1
|
Xu J, Wu D, Yang J, Zhao Y, Liu X, Chang Y, Tang Y, Sun F, Zhao Y. Adult Outpatients with Long COVID Infected with SARS-CoV-2 Omicron Variant. Part 1: Oral Microbiota Alterations. Am J Med 2025; 138:732-741.e2. [PMID: 39151680 DOI: 10.1016/j.amjmed.2024.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/27/2024] [Accepted: 07/30/2024] [Indexed: 08/19/2024]
Abstract
BACKGROUND Many individuals experience long COVID after SARS-CoV-2 infection. As microbiota can influence health, it may change with COVID-19. This study investigated differences in oral microbiota between COVID-19 patients with and without long COVID. METHODS Based on a prospective follow-up investigation, this nested case-control study evaluated the differences in oral microbiota in individuals with and without long COVID (Symptomatic and Asymptomatic groups), which were assessed by 16S rRNA sequencing on tongue coating samples. A predictive model was established using machine learning based on specific differential microbial communities. RESULTS One-hundred-and-eight patients were included (n=54 Symptomatic group). The Symptomatic group had higher Alpha diversity indices (observed_otus, Chao1, Shannon, and Simpson indices), differences in microbial composition (Beta diversity), and microbial dysbiosis with increased diversity and relative abundance of pathogenic bacteria. Marker bacteria (c__Campylobacterota, o__Coriobacteriales, o__Pseudomonadales, and o__Campylobacterales) were associated with long COVID by linear discriminant analysis effect size and receiver operating characteristic curves (AUC 0.821). CONCLUSION There were distinct variations in oral microbiota between COVID-19 patients with and without long COVID. Changes in oral microbiota may indicate long COVID.
Collapse
Affiliation(s)
- Jianchao Xu
- Hebei University of Chinese Medicine, Shijiazhuang, China; Shijiazhuang People's Hospital, Shijiazhuang, China
| | - Di Wu
- Hebei University of Chinese Medicine, Shijiazhuang, China; The Traditional Chinese Medicine Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jie Yang
- Hebei General Hospital, Shijiazhuang, China
| | - Yinuo Zhao
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Xuzhao Liu
- Handan Hospital of Integrated Chinese and Western Medicine, Handan, China
| | - Yingying Chang
- The Traditional Chinese Medicine Hospital of Shijiazhuang, Shijiazhuang, China
| | - Yao Tang
- Wuhan Metware Biotechnology Co, Ltd, Wuhan, China
| | - Feng Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China; Key Laboratory of Epidemiology of Major Diseases (Peking University), Beijing, China
| | - Yubin Zhao
- Hebei University of Chinese Medicine, Shijiazhuang, China; Shijiazhuang People's Hospital, Shijiazhuang, China; Shijiazhuang College of Applied Technology, China.
| |
Collapse
|
2
|
Yang YH, Yu JJ, Han HY, Chang WM, Wang CW. Ex-vivo investigation of human salivary microbial growth with lysogeny broth for translational research-A pilot study. J Dent Sci 2025; 20:437-443. [PMID: 39873074 PMCID: PMC11762923 DOI: 10.1016/j.jds.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/12/2024] [Indexed: 01/30/2025] Open
Abstract
Background/purpose Salivary microbiome has become a surrogate indicator of oral disease due to its collective reservoirs and convenience in sampling. However, failed clinical trials often lead to wastes of resources, indicating a need for preclinical models. In this pilot study, we aimed to compare the salivary microbiome by metagenomics analysis before and after lysogeny broth culture for prospective translational studies. Materials and methods The study cohort included seven patients with severe periodontitis (Stage III/IV, Grade C), from whom unstimulated saliva was collected. The salivary microbiome was sequenced over the 16S rRNA gene V3-V4 hypervariable regions at baseline and after 6 hours of lysogeny broth culture. Results The results revealed changes in salivary microbiome and reduced bacterial diversity after culture, mainly due to the expansion of genera Neisseria (Median (Mdn) 15.95% to 37.52%, P < 0.05), Rothia (Mdn 10.21% to 16.32%, P < 0.05), and Haemophilus (Mdn 5.88% to 13.25%, P < 0.05). Periodontitis-related pathogens such as phyla Bacteroidetes, Fusobacteria and Spirochaetes were identified, while genera Porphyromonas, Parvimonas, Peptostreptococcus, and Campylobacter showed a decrease after lysogeny broth culture. Caries-related pathogens, including genera Veillonella, Leptotrichia, and species Haemophilus parainfluenzae and Streptococcus salivarius, were also detected. Conclusion This pilot study revealed that periodontitis- and caries-related bacteria could be identified in the saliva at baseline and after 6 hours ex-vivo culture with lysogeny broth. Our findings also suggested that lysogeny broth favored the growth of specific genera and may serve as a reference to monitor short-term modulation of these bacteria in salivary microbiome.
Collapse
Affiliation(s)
- Yu-Hsin Yang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jing-Jie Yu
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hsin-Ying Han
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Min Chang
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chin-Wei Wang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Periodontics, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
3
|
Tynior W, Kłósek M, Salatino S, Cuber P, Hudy D, Nałęcz D, Chan YT, Gustave C, Strzelczyk JK. Metagenomic Analysis of the Buccal Microbiome by Nanopore Sequencing Reveals Structural Differences in the Microbiome of a Patient with Molar Incisor Hypomineralization (MIH) Compared to a Healthy Child-Case Study. Int J Mol Sci 2024; 25:13143. [PMID: 39684853 DOI: 10.3390/ijms252313143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 11/29/2024] [Accepted: 12/03/2024] [Indexed: 12/18/2024] Open
Abstract
Molar incisor hypomineralization (MIH) is a qualitative developmental defect that affects the enamel tissue of permanent molars and can also occur in permanent incisors. Enamel affected by MIH has reduced hardness, increased porosity, and a higher organic content than unaffected enamel. These characteristics predispose the enamel to accumulation of bacteria and a higher prevalence of caries lesions. Through a groundbreaking metagenomic analysis of the buccal mucosal sample from a patient with MIH, we explored the intricacies of its microbiome compared to a healthy control using state-of-the-art nanopore long-read sequencing. Out of the 210 bacterial taxa identified in the MIH microbiome, we found Streptococcus and Haemophilus to be the most abundant genera. The bacteria with the highest read counts in the patient with MIH included Streptococcus mitis, Haemophilus parainfluenzae, Streptococcus pneumoniae, Rothia dentocariosa, and Gemella haemolysans. Our results revealed a striking contrast between healthy and MIH affected children, with a higher dominance and number of pathogenic species (S. pneumoniae, H. influenzae, and N. meningitidis) and reduced diversity in the MIH-affected patient. This distinct microbial profile not only sheds light on MIH-affected patients, but paves the way for future research, inspiring deeper understanding and larger scale studies.
Collapse
Affiliation(s)
- Wojciech Tynior
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, 19 Jordana St., 41-808 Zabrze, Poland
| | - Małgorzata Kłósek
- Department of Microbiology and Immunology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, 19 Jordana St., 41-808 Zabrze, Poland
| | - Silvia Salatino
- Molecular Biology Laboratories, Science and Innovation Platforms, Natural History Museum, London SW7 5BD, UK
| | - Piotr Cuber
- Molecular Biology Laboratories, Science and Innovation Platforms, Natural History Museum, London SW7 5BD, UK
| | - Dorota Hudy
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, 19 Jordana St., 41-808 Zabrze, Poland
| | - Dariusz Nałęcz
- Department of Otolaryngology and Maxillofacial Surgery, St. Vincent De Paul Hospital, 1 Wójta Radtkego St., 81-348 Gdynia, Poland
| | - Yuen-Ting Chan
- Molecular Biology Laboratories, Science and Innovation Platforms, Natural History Museum, London SW7 5BD, UK
| | - Carla Gustave
- Molecular Biology Laboratories, Science and Innovation Platforms, Natural History Museum, London SW7 5BD, UK
| | - Joanna Katarzyna Strzelczyk
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, 19 Jordana St., 41-808 Zabrze, Poland
| |
Collapse
|
4
|
Zelasko S, Swaney MH, Sandstrom S, Davenport TC, Seroogy CM, Gern JE, Kalan LR, Currie CR. Upper respiratory microbial communities of healthy populations are shaped by niche and age. MICROBIOME 2024; 12:206. [PMID: 39425237 PMCID: PMC11490146 DOI: 10.1186/s40168-024-01940-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 09/23/2024] [Indexed: 10/21/2024]
Abstract
BACKGROUND Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and intermicrobial interactions across healthy 24-month-old infant (n = 229) and adult (n = 100) populations. RESULTS We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity. CONCLUSIONS In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functions related to colonization resistance, with important implications for host health across the lifespan. Video Abstract.
Collapse
Affiliation(s)
- Susan Zelasko
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
| | - Mary Hannah Swaney
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Timothy C Davenport
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christine M Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lindsay R Kalan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada.
| |
Collapse
|
5
|
de Palma TH, Powers C, McPartland MJ, Mark Welch J, Ramsey M. Essential genes for Haemophilus parainfluenzae survival and biofilm growth. mSystems 2024; 9:e0067424. [PMID: 39166876 PMCID: PMC11406952 DOI: 10.1128/msystems.00674-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 07/21/2024] [Indexed: 08/23/2024] Open
Abstract
Haemophilus parainfluenzae (Hp) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and oral isolate EL1 (Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCEHaemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.
Collapse
Affiliation(s)
- Thais H de Palma
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Chris Powers
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Morgan J McPartland
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Jessica Mark Welch
- Department of Microbiology, ADA Forsyth Institute, Cambridge, Massachusetts, USA
| | - Matthew Ramsey
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| |
Collapse
|
6
|
Zheng Y, Yang Y, Liu X, Liu P, Li X, Zhang M, Zhou E, Zhao Z, Wang X, Zhang Y, Zheng B, Yan Y, Liu Y, Xu D, Cao L. Accelerated corrosion of 316L stainless steel in a simulated oral environment via extracellular electron transfer and acid metabolites of subgingival microbiota. Bioact Mater 2024; 35:56-66. [PMID: 38283387 PMCID: PMC10810744 DOI: 10.1016/j.bioactmat.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/26/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024] Open
Abstract
316L stainless steel (SS) is widely applied as microimplant anchorage (MIA) due to its excellent mechanical properties. However, the risk that the oral microorganisms can corrode 316L SS is fully neglected. Microbiologically influenced corrosion (MIC) of 316L SS is essential to the health and safety of all patients because the accelerated corrosion caused by the oral microbiota can trigger the release of Cr and Ni ions. This study investigated the corrosion behavior and mechanism of subgingival microbiota on 316L SS by 16S rRNA and metagenome sequencing, electrochemical measurements, and surface characterization techniques. Multispecies biofilms were formed by the oral subgingival microbiota in the simulated oral anaerobic environment on 316L SS surfaces, significantly accelerating the corrosion in the form of pitting. The microbiota samples collected from the subjects differed in biofilm compositions, corrosion behaviors, and mechanisms. The oral subgingival microbiota contributed to the accelerated corrosion of 316L SS via acidic metabolites and extracellular electron transfer. Our findings provide a new insight into the underlying mechanisms of oral microbial corrosion and guide the design of oral microbial corrosion-resistant materials.
Collapse
Affiliation(s)
- Ying Zheng
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Yi Yang
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China
- State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang, China
| | - Xianbo Liu
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Pan Liu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China
- State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang, China
| | - Xiangyu Li
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China
- State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang, China
| | - Mingxing Zhang
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China
- State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang, China
| | - Enze Zhou
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China
- State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang, China
| | - Zhenjin Zhao
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Xue Wang
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Yuanyuan Zhang
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Bowen Zheng
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Yuwen Yan
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Yi Liu
- School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Dake Xu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang, China
- State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang, China
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China
| | - Liu Cao
- College of Basic Medical Sciences, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, China
- Institute of Health Sciences, China Medical University, Shenyang, China
| |
Collapse
|
7
|
Zelasko S, Swaney MH, Sandstrom S, Davenport TC, Seroogy CM, Gern JE, Kalan LR, Currie CR. Upper respiratory microbial communities of healthy populations are shaped by niche and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.14.589416. [PMID: 38645133 PMCID: PMC11030450 DOI: 10.1101/2024.04.14.589416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations. Results We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity. Conclusions In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.
Collapse
Affiliation(s)
- Susan Zelasko
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mary Hannah Swaney
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy C. Davenport
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christine M. Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
8
|
Giacomini JJ, Torres-Morales J, Tang J, Dewhirst FE, Borisy GG, Mark Welch JL. Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity. Microbiol Spectr 2024; 12:e0401723. [PMID: 38488280 PMCID: PMC10986600 DOI: 10.1128/spectrum.04017-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/26/2024] [Indexed: 04/06/2024] Open
Abstract
Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility. IMPORTANCE Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.
Collapse
Affiliation(s)
| | | | - Jonathan Tang
- The Forsyth Institute, Cambridge, Massachusetts, USA
| | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, Massachusetts, USA
- Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | | | - Jessica L. Mark Welch
- The Forsyth Institute, Cambridge, Massachusetts, USA
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| |
Collapse
|
9
|
de Palma TH, Powers C, McPartland MJ, Welch JM, Ramsey M. Essential genes for Haemophilus parainfluenzae survival and biofilm growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.587483. [PMID: 38585970 PMCID: PMC10996682 DOI: 10.1101/2024.03.31.587483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Haemophilus parainfluenzae ( Hp ) is a Gram-negative, pleomorphic rod, highly prevalent and abundant as a commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the tongue dorsum, keratinized gingiva, and the supragingival plaque biofilm. As a member of the HACEK group, Hp is also known to cause infective endocarditis. Additionally, case reports have identified Hp as the causative agent of meningitis, septic arthritis, chronic osteomyelitis, septicemia, and a variety of other infectious diseases. Little is known about how Hp interacts with its neighbors in the healthy biofilm nor about its mechanisms of pathogenesis as an extraoral opportunistic pathogen. To address these unknowns, we identified the essential genomes of two Hp strains and the conditionally essential genes for their growth in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain ( Hp 392) and a commensal oral isolate EL1 ( Hp EL1), we show that the essential genome of Hp 392 and Hp EL1 is composed of 395 and 384 genes, respectively. The core essential genome, consisting of 341 essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains of Hp . Additionally, RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic biofilm survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo oral habitat. Further, the creation of this library presents a valuable tool for further investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.
Collapse
|
10
|
Sikdar R, Beauclaire MV, Lima BP, Herzberg MC, Elias MH. N-acyl homoserine lactone signaling modulates bacterial community associated with human dental plaque. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585217. [PMID: 38559107 PMCID: PMC10980036 DOI: 10.1101/2024.03.15.585217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
N-acyl homoserine lactones (AHLs) are small diffusible signaling molecules that mediate a cell density-dependent bacterial communication system known as quorum sensing (QS). AHL-mediated QS regulates gene expression to control many critical bacterial behaviors including biofilm formation, pathogenicity, and antimicrobial resistance. Dental plaque is a complex multispecies oral biofilm formed by successive colonization of the tooth surface by groups of commensal, symbiotic, and pathogenic bacteria, which can contribute to tooth decay and periodontal diseases. While the existence and roles of AHL-mediated QS in oral microbiota have been debated, recent evidence indicates that AHLs play significant roles in oral biofilm development and community dysbiosis. The underlying mechanisms, however, remain poorly characterized. To better understand the importance of AHL signaling in dental plaque formation, we manipulated AHL signaling by adding AHL lactonases or exogenous AHL signaling molecules. We find that AHLs can be detected in dental plaque grown under 5% CO2 conditions, but not when grown under anaerobic conditions, and yet anaerobic cultures are still responsive to AHLs. QS signal disruption using lactonases leads to changes in microbial population structures in both planktonic and biofilm states, changes that are dependent on the substrate preference of the used lactonase but mainly result in the increase in the abundance of commensal and pioneer colonizer species. Remarkably, the opposite manipulation, that is the addition of exogenous AHLs increases the abundance of late colonizer bacterial species. Hence, this work highlights the importance of AHL-mediated QS in dental plaque communities, its potential different roles in anaerobic and aerobic parts of dental plaque, and underscores the potential of QS interference in the control of periodontal diseases.
Collapse
Affiliation(s)
- Rakesh Sikdar
- Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Mai V. Beauclaire
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Bruno P. Lima
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark C. Herzberg
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mikael H. Elias
- Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, MN 55108, USA
| |
Collapse
|
11
|
Chen D, Chew D, Xiang Q, Lam T, Dai Y, Liu J, Wang L, He T, Strand R, Zhang X, Lim L, Xu J, Shi Y, Dong W. Interactions and effects of a stannous-containing sodium fluoride dentifrice on oral pathogens and the oral microbiome. Front Microbiol 2024; 15:1327913. [PMID: 38426054 PMCID: PMC10902866 DOI: 10.3389/fmicb.2024.1327913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024] Open
Abstract
Numerous studies have investigated the effects of stannous ions on specific microbes and their efficacy in reducing dental plaque. Nonetheless, our understanding of their impact on the oral microbiome is still a subject of ongoing exploration. Therefore, this study sought to evaluate the effects of a stannous-containing sodium fluoride dentifrice in comparison to a zinc-containing sodium fluoride dentifrice and a control group on intact, healthy oral biofilms. Utilizing the novel 2bRAD-M approach for species-resolved metagenomics, and FISH/CLSM with probes targeting periodontal and caries associated species alongside Sn2+ and Zn2+ ions, we collected and analyzed in situ biofilms from 15 generally healthy individuals with measurable dental plaque and treated the biofilms with dentifrices to elucidate variations in microbial distribution. Although significant shifts in the microbiome upon treatment were not observed, the use of a stannous-containing sodium fluoride dentifrice primarily led to an increase in health-associated commensal species and decrease in pathogenic species. Notably, FISH/CLSM analysis highlighted a marked reduction in representative species associated with periodontitis and caries following treatment with the use of a stannous-containing sodium fluoride dentifrice, as opposed to a zinc-containing sodium fluoride dentifrice and the control group. Additionally, Sn2+ specific intracellular imaging reflected the colocalization of Sn2+ ions with P. gingivalis but not with other species. In contrast, Zn2+ ions exhibited non-specific binding, thus suggesting that Sn2+ could exhibit selective binding toward pathogenic species. Altogether, our results demonstrate that stannous ions could help to maintain a healthy oral microbiome by preferentially targeting certain pathogenic bacteria to reverse dysbiosis and underscores the importance of the continual usage of such products as a preventive measure for oral diseases and the maintenance of health.
Collapse
Affiliation(s)
- Danyan Chen
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Periodontology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Stomatology, Yiwu Central Hospital, Yiwu, Zhejiang, China
| | - Dillon Chew
- Singapore Innovation Center, The Procter & Gamble Company, Singapore, Singapore
| | - Qianfeng Xiang
- Department of Dentistry-Regenerative Biomaterials, Radboud University Medical Center, Nijmegen, Netherlands
| | - TzeHau Lam
- Singapore Innovation Center, The Procter & Gamble Company, Singapore, Singapore
| | - Yajie Dai
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Jiquan Liu
- Singapore Innovation Center, The Procter & Gamble Company, Singapore, Singapore
| | - Lijiang Wang
- Procter & Gamble Technology Co. Ltd, Beijing, China
| | - Tao He
- The Procter & Gamble Company, Mason, OH, United States
| | - Ross Strand
- Singapore Innovation Center, The Procter & Gamble Company, Singapore, Singapore
| | - Xiaolan Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Linda Lim
- Singapore Innovation Center, The Procter & Gamble Company, Singapore, Singapore
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yunming Shi
- Procter & Gamble Technology Co. Ltd, Beijing, China
| | - Weili Dong
- State Key Laboratory of Oral and Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Periodontology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| |
Collapse
|
12
|
Baker JL, Mark Welch JL, Kauffman KM, McLean JS, He X. The oral microbiome: diversity, biogeography and human health. Nat Rev Microbiol 2024; 22:89-104. [PMID: 37700024 PMCID: PMC11084736 DOI: 10.1038/s41579-023-00963-6] [Citation(s) in RCA: 148] [Impact Index Per Article: 148.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2023] [Indexed: 09/14/2023]
Abstract
The human oral microbiota is highly diverse and has a complex ecology, comprising bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and highly structured biogeography that shapes metabolic exchange on a local scale and results from the diverse microenvironments present in the oral cavity. The oral microbiota also interfaces with the immune system of the human host and has an important role in not only the health of the oral cavity but also systemic health. In this Review, we highlight recent advances including novel insights into the biogeography of several oral niches at the species level, as well as the ecological role of candidate phyla radiation bacteria and non-bacterial members of the oral microbiome. In addition, we summarize the relationship between the oral microbiota and the pathology of oral diseases and systemic diseases. Together, these advances move the field towards a more holistic understanding of the oral microbiota and its role in health, which in turn opens the door to the study of novel preventive and therapeutic strategies.
Collapse
Affiliation(s)
- Jonathon L Baker
- Oregon Health & Science University, Portland, OR, USA
- J. Craig Venter Institute, La Jolla, CA, USA
- UC San Diego School of Medicine, La Jolla, CA, USA
| | - Jessica L Mark Welch
- The Forsyth Institute, Cambridge, MA, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
| | | | | | - Xuesong He
- The Forsyth Institute, Cambridge, MA, USA.
- Harvard School of Dental Medicine, Boston, MA, USA.
| |
Collapse
|
13
|
Fujimoto A, Fujii K, Suido H, Fukuike H, Miyake N, Suzuki H, Eguchi T, Tobata H. Changes in oral microflora following 0.3% cetylpyridinium chloride-containing mouth spray intervention in adult volunteers after professional oral care: Randomized clinical study. Clin Exp Dent Res 2023; 9:1034-1043. [PMID: 38041504 PMCID: PMC10728501 DOI: 10.1002/cre2.810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 12/03/2023] Open
Abstract
OBJECTIVES This study explored the changes in bacterial flora composition and total bacterial count in the saliva and tongue coating, along with the change in the tongue coating index (TCI) following an intervention with 0.3% cetylpyridinium chloride (CPC) mouth spray after professional oral care. MATERIALS AND METHODS Fifty-two adult volunteers aged 30-60 years were equally divided into CPC spray (n = 26) and control (n = 26) groups. All subjects underwent scaling and polishing. The CPC spray group was administered four puffs of CPC spray to the tongue dorsum four times a day for 3 weeks. The control group performed only routine daily oral care (brushing) and did not use any other spray. Bacteriological evaluation of saliva and tongue coating was performed using 16S ribosomal RNA gene sequencing and quantitative polymerase chain reaction. The tongue coating was evaluated to calculate the TCI. A per-protocol analysis was conducted for 44 subjects (CPC spray group, n = 23; control group, n = 21). RESULTS At 1 and 3 weeks after CPC spray use, the flora of the saliva and tongue coating changed; the genus Haemophilus was dominant in the CPC spray group, whereas the genus Saccharibacteria was dominant in the control group. The sampling time differed among individual participants, which may have affected the bacterial counts. There was no significant intragroup change in TCI in either group. CONCLUSIONS CPC spray affected the bacterial flora in the saliva and tongue coating, particularly with respect to an increase in the abundance of Haemophilus. However, CPC spray did not change the TCI. These results suggest that it may be optimal to combine CPC spray with a physical cleaning method such as using a tongue brush or scraper. Clinical Trial Registration: University Hospital Medical Information Network UMIN000041140.
Collapse
Affiliation(s)
- Ai Fujimoto
- Research and Development, Sunstar Inc.OsakaJapan
| | - Kana Fujii
- Research and Development, Sunstar Inc.OsakaJapan
| | - Hirohisa Suido
- Department of Health and Nutrition, Faculty of Health ScienceKyoto Koka Women's UniversityKyotoJapan
| | - Hisae Fukuike
- Oral Health Promotion, Affiliated with the Sunstar FoundationOsakaJapan
| | - Naoko Miyake
- Sunstar Senri Dental Clinic, Affiliated with the Sunstar FoundationOsakaJapan
| | - Hidenori Suzuki
- Sunstar Senri Dental Clinic, Affiliated with the Sunstar FoundationOsakaJapan
| | - Toru Eguchi
- Research and Development, Sunstar Inc.OsakaJapan
| | | |
Collapse
|
14
|
Labossiere A, Ramsey M, Merritt J, Kreth J. Molecular commensalism-how to investigate underappreciated health-associated polymicrobial communities. mBio 2023; 14:e0134223. [PMID: 37754569 PMCID: PMC10653818 DOI: 10.1128/mbio.01342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
The study of human commensal bacteria began with the first observation of prokaryotes >340 years ago. Since then, the study of human-associated microbes has been justifiably biased toward the study of infectious pathogens. However, the role of commensal microbes has in recent years begun to be understood with some appreciation of them as potential protectors of host health rather than bystanders. As our understanding of these valuable microbes grows, it highlights how much more remains to be learned about them and their roles in maintaining health. We note here that a thorough framework for the study of commensals, both in vivo and in vitro is overall lacking compared to well-developed methodologies for pathogens. The modification and application of methods for the study of pathogens can work well for the study of commensals but is not alone sufficient to properly characterize their relationships. This is because commensals live in homeostasis with the host and within complex communities. One difficulty is determining which commensals have a quantifiable impact on community structure and stability as well as host health, vs benign microbes that may indeed serve only as bystanders. Human microbiomes are composed of bacteria, archaea, fungi, and viruses. This review focuses particularly on oral bacteria, yet many of the principles of commensal impacts on host health observed in the mouth can translate well to other host sites. Here, we discuss the value of commensals, the shortcomings involved in model systems for their study, and some of the more notable impacts they have upon not only each other but host health.
Collapse
Affiliation(s)
- Alex Labossiere
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Matthew Ramsey
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Justin Merritt
- Biomaterial and Biomedical Sciences, Oregon Health and Science University, School of Dentistry, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Jens Kreth
- Biomaterial and Biomedical Sciences, Oregon Health and Science University, School of Dentistry, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health and Science University, Portland, Oregon, USA
| |
Collapse
|
15
|
Zuber P, Kreth J. Aspects of oral streptococcal metabolic diversity: Imagining the landscape beneath the fog. Mol Microbiol 2023; 120:508-524. [PMID: 37329112 DOI: 10.1111/mmi.15106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023]
Abstract
It is widely acknowledged that the human-associated microbial community influences host physiology, systemic health, disease progression, and even behavior. There is currently an increased interest in the oral microbiome, which occupies the entryway to much of what the human initially encounters from the environment. In addition to the dental pathology that results from a dysbiotic microbiome, microbial activity within the oral cavity exerts significant systemic effects. The composition and activity of the oral microbiome is influenced by (1) host-microbial interactions, (2) the emergence of niche-specific microbial "ecotypes," and (3) numerous microbe-microbe interactions, shaping the underlying microbial metabolic landscape. The oral streptococci are central players in the microbial activity ongoing in the oral cavity, due to their abundance and prevalence in the oral environment and the many interspecies interactions in which they participate. Streptococci are major determinants of a healthy homeostatic oral environment. The metabolic activities of oral Streptococci, particularly the metabolism involved in energy generation and regeneration of oxidative resources vary among the species and are important factors in niche-specific adaptations and intra-microbiome interactions. Here we summarize key differences among streptococcal central metabolic networks and species-specific differences in how the key glycolytic intermediates are utilized.
Collapse
Affiliation(s)
- Peter Zuber
- Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
| | - Jens Kreth
- School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
| |
Collapse
|
16
|
Abstract
Microbial species colonizing host ecosystems in health or disease rarely do so alone. Organisms conglomerate into dynamic heterotypic communities or biofilms in which interspecies and interkingdom interactions drive functional specialization of constituent species and shape community properties, including nososymbiocity or pathogenic potential. Cell-to-cell binding, exchange of signaling molecules, and nutritional codependencies can all contribute to the emergent properties of these communities. Spatial constraints defined by community architecture also determine overall community function. Multilayered interactions thus occur between individual pairs of organisms, and the relative impact can be determined by contextual cues. Host responses to heterotypic communities and impact on host surfaces are also driven by the collective action of the community. Additionally, the range of interspecies interactions can be extended by bacteria utilizing host cells or host diet to indirectly or directly influence the properties of other organisms and the community microenvironment. In contexts where communities transition to a dysbiotic state, their quasi-organismal nature imparts adaptability to nutritional availability and facilitates resistance to immune effectors and, moreover, exploits inflammatory and acidic microenvironments for their persistence.
Collapse
Affiliation(s)
- Richard J. Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, USA
| | - George Hajishengallis
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hyun Koo
- Department of Orthodontics and Divisions of Pediatric Dentistry and Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
17
|
Hajishengallis G, Lamont RJ, Koo H. Oral polymicrobial communities: Assembly, function, and impact on diseases. Cell Host Microbe 2023; 31:528-538. [PMID: 36933557 PMCID: PMC10101935 DOI: 10.1016/j.chom.2023.02.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Oral microbial communities assemble into complex spatial structures. The sophisticated physical and chemical signaling systems underlying the community enable their collective functional regulation as well as the ability to adapt by integrating environmental information. The combined output of community action, as shaped by both intra-community interactions and host and environmental variables, dictates homeostatic balance or dysbiotic disease such as periodontitis and dental caries. Oral polymicrobial dysbiosis also exerts systemic effects that adversely affect comorbidities, in part due to ectopic colonization of oral pathobionts in extra-oral tissues. Here, we review new and emerging concepts that explain the collective functional properties of oral polymicrobial communities and how these impact health and disease both locally and systemically.
Collapse
Affiliation(s)
- George Hajishengallis
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, USA.
| | - Hyun Koo
- Department of Orthodontics and Divisions of Pediatric Dentistry and Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA; Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
18
|
Kreth J, Merritt J. Illuminating the oral microbiome and its host interactions: tools and approaches for molecular ecological studies. FEMS Microbiol Rev 2023; 47:fuac052. [PMID: 36564013 PMCID: PMC9936263 DOI: 10.1093/femsre/fuac052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022] Open
Abstract
A more comprehensive understanding of oral diseases like caries and periodontitis is dependent on an intimate understanding of the microbial ecological processes that are responsible for disease development. With this review, we provide a comprehensive overview of relevant molecular ecology techniques that have played critical roles in the current understanding of human oral biofilm development, interspecies interactions, and microbiome biogeography. The primary focus is on relevant technologies and examples available in the oral microbiology literature. However, most, if not all, of the described technologies should be readily adaptable for studies of microbiomes from other mucosal sites in the body. Therefore, this review is intended to serve as a reference guide used by microbiome researchers as they inevitably transition into molecular mechanistic studies of the many significant phenotypes observed clinically.
Collapse
Affiliation(s)
- Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, MRB433, 3181 SW Sam Jackson Park Rd., #L595, Portland, OR 97239, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, MRB433, 3181 SW Sam Jackson Park Rd., #L595, Portland, OR 97239, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States
| |
Collapse
|
19
|
Morillo-Lopez V, Sjaarda A, Islam I, Borisy GG, Mark Welch JL. Corncob structures in dental plaque reveal microhabitat taxon specificity. MICROBIOME 2022; 10:145. [PMID: 36064650 PMCID: PMC9446765 DOI: 10.1186/s40168-022-01323-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 07/07/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND The human mouth is a natural laboratory for studying how bacterial communities differ across habitats. Different bacteria colonize different surfaces in the mouth-teeth, tongue dorsum, and keratinized and non-keratinized epithelia-despite the short physical distance between these habitats and their connection through saliva. We sought to determine whether more tightly defined microhabitats might have more tightly defined sets of resident bacteria. A microhabitat may be characterized, for example, as the space adjacent to a particular species of bacterium. Corncob structures of dental plaque, consisting of coccoid bacteria bound to filaments of Corynebacterium cells, present an opportunity to analyze the community structure of one such well-defined microhabitat within a complex natural biofilm. Here, we investigate by fluorescence in situ hybridization and spectral imaging the composition of the cocci decorating the filaments. RESULTS The range of taxa observed in corncobs was limited to a small subset of the taxa present in dental plaque. Among four major groups of dental plaque streptococci, two were the major constituents of corncobs, including one that was the most abundant Streptococcus species in corncobs despite being relatively rare in dental plaque overall. Images showed both Streptococcus types in corncobs in all individual donors, suggesting that the taxa have different ecological roles or that mechanisms exist for stabilizing the persistence of functionally redundant taxa in the population. Direct taxon-taxon interactions were observed not only between the Streptococcus cells and the central corncob filament but also between Streptococcus cells and the limited subset of other plaque bacteria detected in the corncobs, indicating species ensembles involving these taxa as well. CONCLUSIONS The spatial organization we observed in corncobs suggests that each of the microbial participants can interact with multiple, albeit limited, potential partners, a feature that may encourage the long-term stability of the community. Additionally, our results suggest the general principle that a precisely defined microhabitat will be inhabited by a small and well-defined set of microbial taxa. Thus, our results are important for understanding the structure and organizing principles of natural biofilms and lay the groundwork for future work to modulate and control biofilms for human health. Video Abstract.
Collapse
Affiliation(s)
- Viviana Morillo-Lopez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543 USA
| | - Alexandra Sjaarda
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543 USA
| | - Imon Islam
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543 USA
| | - Gary G. Borisy
- Present Address: Department of Microbiology, The Forsyth Institute, Cambridge, MA 02139 USA
| | - Jessica L. Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543 USA
- Present Address: Department of Microbiology, The Forsyth Institute, Cambridge, MA 02139 USA
| |
Collapse
|
20
|
Reis Ferreira M, Pasto A, Ng T, Patel V, Guerrero Urbano T, Sears C, Wade WG. The microbiota and radiotherapy for head and neck cancer: What should clinical oncologists know? Cancer Treat Rev 2022; 109:102442. [PMID: 35932549 DOI: 10.1016/j.ctrv.2022.102442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/23/2022]
Abstract
Radiotherapy is a linchpin in head and neck squamous cell carcinoma (HN-SCC) treatment. Modulating tumour and/or normal tissue biology offers opportunities to further develop HN-SCC radiotherapy. The microbiota, which can exhibit homeostatic properties and be a modulator of immunity, has recently received considerable interest from the Oncology community. Microbiota research in head and neck oncology has also flourished. However, available data are difficult to interpret for clinical and radiation oncologists. In this review, we focus on how microbiota research can contribute to the improvement of radiotherapy for HN-SCC, focusing on how current and future research can be translated back to the clinic. We include in-depth discussions about the microbiota, its multiple habitats and relevance to human physiology, mechanistic interactions with HN-SCC, available evidence on microbiota and HNC oncogenesis, efficacy and toxicity of treatment. We discuss clinically-relevant areas such as the role of the microbiota as a predictive and prognostic biomarker, as well as the potential of leveraging the microbiota and its interactions with immunity to improve treatment results. Importantly, we draw parallels with other cancers where research is more mature. We map out future directions of research and explain clinical implications in detail.
Collapse
Affiliation(s)
- Miguel Reis Ferreira
- King's College London, London, UK; Guys and St Thomas NHS Foundation Trust, London, UK.
| | | | - Tony Ng
- King's College London, London, UK
| | - Vinod Patel
- King's College London, London, UK; Guys and St Thomas NHS Foundation Trust, London, UK
| | | | - Cynthia Sears
- Johns Hopkins University School of Medicine and the Bloomberg School of Public Health, Baltimore, USA
| | | |
Collapse
|
21
|
Li Q, Zhou F, Su Z, Li Y, Li J. Corynebacterium matruchotii: A Confirmed Calcifying Bacterium With a Potentially Important Role in the Supragingival Plaque. Front Microbiol 2022; 13:940643. [PMID: 35875585 PMCID: PMC9298747 DOI: 10.3389/fmicb.2022.940643] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
Corynebacterium matruchotii is a reported calcifying bacterium that can usually be isolated from dental calculus and induce mineralization in vitro. In recent years, based on in situ hybridization probe and sequencing technology, researchers have discovered the central "pillar" role of C. matruchotii in supragingival plaque, and many studies focused on bacterial interactions in the biofilm structure dominated by C. matruchotii have been conducted. Besides, C. matruchotii seems to be an indicator of "caries-free" oral status according to imaging and sequencing studies. Therefore, in this review, we summarize C. matruchotii 's role in supragingival plaque based on the structure, interactions, and potential connections with oral diseases.
Collapse
Affiliation(s)
- Qinyang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fangjie Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhifei Su
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
22
|
Strategies to Combat Caries by Maintaining the Integrity of Biofilm and Homeostasis during the Rapid Phase of Supragingival Plaque Formation. Antibiotics (Basel) 2022; 11:antibiotics11070880. [PMID: 35884135 PMCID: PMC9312143 DOI: 10.3390/antibiotics11070880] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 02/06/2023] Open
Abstract
Bacteria in the oral cavity, including commensals and opportunistic pathogens, are organized into highly specialized sessile communities, coexisting in homeostasis with the host under healthy conditions. A dysbiotic environment during biofilm evolution, however, allows opportunistic pathogens to become the dominant species at caries-affected sites at the expense of health-associated taxa. Combining tooth brushing with dentifrices or rinses combat the onset of caries by partially removes plaque, but resulting in the biofilm remaining in an immature state with undesirables’ consequences on homeostasis and oral ecosystem. This leads to the need for therapeutic pathways that focus on preserving balance in the oral microbiota and applying strategies to combat caries by maintaining biofilm integrity and homeostasis during the rapid phase of supragingival plaque formation. Adhesion, nutrition, and communication are fundamental in this phase in which the bacteria that have survived these adverse conditions rebuild and reorganize the biofilm, and are considered targets for designing preventive strategies to guide the biofilm towards a composition compatible with health. The present review summarizes the most important advances and future prospects for therapies based on the maintenance of biofilm integrity and homeostasis as a preventive measure of dysbiosis focused on these three key factors during the rapid phase of plaque formation.
Collapse
|