong 518020, China
| | - Shandan He
- Department of Stomatology, Shenzhen People's Hospital, Second Clinical Medical School of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong 518020, China
| | - Fei He
- Department of Stomatology, Shenzhen People's Hospital, Second Clinical Medical School of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong 518020, China
| | - Xiaoyun Wu
- Shenzhen People's Hospital, Second Clinical Medical School of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong 518020, China
| | - Yuyan Zheng
- Department of Stomatology, Shenzhen People's Hospital, Second Clinical Medical School of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong 518020, China
| |
Collapse
|
9
|
Ahannach S, Spacova I, Decorte R, Jehaes E, Lebeer S. At the Interface of Life and Death: Post-mortem and Other Applications of Vaginal, Skin, and Salivary Microbiome Analysis in Forensics. Front Microbiol 2021; 12:694447. [PMID: 34394033 PMCID: PMC8355522 DOI: 10.3389/fmicb.2021.694447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022] Open
Abstract
Microbial forensics represents a promising tool to strengthen traditional forensic investigative methods and fill related knowledge gaps. Large-scale microbiome studies indicate that microbial fingerprinting can assist forensics in areas such as trace evidence, source tracking, geolocation, and circumstances of death. Nevertheless, the majority of forensic microbiome studies focus on soil and internal organ samples, whereas the microbiome of skin, mouth, and especially vaginal samples that are routinely collected in sexual assault and femicide cases remain underexplored. This review discusses the current and emerging insights into vaginal, skin, and salivary microbiome-modulating factors during life (e.g., lifestyle and health status) and after death (e.g., environmental influences and post-mortem interval) based on next-generation sequencing. We specifically highlight the key aspects of female reproductive tract, skin, and mouth microbiome samples relevant in forensics. To fill the current knowledge gaps, future research should focus on the degree to which the post-mortem succession rate and profiles of vaginal, skin, and saliva microbiota are sensitive to abiotic and biotic factors, presence or absence of oxygen and other gases, and the nutrient richness of the environment. Application of this microbiome-related knowledge could provide valuable complementary data to strengthen forensic cases, for example, to shed light on the circumstances surrounding death with (post-mortem) microbial fingerprinting. Overall, this review synthesizes the present knowledge and aims to provide a framework to adequately comprehend the hurdles and potential application of vaginal, skin, and salivary post-mortem microbiomes in forensic investigations.
Collapse
Affiliation(s)
- Sarah Ahannach
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Ronny Decorte
- Laboratory of Forensic Genetics, Department of Forensic Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium
| | - Els Jehaes
- Forensic DNA Laboratory, Department of Forensic Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
10
|
Willis JR, Saus E, Iraola-Guzmán S, Cabello-Yeves E, Ksiezopolska E, Cozzuto L, Bejarano LA, Andreu-Somavilla N, Alloza-Trabado M, Blanco A, Puig-Sola A, Broglio E, Carolis C, Ponomarenko J, Hecht J, Gabaldón T. Citizen-science based study of the oral microbiome in Cystic fibrosis and matched controls reveals major differences in diversity and abundance of bacterial and fungal species. J Oral Microbiol 2021; 13:1897328. [PMID: 34104346 PMCID: PMC8143623 DOI: 10.1080/20002297.2021.1897328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Introduction: Cystic fibrosis (CF) is an autosomal genetic disease, associated with the production of excessively thick mucosa and with life-threatening chronic lung infections. The microbiota of the oral cavity can act as a reservoir or as a barrier for infectious microorganisms that can colonize the lungs. However, the specific composition of the oral microbiome in CF is poorly understood.Methods: In collaboration with CF associations in Spain, we collected oral rinse samples from 31 CF persons (age range 7-47) and matched controls, and then performed 16S rRNA metabarcoding and high-throughput sequencing, combined with culture and proteomics-based identification of fungi to survey the bacterial and fungal oral microbiome.Results: We found that CF is associated with less diverse oral microbiomes, which were characterized by higher prevalence of Candida albicans and differential abundances of a number of bacterial taxa that have implications in both the connection to lung infections in CF, as well as potential oral health concerns, particularly periodontitis and dental caries.Conclusion: Overall, our study provides a first global snapshot of the oral microbiome in CF. Future studies are required to establish the relationships between the composition of the oral and lung microbiomes in CF.
Collapse
Affiliation(s)
- Jesse R Willis
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ester Saus
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Susana Iraola-Guzmán
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elena Cabello-Yeves
- Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ewa Ksiezopolska
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luis A Bejarano
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nuria Andreu-Somavilla
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Miriam Alloza-Trabado
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andrea Blanco
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Puig-Sola
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elisabetta Broglio
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carlo Carolis
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| |
Collapse
|
11
|
Alia-García E, Ponce-Alonso M, Saralegui C, Halperin A, Cortés MP, Baquero MR, Parra-Pecharromán D, Galeano J, del Campo R. Machine Learning Study in Caries Markers in Oral Microbiota from Monozygotic Twin Children. Diagnostics (Basel) 2021; 11:diagnostics11050835. [PMID: 34066599 PMCID: PMC8148599 DOI: 10.3390/diagnostics11050835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022] Open
Abstract
In recent years, the etiology of caries has evolved from a simplistic infectious perspective based on Streptococcus mutans and/or Lactobacillus activity, to a multifactorial disease involving a complex oral microbiota, the human genetic background and the environment. The aim of this work was to identify bacterial markers associated with early caries using massive 16S rDNA. To minimize the other factors, the composition of the oral microbiota of twins in which only one of them had caries was compared with their healthy sibling. Twenty-one monozygotic twin pairs without a previous diagnosis of caries were recruited in the context of their orthodontic treatment and divided into two categories: (1) caries group in which only one of the twins had caries; and (2) control group in which neither of the twins had caries. Each participant contributed a single oral lavage sample in which the bacterial composition was determined by 16S rDNA amplification and further high-throughput sequencing. Data analysis included statistical comparison of alpha and beta diversity, as well as differential taxa abundance between groups. Our results show that twins of the control group have a closer bacterial composition than those from the caries group. However, statistical differences were not detected and we were unable to find any particular bacterial marker by 16S rDNA high-throughput sequencing that could be useful for prevention strategies. Although these results should be validated in a larger population, including children from other places or ethnicities, we conclude that the occurrence of caries is not related to the increase of any particular bacterial population.
Collapse
Affiliation(s)
- Esther Alia-García
- Facultad de Ciencias de la Salud, Universidad Alfonso X El Sabio, Villanueva de la Cañada, 28691 Madrid, Spain; (E.A.-G.); (M.P.C.); (M.R.B.); (D.P.-P.); (R.d.C.)
| | - Manuel Ponce-Alonso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28034 Madrid, Spain; (M.P.-A.); (C.S.); (A.H.)
| | - Claudia Saralegui
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28034 Madrid, Spain; (M.P.-A.); (C.S.); (A.H.)
| | - Ana Halperin
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28034 Madrid, Spain; (M.P.-A.); (C.S.); (A.H.)
| | - Marta Paz Cortés
- Facultad de Ciencias de la Salud, Universidad Alfonso X El Sabio, Villanueva de la Cañada, 28691 Madrid, Spain; (E.A.-G.); (M.P.C.); (M.R.B.); (D.P.-P.); (R.d.C.)
| | - María Rosario Baquero
- Facultad de Ciencias de la Salud, Universidad Alfonso X El Sabio, Villanueva de la Cañada, 28691 Madrid, Spain; (E.A.-G.); (M.P.C.); (M.R.B.); (D.P.-P.); (R.d.C.)
| | - David Parra-Pecharromán
- Facultad de Ciencias de la Salud, Universidad Alfonso X El Sabio, Villanueva de la Cañada, 28691 Madrid, Spain; (E.A.-G.); (M.P.C.); (M.R.B.); (D.P.-P.); (R.d.C.)
- Departamento de Biología, Servicio de Criminalística, Dirección General de la Guardia Civil, 28003 Madrid, Spain
| | - Javier Galeano
- Complex Systems Group, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- Correspondence:
| | - Rosa del Campo
- Facultad de Ciencias de la Salud, Universidad Alfonso X El Sabio, Villanueva de la Cañada, 28691 Madrid, Spain; (E.A.-G.); (M.P.C.); (M.R.B.); (D.P.-P.); (R.d.C.)
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28034 Madrid, Spain; (M.P.-A.); (C.S.); (A.H.)
| |
Collapse
|
12
|
Rahne M, Basic A, Almståhl A. Explorative study on Lactobacillus species and their acid-producing capacity and anti-microbial activity in head and neck cancer patients. Clin Exp Dent Res 2021; 7:924-933. [PMID: 33787075 PMCID: PMC8543467 DOI: 10.1002/cre2.426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVE To determine acid-producing capacity and anti-microbial activity of Lactobacillus species collected pretreatment and post treatment in head and neck cancer patients. MATERIAL AND METHODS Lactobacillus isolates from 21 patients pretreatment and post treatment were identified using molecular methods. The patients' stimulated salivary secretion was determined pretreatment, and 6 and 12 months post treatment and caries lesions/new filled surfaces registered at 24 months post treatment. The acid-producing capacity of the Lactobacillus isolate was analyzed using a colorimetric fermentation test in microtiter plates. The anti-microbial activity of the isolates against Streptococcus mutans associated with caries, and against the mucosal pathogens Staphylococcus aureus, Candida albicans, and Enterococcus faecalis was analyzed by determining inhibitory zones on agar plates. RESULTS The most frequent species were L. paracasei (n = 21), L. casei/rhamnosus (n = 17) and L. fermentum (n = 10). Sixty-seven percent of the patients harbored L. paracasei either at 6 or 12 months post radiotherapy. The corresponding figures for L. casei/rhamnosus and L. fermentum were 62% and 33%. L. paracasei strains showed the best acid-producing capacity and L. fermentum strains the lowest. Strong acid-producing capacity was most common among isolates collected at 6 months post treatment. Seventy-two percent of the strains showed an anti-microbial activity against S. mutans, one strain against S. aureus and none against C. albicans or E. faecalis. CONCLUSION The most frequent species isolated from head and neck cancer patients both pretreatment and post treatment were L. paracasei, L. casei/rhamnosus, and L. fermentum. L. paracasei showed the best acid-producing capacity and the highest proportion with anti-microbial activity against S. mutans.
Collapse
Affiliation(s)
- Matilda Rahne
- Department of Oral Microbiology and Immunology, Institute of Odontology, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Amina Basic
- Department of Oral Microbiology and Immunology, Institute of Odontology, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Annica Almståhl
- Department of Oral Microbiology and Immunology, Institute of Odontology, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| |
Collapse
|
13
|
Relvas M, Regueira-Iglesias A, Balsa-Castro C, Salazar F, Pacheco JJ, Cabral C, Henriques C, Tomás I. Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models. Sci Rep 2021; 11:929. [PMID: 33441710 PMCID: PMC7806737 DOI: 10.1038/s41598-020-79875-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
The present study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental and periodontal disease and the combination of both (hereinafter referred to as oral disease), in terms of bacterial diversity, co-occurrence network patterns and predictive models. Our scale of overall oral health was used to produce a convenience sample of 81 patients from 270 who were initially recruited. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 × 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the phyloseq, DESeq2, Microbiome, SpiecEasi, igraph, MixOmics packages. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or oral disease, especially in high grades. Supragingival dental parameters influence the microbiota’s abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that oral health has on the salivary microbiome. The possible keystone OTUs are different in the oral health and disease, and even these vary between dental and periodontal disease: half of them belongs to the core microbiome and are independent of the abundance parameters. The salivary microbiome, involving a considerable number of OTUs, shows an excellent discriminatory potential for distinguishing different grades of dental, periodontal or oral disease; considering the number of predictive OTUs, the best model is that which predicts the combined dental and periodontal status.
Collapse
Affiliation(s)
- M Relvas
- Institute of Research and Advanced Training in Health Sciences and Tecnologies (IINFACTS), IUCS-Cespu-Instituto Universitário de Ciencias da Saúde, Gandra, Paredes, Portugal
| | - A Regueira-Iglesias
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Health Research Institute of Santiago (IDIS), Universidade de Santiago de Compostela, Galicia, 15872, Santiago de Compostela, Spain
| | - C Balsa-Castro
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Health Research Institute of Santiago (IDIS), Universidade de Santiago de Compostela, Galicia, 15872, Santiago de Compostela, Spain
| | - F Salazar
- Institute of Research and Advanced Training in Health Sciences and Tecnologies (IINFACTS), IUCS-Cespu-Instituto Universitário de Ciencias da Saúde, Gandra, Paredes, Portugal
| | - J J Pacheco
- Institute of Research and Advanced Training in Health Sciences and Tecnologies (IINFACTS), IUCS-Cespu-Instituto Universitário de Ciencias da Saúde, Gandra, Paredes, Portugal
| | - C Cabral
- Institute of Research and Advanced Training in Health Sciences and Tecnologies (IINFACTS), IUCS-Cespu-Instituto Universitário de Ciencias da Saúde, Gandra, Paredes, Portugal
| | - C Henriques
- Institute of Research and Advanced Training in Health Sciences and Tecnologies (IINFACTS), IUCS-Cespu-Instituto Universitário de Ciencias da Saúde, Gandra, Paredes, Portugal
| | - I Tomás
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Health Research Institute of Santiago (IDIS), Universidade de Santiago de Compostela, Galicia, 15872, Santiago de Compostela, Spain.
| |
Collapse
|
14
|
Pappa E, Vougas K, Zoidakis J, Vastardis H. Proteomic advances in salivary diagnostics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140494. [DOI: 10.1016/j.bbapap.2020.140494] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/21/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022]
|
15
|
Chen W, Jiang Q, Yan G, Yang D. The oral microbiome and salivary proteins influence caries in children aged 6 to 8 years. BMC Oral Health 2020; 20:295. [PMID: 33115458 PMCID: PMC7592381 DOI: 10.1186/s12903-020-01262-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 09/23/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Oral microbiome and salivary proteins play a critical role in the occurrence and development of caries. In this study, we used metagenomic and metaproteomic analyses to explore the microbiological and proteinic biomarkers and investigate the etiology of caries in 6-8 years old children. Our study aims to offer a better comprehension of these factors and the relationship with caries, and these findings might facilitate caries risk assessment and provide a basis for future prevention strategies. METHODS Children 6 to 8 years old living in rural isolated areas including 40 caries-active subjects and 40 caries-free subjects were recruited. Supragingival plaque and unstimulated saliva were collected for 16S rDNA pyrosequencing and isobaric tags for relative and absolute quantitation (iTRAQ) technique coupled with quantitative nano-flow liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. RESULTS We found 6 phyla and 13 genera predominant in all the samples, and differences in relative abundances can be observed. The Alpha diversity analysis demonstrated that the richness and diversity of the bacterial communities were similar between children with caries-free and caries-active groups; LEfSe detected differences in the bacterial community including Dialister, Selenomonas, Actinomyces, and Mogibacterium in the caries-active group (P < 0.05) and Capnocytophaga, Fusobacterium, Desulfuromonadales, Haemophilus, and Porphyromonas in the caries-free group(P < 0.05). The core microbiome was defined as 18 predominant genera in children with caries. The results of the salivary proteome identified 9135 unique peptides and 1662 proteins group from 20 salivary samples. Two hundred fifty-eight proteins were differentially expressed between the caries-free and caries-active groups. CONCLUSIONS The diversity of the microbial community has little effect on caries but some bacteria with different relative abundance between the caries-active and caries-free group could be considered as potential biomarkers for children with caries. In addition, as a critical host factor of caries, the salivary proteins are different in caries-free and caries-active groups.
Collapse
Affiliation(s)
- Wang Chen
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| | - Qian Jiang
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| | - Guowei Yan
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| | - Deqin Yang
- College of Stomatology, Chongqing Medical University, Chongqing, China. .,Chongqing key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China.
| |
Collapse
|
16
|
Damé-Teixeira N, Parolo CCF, Malz M, Devine DA, DO T. Gene expression profile of Scardovia spp. in the metatranscriptome of root caries. Braz Oral Res 2020; 34:e042. [PMID: 32401932 DOI: 10.1590/1807-3107bor-2020.vol34.0042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/16/2020] [Indexed: 11/22/2022] Open
Abstract
A few investigations of caries biofilms have identified Scardovia spp.; however, little is known about its involvement in caries pathogenesis. The purpose of this study was to assess the gene expression profile of Scardovia spp. in root caries, and compare it with other microorganisms. Clinical samples from active root caries lesions were collected. Microbial mRNA was isolated and cDNA sequenced. The function and composition of the Scardovia were investigated using two methods: a) de novo assembly of the read data and mapping to contigs, and b) reads mapping to reference genomes. Pearson correlation was performed (p < 0.05). Proportion of Scardovia inopinata and Scardovia wiggsiae sequences ranged from 0-6% in the root caries metatranscriptome. There was a positive correlation between the transcriptome of Lactobacillus spp. and Scardovia spp. (r = 0.70; p = 0.03), as well as with other Bifidobacteriaceae (r = 0.91; p = 0.0006). Genes that code for fructose 6-phosphate phosphoketolase (the key enzyme for "Bifid shunt"), as well as ABC transporters and glycosyl-hydrolases were highly expressed. In conclusion, "Bifid shunt" and starch metabolism are involved in carbohydrate metabolism of S. inopinata and S. wiggsiae in root caries. There is a positive correlation between the metabolism abundance of Lactobacillus spp., Bifidobacteriaceae members, and Scardovia in root caries.
Collapse
Affiliation(s)
- Naile Damé-Teixeira
- Universidade de Brasília - UnB, Faculty of Heath Sciences, Department of Dentistry, Brasília, DF, Brazil
| | - Clarissa Cavalcanti Fatturi Parolo
- Univeridade Federal do Rio Grande do Sul - UFRGS, Faculty of Dentistry, Department of Social and Preventive Dentistry, Porto Alegre, RS, Brazil
| | - Marisa Malz
- Univeridade Federal do Rio Grande do Sul - UFRGS, Faculty of Dentistry, Department of Social and Preventive Dentistry, Porto Alegre, RS, Brazil
| | - Deirdre Ann Devine
- University of Leeds, School of Dentistry, Division of Oral Biology, Leeds, England
| | - Thuy DO
- University of Leeds, School of Dentistry, Division of Oral Biology, Leeds, England
| |
Collapse
|
17
|
Belstrøm D. The salivary microbiota in health and disease. J Oral Microbiol 2020; 12:1723975. [PMID: 32128039 PMCID: PMC7034443 DOI: 10.1080/20002297.2020.1723975] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 12/19/2022] Open
Abstract
The salivary microbiota (SM), comprising bacteria shed from oral surfaces, has been shown to be individualized, temporally stable and influenced by diet and lifestyle. SM reflects local bacterial alterations of the supragingival and subgingival microbiota, and periodontitis and dental-caries associated characteristics of SM have been reported. Also, data suggest an impact of systemic diseases on SM as demonstrated in patients with a wide variety of systemic diseases including diabetes, cancer, HIV and rheumatoid arthritis. The presence of systemic diseases seems to influence salivary levels of specific bacterial species, as well as α- and β-diversity of SM. The composition of SM might thereby potentially mirror oral and general health status. The contentious development of advanced molecular techniques such as metagenomics, metatranscriptomics and metabolomics has enabled the possibility to address bacterial functions rather than presence in microbial samples. However, at present only a few studies have employed such techniques on SM to reveal functional and metabolic characteristics in oral health and disease. Future studies are therefore warranted to illuminate the possible impact of metabolic functions of SM on oral and general health status. Ultimately, such an approach has the possibility to reveal novel and personalized therapeutic avenues in oral and general medicine.
Collapse
Affiliation(s)
- Daniel Belstrøm
- Section for Periodontology and Microbiology, Department of Odontology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
18
|
Zhao R, Huang R, Long H, Li Y, Gao M, Lai W. The dynamics of the oral microbiome and oral health among patients receiving clear aligner orthodontic treatment. Oral Dis 2020; 26:473-483. [PMID: 31418980 DOI: 10.1111/odi.13175] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 02/05/2023]
Abstract
OBJECTIVES This 6-month prospective clinical study assessed the impacts of Invisalign appliances on the oral bacterial community and oral health of patients. METHODS Salivary samples were obtained from twenty-five adult patients receiving Invisalign aligner treatment before the treatment (Group B) and at a 6-month follow-up (Group P). The bacterial composition of each sample was determined using Illumina MiSeq sequencing of the bacterial 16S rRNA. Intra- and intergroup biodiversity was analyzed. Clinical periodontal parameters and daily oral hygiene habits were recorded. RESULTS Reduction in plaque, increased daily brushing frequency, and decreased dessert intake were observed in Group P compared with that in Group B. A total of 1,853,952 valid reads were obtained from the 50 salivary samples, with 37,904 sequences per sample. No significant differences were detected in the intra- and intergroup biodiversity comparisons between the two groups. By clustering, 8,885 OTUs were identified and categorized into six major phyla: Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, Actinobacteria, and Candidate_division_TM7_norank. At the genus level, compared with Group B, Group P demonstrated significantly increased Bacillus abundance and decreased Prevotella abundance. CONCLUSIONS Our results suggested that the general biodiversity and salivary microbial community structure did not change significantly and that patients had increased beneficial oral hygiene habits and awareness during the first six months of Invisalign treatment. Hence, on the basis of this study, it appears that Invisalign aligner treatment did not induce deterioration of oral health nor significant biodiversity changes in oral bacterial communities, assuming that detailed oral hygiene instructions for both teeth and aligners were provided.
Collapse
Affiliation(s)
- Rui Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Renhuan Huang
- Department of Orthodontics, Tenth People's Hospital, Shanghai, China
| | - Hu Long
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yan Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Meiya Gao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wenli Lai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
19
|
Comparison of oral microbiome profiles in stimulated and unstimulated saliva, tongue, and mouth-rinsed water. Sci Rep 2019; 9:16124. [PMID: 31695050 PMCID: PMC6834574 DOI: 10.1038/s41598-019-52445-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/12/2019] [Indexed: 01/07/2023] Open
Abstract
Epidemiological studies using saliva have revealed relationships between the oral microbiome and many oral and systemic diseases. However, when collecting from a large number of participants such as a large-scale cohort study, the time it takes to collect saliva can be a problem. Mouth-rinsed water, which is water that has been used to rinse the oral cavity, can be used as an alternative method for collecting saliva for oral microbiome analysis because it can be collected in a shorter time than saliva. The purpose of this study was to verify whether mouth-rinsed water is a suitable saliva substitute for analyzing the oral microbiome. We collected samples of mouth-rinsed water, stimulated saliva, unstimulated saliva, and tongue coating from 10 systemic healthy participants, and compared the microbial diversity and composition of the samples using next-generation sequencing of 16S rRNA-encoding genes. The results showed that the microbial diversity of mouth-rinsed water was similar to that of unstimulated and stimulated saliva, and significantly higher than that of tongue-coating samples. The microbial composition at the species level of mouth-rinsed water also showed a very high correlation with the composition of unstimulated and stimulated saliva. These results suggest that the mouth-rinsed water is a suitable collection method instead of saliva for oral microbiome analysis.
Collapse
|
20
|
Philip N, Leishman SJ, Bandara HMHN, Healey DL, Walsh LJ. Randomized Controlled Study to Evaluate Microbial Ecological Effects of CPP-ACP and Cranberry on Dental Plaque. JDR Clin Trans Res 2019; 5:118-126. [PMID: 31283892 DOI: 10.1177/2380084419859871] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Ecological approaches to dental caries prevention play a key role in attaining long-term control over the disease and maintaining a symbiotic oral microbiome. OBJECTIVES This study aimed to investigate the microbial ecological effects of 2 interventional dentifrices: a casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) dentifrice and the same dentifrice supplemented with a polyphenol-rich cranberry extract. METHODS The interventional toothpastes were compared with each other and with an active control fluoride dentifrice in a double-blinded randomized controlled trial. Real-time quantitative polymerase chain reaction (qPCR) analysis was used to determine changes in the bacterial loads of 14 key bacterial species (8 caries associated and 6 health associated) in the dental plaque of trial participants after they used the dentifrices for 5 to 6 wk. RESULTS From the baseline to the recall visit, significant differences were observed between the treatment groups in the bacterial loads of 2 caries-associated bacterial species (Streptococcus mutans [P < 0.001] and Veillonella parvula [P < 0.001]) and 3 health-associated bacterial species (Corynebacterium durum [P = 0.008], Neisseria flavescens [P = 0.005], and Streptococcus sanguinis [P < 0.001]). Compared to the fluoride control dentifrice, the CPP-ACP dentifrice demonstrated significant differences for S. mutans (P = 0.032), C. durum (P = 0.007), and S. sanguinis (P < 0.001), while combination CPP-ACP-cranberry dentifrice showed significant differences for S. mutans (P < 0.001), V. parvula (P < 0.001), N. flavescens (P = 0.003), and S. sanguinis (P < 0.001). However, no significant differences were observed in the bacterial load comparisons between the CPP-ACP and combination dentifrices for any of the targeted bacterial species (P > 0.05). CONCLUSIONS Overall, the results indicate that dentifrices containing CPP-ACP and polyphenol-rich cranberry extracts can influence a species-level shift in the ecology of the oral microbiome, resulting in a microbial community less associated with dental caries (Australian New Zealand Clinical Trial Registry ANZCTR 12618000095268). KNOWLEDGE TRANSFER STATEMENT The results of this randomized controlled trial indicate that dentifrices containing casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) and polyphenol-rich cranberry extracts were able to beneficially modulate the microbial ecology of dental plaque in a group of high caries-risk patients. This could contribute toward lowering the risk of developing new caries lesions, an important goal sought by patients, clinicians, and policy makers.
Collapse
Affiliation(s)
- N Philip
- The University of Queensland School of Dentistry, Brisbane, Australia
| | - S J Leishman
- The University of Queensland School of Dentistry, Brisbane, Australia
| | | | - D L Healey
- The University of Queensland School of Dentistry, Brisbane, Australia
| | - L J Walsh
- The University of Queensland School of Dentistry, Brisbane, Australia
| |
Collapse
|
21
|
Chattopadhyay I, Verma M, Panda M. Role of Oral Microbiome Signatures in Diagnosis and Prognosis of Oral Cancer. Technol Cancer Res Treat 2019; 18:1533033819867354. [PMID: 31370775 PMCID: PMC6676258 DOI: 10.1177/1533033819867354] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/15/2019] [Accepted: 06/27/2019] [Indexed: 12/11/2022] Open
Abstract
Despite advancement in cancer treatment, oral cancer has a poor prognosis and is often detected at late stage. To overcome these challenges, investigators should search for early diagnostic and prognostic biomarkers. More than 700 bacterial species reside in the oral cavity. The oral microbiome population varies by saliva and different habitats of oral cavity. Tobacco, alcohol, and betel nut, which are causative factors of oral cancer, may alter the oral microbiome composition. Both pathogenic and commensal strains of bacteria have significantly contributed to oral cancer. Numerous bacterial species in the oral cavity are involved in chronic inflammation that lead to development of oral carcinogenesis. Bacterial products and its metabolic by-products may induce permanent genetic alterations in epithelial cells of the host that drive proliferation and/or survival of epithelial cells. Porphyromonas gingivalis and Fusobacterium nucleatum induce production of inflammatory cytokines, cell proliferation, and inhibition of apoptosis, cellular invasion, and migration thorough host cell genomic alterations. Recent advancement in metagenomic technologies may be useful in identifying oral cancer-related microbiome, their genomes, virulence properties, and their interaction with host immunity. It is very important to address which bacterial species is responsible for driving oral carcinogenesis. Alteration in the oral commensal microbial communities have potential application as a diagnostic tool to predict oral squamous cell carcinoma. Clinicians should be aware that the protective properties of the resident microflora are beneficial to define treatment strategies. To develop highly precise and effective therapeutic approaches, identification of specific oral microbiomes may be required. In this review, we narrate the role of microbiome in the progression of oral cancer and its role as an early diagnostic and prognostic biomarker for oral cancer.
Collapse
Affiliation(s)
- Indranil Chattopadhyay
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Madhusmita Panda
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| |
Collapse
|
22
|
Willis JR, González-Torres P, Pittis AA, Bejarano LA, Cozzuto L, Andreu-Somavilla N, Alloza-Trabado M, Valentín A, Ksiezopolska E, Company C, Onywera H, Montfort M, Hermoso A, Iraola-Guzmán S, Saus E, Labeeuw A, Carolis C, Hecht J, Ponomarenko J, Gabaldón T. Citizen science charts two major "stomatotypes" in the oral microbiome of adolescents and reveals links with habits and drinking water composition. MICROBIOME 2018; 6:218. [PMID: 30522523 PMCID: PMC6284318 DOI: 10.1186/s40168-018-0592-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 11/06/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral microbiome of 1500 adolescents around Spain and its relationships with lifestyle, diet, hygiene, and socioeconomic and environmental parameters. RESULTS Our results provide a detailed snapshot of the adolescent oral microbiome and how it varies with lifestyle and other factors. In addition to hygiene and dietary habits, we found that the composition of tap water was related to important changes in the abundance of several bacterial genera. This points to an important role of drinking water in shaping the oral microbiota, which has been so far poorly explored. Overall, the microbiome samples of our study can be clustered into two broad compositional patterns (stomatotypes), driven mostly by Neisseria and Prevotella, respectively. These patterns show striking similarities with those found in unrelated populations. CONCLUSIONS We hypothesize that these stomatotypes represent two possible global optimal equilibria in the oral microbiome that reflect underlying constraints of the human oral niche. As such, they should be found across a variety of geographical regions, lifestyles, and ages.
Collapse
Affiliation(s)
- Jesse R Willis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Pedro González-Torres
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Alexandros A Pittis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Luis A Bejarano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Nuria Andreu-Somavilla
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Miriam Alloza-Trabado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Antonia Valentín
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - Ewa Ksiezopolska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Carlos Company
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Harris Onywera
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town (UCT), Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Magda Montfort
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Antonio Hermoso
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Susana Iraola-Guzmán
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Ester Saus
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Annick Labeeuw
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Carlo Carolis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| |
Collapse
|
23
|
Rafeek R, Carrington CVF, Gomez A, Harkins D, Torralba M, Kuelbs C, Addae J, Moustafa A, Nelson KE. Xylitol and sorbitol effects on the microbiome of saliva and plaque. J Oral Microbiol 2018; 11:1536181. [PMID: 30598728 PMCID: PMC6225370 DOI: 10.1080/20002297.2018.1536181] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 02/07/2023] Open
Abstract
Chewing gum containing xylitol may help prevent caries by reducing levels of mutans streptococci (MS) and lactobacilli in saliva and plaque. Very little is known about other species which are possibly beneficial to oral health. In this study, we employed high-throughput sequencing of the 16S rRNA gene to profile microbial communities of saliva and plaque following short-term consumption of xylitol and sorbitol containing chewing gum. Participants (n = 30) underwent a washout period and were randomly assigned to one of two groups. Each group chewed either xylitol or sorbitol gum for three weeks, before undergoing a second four-week washout period after which they switched to the alternate gum for three weeks. Analysis of samples collected before and after each intervention identified distinct plaque and saliva microbial communities that altered dependent on the order in which gum treatments were given. Neither the xylitol nor sorbitol treatments significantly affected the bacterial composition of plaque. Lactobacilli were undetected and the number of Streptococcus mutans sequence reads was very low and unaffected by either xylitol or sorbitol. However, sorbitol affected several other streptococcal species in saliva including increasing the abundance of S. cristatus, an oral commensal shown to inhibit bacteria associated with chronic periodontitis.
Collapse
Affiliation(s)
- Reisha Rafeek
- School of Dentistry, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Andres Gomez
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | - Derek Harkins
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | - Manolito Torralba
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | - Claire Kuelbs
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| | - Jonas Addae
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Ahmed Moustafa
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Biology, The American University in Cairo, New Cairo, Egypt
| | - Karen E Nelson
- Department of Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, USA
| |
Collapse
|
24
|
Lun H, Yang W, Zhao S, Jiang M, Xu M, Liu F, Wang Y. Altered gut microbiota and microbial biomarkers associated with chronic kidney disease. Microbiologyopen 2018; 8:e00678. [PMID: 30088332 PMCID: PMC6460263 DOI: 10.1002/mbo3.678] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/25/2018] [Accepted: 05/22/2018] [Indexed: 01/06/2023] Open
Abstract
The present study aimed to determine the differences in gut microbiota between patients with chronic kidney disease (CKD) and healthy controls (HC) and search for better microbial biomarkers associated with CKD. The 16S rRNA gene sequencing approach was used to investigate the differences in gut microbiota between the CKD and HC groups. The study found that 12 phylotypes were overrepresented in the CKD group and 19 in the HC group at the genus level. Furthermore, genera Lachnospira and Ruminococcus_gnavus performed the best in differentiating between HC and CKD populations. In addition, this novel study found that the genera Holdemanella, Megamonas, Prevotella 2, Dielma, and Scardovia were associated with the progression of CKD and hemodialysis. In conclusion, the composition of gut microbiota was different in CKD populations compared with healthy populations, and Lachnospira and R._gnavus were better microbial biomarkers. In addition, five phylotypes, including Holdemanella, Megamonas, Prevotella2, Dielma, and Scardovia, served as an indicator of the progression of CKD and hemodialysis. However, large‐scale prospective studies should be performed to identify the reliability of the set of these phylotypes as biomarkers.
Collapse
Affiliation(s)
- Hengzhong Lun
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China.,The Department of Clinical Laboratory, Taian City Central Hospital, Taian, Shandong, China
| | - Weihua Yang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Shuping Zhao
- The Department of Clinical Laboratory, Taian City Central Hospital, Taian, Shandong, China
| | - Meijie Jiang
- The Department of Clinical Laboratory, Taian City Central Hospital, Taian, Shandong, China
| | - Mingjie Xu
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Fenfen Liu
- The Department of Nephrology, Taian City Central Hospital, Taian, Shandong, China
| | - Yunshan Wang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
| |
Collapse
|
25
|
Burczynska A, Dziewit L, Decewicz P, Struzycka I, Wroblewska M. Application of Metagenomic Analyses in Dentistry as a Novel Strategy Enabling Complex Insight into Microbial Diversity of the Oral Cavity. Pol J Microbiol 2018; 66:9-15. [PMID: 29359689 DOI: 10.5604/17331331.1234988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The composition of the oral microbiome in healthy individuals is complex and dynamic, and depends on many factors, such as anatomical location in the oral cavity, diet, oral hygiene habits or host immune responses. It is estimated at present that worldwide about 2 billion people suffer from diseases of the oral cavity, mainly periodontal disease and dental caries. Importantly, the oral microflora involved in local infections may spread and cause systemic, even life-threatening infections. In search for etiological agents of infections in dentistry, traditional approaches are not sufficient, as about 50% of oral bacteria are not cultivable. Instead, metagenomic analyses are particularly useful for studies of the complex oral microbiome - both in healthy individuals, and in patients with oral and dental diseases. In this paper we review the current and future applications of metagenomic studies in evaluation of both the composition of the oral microbiome as well as its potential pathogenic role in infections in dentistry.
Collapse
Affiliation(s)
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland
| | - Przemysław Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland; Research and Development for Life Sciences Ltd., Poland
| | - Izabela Struzycka
- Department of Comprehensive Dental Care, Medical University of Warsaw, Poland
| | - Marta Wroblewska
- Department of Dental Microbiology, Medical University of Warsaw, Poland; Department of Microbiology, Central Clinical Hospital in Warsaw, Poland
| |
Collapse
|
26
|
Villmones HC, Haug ES, Ulvestad E, Grude N, Stenstad T, Halland A, Kommedal Ø. Species Level Description of the Human Ileal Bacterial Microbiota. Sci Rep 2018; 8:4736. [PMID: 29549283 PMCID: PMC5856834 DOI: 10.1038/s41598-018-23198-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/06/2018] [Indexed: 02/07/2023] Open
Abstract
The small bowel is responsible for most of the body’s nutritional uptake and for the development of intestinal and systemic tolerance towards microbes. Nevertheless, the human small bowel microbiota has remained poorly characterized, mainly owing to sampling difficulties. Sample collection directly from the distal ileum was performed during radical cystectomy with urinary diversion. Material from the ileal mucosa were analysed using massive parallel sequencing of the 16S rRNA gene. Samples from 27 Caucasian patients were included. In total 280 unique Operational Taxonomic Units were identified, whereof 229 could be assigned to a species or a species group. The most frequently detected bacteria belonged to the genera Streptococcus, Granulicatella, Actinomyces, Solobacterium, Rothia, Gemella and TM7(G-1). Among these, the most abundant species were typically streptococci within the mitis and sanguinis groups, Streptococcus salivarius, Rothia mucilaginosa and Actinomyces from the A. meyeri/odontolyticus group. The amounts of Proteobacteria and strict anaerobes were low. The microbiota of the distal part of the human ileum is oral-like and strikingly different from the colonic microbiota. Although our patient population is elderly and hospitalized with a high prevalence of chronic conditions, our results provide new and valuable insights into a lesser explored part of the human intestinal ecosystem.
Collapse
Affiliation(s)
| | | | - Elling Ulvestad
- Department of Microbiology, Haukeland University Hospital, 5021, Bergen, Norway.,Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Nils Grude
- Department of Microbiology, Vestfold Hospital Trust, 3103, Tønsberg, Norway
| | - Tore Stenstad
- Department of Infectious Medicine, Vestfold Hospital Trust, 3103, Tønsberg, Norway
| | - Adrian Halland
- Department of Urology, Vestfold Hospital Trust, 3103, Tønsberg, Norway
| | - Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, 5021, Bergen, Norway
| |
Collapse
|
27
|
Bowen WH, Burne RA, Wu H, Koo H. Oral Biofilms: Pathogens, Matrix, and Polymicrobial Interactions in Microenvironments. Trends Microbiol 2018; 26:229-242. [PMID: 29097091 PMCID: PMC5834367 DOI: 10.1016/j.tim.2017.09.008] [Citation(s) in RCA: 518] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/26/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023]
Abstract
Biofilms are microbial communities embedded within an extracellular matrix, forming a highly organized structure that causes many human infections. Dental caries (tooth decay) is a polymicrobial biofilm disease driven by the diet and microbiota-matrix interactions that occur on a solid surface. Sugars fuel the emergence of pathogens, the assembly of the matrix, and the acidification of the biofilm microenvironment, promoting ecological changes and concerted multispecies efforts that are conducive to acid damage of the mineralized tooth tissue. Here, we discuss recent advances in the role of the biofilm matrix and interactions between opportunistic pathogens and commensals in the pathogenesis of dental caries. In addition, we highlight the importance of matrix-producing organisms in fostering a pathogenic habitat where interspecies competition and synergies occur to drive the disease process, which could have implications to other infections associated with polymicrobial biofilms.
Collapse
Affiliation(s)
- William H Bowen
- Center for Oral Biology, Department of Microbiology & Immunology and Environmental Medicine, University of Rochester Medical Center, Rochester, New York, NY, USA; Deceased (15 November 2016)
| | - Robert A Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Hui Wu
- Departments of Microbiology and Pediatric Dentistry, School of Dentistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hyun Koo
- Levy Center for Oral Health, Department of Orthodontics, Divisions of Pediatric Dentistry and Community of Oral Health, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA.
| |
Collapse
|
28
|
Zhou J, Yao Y, Jiao K, Zhang J, Zheng X, Wu F, Hu X, Li J, Yu Z, Zhang G, Jiang N, Li Z. Relationship between Gingival Crevicular Fluid Microbiota and Cytokine Profile in Periodontal Host Homeostasis. Front Microbiol 2017; 8:2144. [PMID: 29163429 PMCID: PMC5672786 DOI: 10.3389/fmicb.2017.02144] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/19/2017] [Indexed: 12/27/2022] Open
Abstract
As potential biomarkers in periodontitis, microbiome, and cytokines have recently been extensively investigated, but combined analyses of the variations between the microbial structure and cytokine composition are rare. The present study aimed to investigate whether there are differences in the combined profile of microbiome and cytokines in individuals with or without periodontitis. The microbiome and cytokine composition in gingival crevicular fluid (GCF) from 16 patients and 15 controls from Jishi Shan (Gansu, China) were analyzed using 454 pyrosequencing and RayBio Quantibody Arrays. The results showed that a higher co-occurrence of genera in periodontitis group compared with the healthy group, as evaluated by Schoener's abundance-based co-occurrence index. C-reactive protein (CRP) was significantly (P < 0.05) higher in the GCF of the periodontitis group while interleukin (IL)-8 was significantly (P < 0.01) higher in the GCF of the healthy group. The Mantel test revealed a significant concordance between cytokines and microbiota, in the healthy group (Mantel statistic r = 0.36, P ≤ 0.05) but not in the periodontitis group (Mantel statistic r = 0.013, P = 0.434). The results were further confirmed by the Procrustes test. Matrix metalloproteinase (MMP)-9, osteoactivin, IL-8, and macrophage inflammatory protein (MIP)-1a were significantly associated with bacterial composition at the phylum, class, order, family, and genus levels. CRP was also associated with bacterial composition at the species level. In conclusion, alterations in the polymicrobial community structure leads to disruption in the healthy correlation between cytokines and microbiomes. This dysbiosis between the microbiota and the immune response could be one of the major etiological mechanisms underlying periodontitis.
Collapse
Affiliation(s)
- Jianye Zhou
- Department of Prosthodontics, Key Laboratory of Oral Diseases of Gansu Province, Northwest University for Nationalities, Lanzhou, China
| | - Yiqing Yao
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Kangli Jiao
- Department of Prosthodontics, Key Laboratory of Oral Diseases of Gansu Province, Northwest University for Nationalities, Lanzhou, China
| | - Jumei Zhang
- Department of Prosthodontics, Key Laboratory of Oral Diseases of Gansu Province, Northwest University for Nationalities, Lanzhou, China
| | - Xin Zheng
- Department of Prosthodontics, Key Laboratory of Oral Diseases of Gansu Province, Northwest University for Nationalities, Lanzhou, China
| | - Fang Wu
- Yinchuan Stomatology Hospital, Yinchuan, China
| | - Xiaopan Hu
- Department of Prosthodontics, Key Laboratory of Oral Diseases of Gansu Province, Northwest University for Nationalities, Lanzhou, China
| | | | - Zhanhai Yu
- Department of Prosthodontics, School of Stomatology, Lanzhou University, Lanzhou, China
| | - Gaosen Zhang
- Department of Soil Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China
| | - Nan Jiang
- Department of Applied Soil Biochemistry, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhiqiang Li
- Department of Prosthodontics, Key Laboratory of Oral Diseases of Gansu Province, Northwest University for Nationalities, Lanzhou, China
| |
Collapse
|
29
|
Mashima I, Theodorea CF, Thaweboon B, Thaweboon S, Scannapieco FA, Nakazawa F. Exploring the salivary microbiome of children stratified by the oral hygiene index. PLoS One 2017; 12:e0185274. [PMID: 28934367 PMCID: PMC5608389 DOI: 10.1371/journal.pone.0185274] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/08/2017] [Indexed: 01/01/2023] Open
Abstract
Poor oral hygiene often leads to chronic diseases such as periodontitis and dental caries resulting in substantial economic costs and diminished quality of life in not only adults but also in children. In this study, the salivary microbiome was characterized in a group of children stratified by the Simplified Oral Hygiene Index (OHI-S). Illumina MiSeq high-throughput sequencing based on the 16S rRNA was utilized to analyze 90 salivary samples (24 Good, 31 Moderate and 35 Poor oral hygiene) from a cohort of Thai children. A total of 38,521 OTUs (Operational Taxonomic Units) with a 97% similarity were characterized in all of the salivary samples. Twenty taxonomic groups (Seventeen genera, two families and one class; Streptococcus, Veillonella, Gemellaceae, Prevotella, Rothia, Porphyromonas, Granulicatella, Actinomyces, TM-7-3, Leptotrichia, Haemophilus, Selenomonas, Neisseria, Megasphaera, Capnocytophaga, Oribacterium, Abiotrophia, Lachnospiraceae, Peptostreptococcus, and Atopobium) were found in all subjects and constituted 94.5-96.5% of the microbiome. Of these twenty genera, the proportion of Streptococcus decreased while Veillonella increased with poor oral hygiene status (P < 0.05). Furthermore, an unassigned species of Veillonella, Veillonella dispar and Veillonella parvula tended to be elevated in the Poor oral hygiene group. This is the first study demonstrating an important association between increase of Veillonella and poor oral hygiene status in children. However, further studies are required to identify the majority of Veillonella at species level in salivary microbiome of the Poor oral hygiene group.
Collapse
Affiliation(s)
- Izumi Mashima
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, Japan
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, New York, United States of America
- Department of Microbiology, School of Dentistry, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| | - Citra F. Theodorea
- Department of Microbiology, School of Dentistry, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
- Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
| | - Boonyanit Thaweboon
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Sroisiri Thaweboon
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Frank A. Scannapieco
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, New York, United States of America
| | - Futoshi Nakazawa
- Department of Microbiology, School of Dentistry, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| |
Collapse
|
30
|
Eriksson L, Lif Holgerson P, Johansson I. Saliva and tooth biofilm bacterial microbiota in adolescents in a low caries community. Sci Rep 2017; 7:5861. [PMID: 28724921 PMCID: PMC5517611 DOI: 10.1038/s41598-017-06221-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/08/2017] [Indexed: 12/16/2022] Open
Abstract
The oral cavity harbours a complex microbiome that is linked to dental diseases and serves as a route to other parts of the body. Here, the aims were to characterize the oral microbiota by deep sequencing in a low-caries population with regular dental care since childhood and search for association with caries prevalence and incidence. Saliva and tooth biofilm from 17-year-olds and mock bacteria communities were analysed using 16S rDNA Illumina MiSeq (v3-v4) and PacBio SMRT (v1-v8) sequencing including validity and reliability estimates. Caries was scored at 17 and 19 years of age. Both sequencing platforms revealed that Firmicutes dominated in the saliva, whereas Firmicutes and Actinobacteria abundances were similar in tooth biofilm. Saliva microbiota discriminated caries-affected from caries-free adolescents, with enumeration of Scardovia wiggsiae, Streptococcus mutans, Bifidobacterium longum, Leptotrichia sp. HOT498, and Selenomonas spp. in caries-affected participants. Adolescents with B. longum in saliva had significantly higher 2-year caries increment. PacBio SMRT revealed Corynebacterium matruchotii as the most prevalent species in tooth biofilm. In conclusion, both sequencing methods were reliable and valid for oral samples, and saliva microbiota was associated with cross-sectional caries prevalence, especially S. wiggsiae, S. mutans, and B. longum; the latter also with the 2-year caries incidence.
Collapse
Affiliation(s)
- Linda Eriksson
- Department of Odontology, section of Cariology, Umeå University, Umeå, Sweden
- Department of Odontology,section of Pedodontics, Umeå University, Umeå, Sweden
| | | | - Ingegerd Johansson
- Department of Odontology, section of Cariology, Umeå University, Umeå, Sweden.
| |
Collapse
|
31
|
Sundin OH, Mendoza-Ladd A, Zeng M, Diaz-Arévalo D, Morales E, Fagan BM, Ordoñez J, Velez P, Antony N, McCallum RW. The human jejunum has an endogenous microbiota that differs from those in the oral cavity and colon. BMC Microbiol 2017; 17:160. [PMID: 28716079 PMCID: PMC5513040 DOI: 10.1186/s12866-017-1059-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/26/2017] [Indexed: 02/07/2023] Open
Abstract
Background The upper half of the human small intestine, known as the jejunum, is the primary site for absorption of nutrient-derived carbohydrates, amino acids, small peptides, and vitamins. In contrast to the colon, which contains 1011–1012 colony forming units of bacteria per ml (CFU/ml), the normal jejunum generally ranges from 103 to 105 CFU per ml. Because invasive procedures are required to access the jejunum, much less is known about its bacterial microbiota. Bacteria inhabiting the jejunal lumen have been investigated by classical culture techniques, but not by culture-independent metagenomics. Results The lumen of the upper jejunum was sampled during enteroscopy of 20 research subjects. Culture on aerobic and anaerobic media gave live bacterial counts ranging from 5.8 × 103 CFU/ml to 8.0 × 106 CFU/ml. DNA from the same samples was analyzed by 16S rRNA gene-specific quantitative PCR, yielding values from 1.5 × 105 to 3.1 × 107 bacterial genomes per ml. When calculated for each sample, estimated bacterial viability ranged from effectively 100% to a low of 0.3%. 16S rRNA metagenomic analysis of uncultured bacteria by Illumina MiSeq sequencing gave detailed microbial composition by phylum, genus and species. The genera Streptococcus, Prevotella, Veillonella and Fusobacterium, were especially abundant, as well as non-oral genera including Escherichia, Klebsiella, and Citrobacter. The jejunum was devoid of the genera Alistipes, Ruminococcus, Faecalibacterium, and other extreme anaerobes abundant in the colon. In patients with higher bacterial loads, there was no significant change in microbial species composition. Conclusions The jejunal lumen contains a distinctive bacterial population consisting primarily of facultative anaerobes and oxygen-tolerant obligate anaerobes similar to those found in the oral cavity. However, the frequent abundance of Enterobacteriaceae represents a major difference from oral microbiota. Although a few genera are shared with the colon, we found no evidence for retrograde movement of the most abundant colonic microbes to the jejunum. Some individuals had much higher bacterial loads, but this was not correlated with decreases in bacterial species diversity or other evidence of dysbiosis. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1059-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Olof H Sundin
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center at El Paso, El Paso, 79905, TX, USA.
| | - Antonio Mendoza-Ladd
- Department of Internal Medicine, Division of Gastroenterology, Texas Tech University Health Sciences Center at El Paso, El Paso, 79905, TX, USA
| | - Mingtao Zeng
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center at El Paso, El Paso, 79905, TX, USA
| | - Diana Diaz-Arévalo
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center at El Paso, El Paso, 79905, TX, USA
| | - Elisa Morales
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center at El Paso, El Paso, 79905, TX, USA
| | - B Matthew Fagan
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center at El Paso, El Paso, 79905, TX, USA
| | - Javier Ordoñez
- Biostatistics Unit, Texas Tech University Health Sciences Center at El Paso, El Paso, 79905, TX, USA
| | - Philip Velez
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center at El Paso, El Paso, 79905, TX, USA
| | - Nishaal Antony
- Department of Internal Medicine, Division of Gastroenterology, Texas Tech University Health Sciences Center at El Paso, El Paso, 79905, TX, USA
| | - Richard W McCallum
- Department of Internal Medicine, Division of Gastroenterology, Texas Tech University Health Sciences Center at El Paso, El Paso, 79905, TX, USA
| |
Collapse
|
32
|
Influences of pH and Iron Concentration on the Salivary Microbiome in Individual Humans with and without Caries. Appl Environ Microbiol 2017; 83:AEM.02412-16. [PMID: 27940544 PMCID: PMC5288818 DOI: 10.1128/aem.02412-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/02/2016] [Indexed: 12/14/2022] Open
Abstract
This study aimed to identify the differences in the oral microbial communities in saliva from patients with and without caries by performing sequencing with the Illumina MiSeq platform, as well as to further assess their relationships with environmental factors (salivary pH and iron concentration). Forty-three volunteers were selected, including 21 subjects with and 22 without caries, from one village in Gansu, China. Based on 966,255 trimmed sequences and clustering at the 97% similarity level, 1,303 species-level operational taxonomic units were generated. The sequencing data for the two groups revealed that (i) particular distribution patterns (synergistic effects or competition) existed in the subjects with and without caries at both the genus and species levels and (ii) both the salivary pH and iron concentration had significant influences on the microbial community structure. IMPORTANCE The significant influences of the oral environment observed in this study increase the current understanding of the salivary microbiome in caries. These results will be useful for expanding research directions and for improving disease diagnosis, prognosis, and therapy.
Collapse
|
33
|
Jiang S, Gao X, Jin L, Lo ECM. Salivary Microbiome Diversity in Caries-Free and Caries-Affected Children. Int J Mol Sci 2016; 17:ijms17121978. [PMID: 27898021 PMCID: PMC5187778 DOI: 10.3390/ijms17121978] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/15/2016] [Accepted: 11/21/2016] [Indexed: 12/26/2022] Open
Abstract
Dental caries (tooth decay) is an infectious disease. Its etiology is not fully understood from the microbiological perspective. This study characterizes the diversity of microbial flora in the saliva of children with and without dental caries. Children (3–4 years old) with caries (n = 20) and without caries (n = 20) were recruited. Unstimulated saliva (2 mL) was collected from each child and the total microbial genomic DNA was extracted. DNA amplicons of the V3-V4 hypervariable region of the bacterial 16S rRNA gene were generated and subjected to Illumina Miseq sequencing. A total of 17 phyla, 26 classes, 40 orders, 80 families, 151 genera, and 310 bacterial species were represented in the saliva samples. There was no significant difference in the microbiome diversity between caries-affected and caries-free children (p > 0.05). The relative abundance of several species (Rothia dentocariosa, Actinomyces graevenitzii, Veillonella sp. oral taxon 780, Prevotella salivae, and Streptococcus mutans) was higher in the caries-affected group than in the caries-free group (p < 0.05). Fusobacterium periodonticum and Leptotrichia sp. oral clone FP036 were more abundant in caries-free children than in caries-affected children (p < 0.05). The salivary microbiome profiles of caries-free and caries-affected children were similar. Salivary counts of certain bacteria such as R. dentocariosa and F. periodonticum may be useful for screening/assessing children’s risk of developing caries.
Collapse
Affiliation(s)
- Shan Jiang
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, 34 Hospital Road, Sai Ying Pun, Hong Kong, China.
| | - Xiaoli Gao
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, 34 Hospital Road, Sai Ying Pun, Hong Kong, China.
| | - Lijian Jin
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, 34 Hospital Road, Sai Ying Pun, Hong Kong, China.
| | - Edward C M Lo
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, 34 Hospital Road, Sai Ying Pun, Hong Kong, China.
| |
Collapse
|