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Brar NK, Dhariwal A, Shekhar S, Junges R, Hakansson AP, Petersen FC. HAMLET, a human milk protein-lipid complex, modulates amoxicillin induced changes in an ex vivo biofilm model of the oral microbiome. Front Microbiol 2024; 15:1406190. [PMID: 39101559 PMCID: PMC11254628 DOI: 10.3389/fmicb.2024.1406190] [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: 03/24/2024] [Accepted: 06/17/2024] [Indexed: 08/06/2024] Open
Abstract
Challenges from infections caused by biofilms and antimicrobial resistance highlight the need for novel antimicrobials that work in conjunction with antibiotics and minimize resistance risk. In this study we investigated the composite effect of HAMLET (human alpha-lactalbumin made lethal to tumor cells), a human milk protein-lipid complex and amoxicillin on microbial ecology using an ex vivo oral biofilm model with pooled saliva samples. HAMLET was chosen due to its multi-targeted antimicrobial mechanism, together with its synergistic effect with antibiotics on single species pathogens, and low risk of resistance development. The combination of HAMLET and low concentrations of amoxicillin significantly reduced biofilm viability, while each of them alone had little or no impact. Using a whole metagenomics approach, we found that the combination promoted a remarkable shift in overall microbial composition compared to the untreated samples. A large proportion of the bacterial species in the combined treatment were Lactobacillus crispatus, a species with probiotic effects, whereas it was only detected in a minor fraction in untreated samples. Although resistome analysis indicated no major shifts in alpha-diversity, the results showed the presence of TEM beta-lactamase genes in low proportions in all treated samples but absence in untreated samples. Our study illustrates HAMLET's capability to alter the effects of amoxicillin on the oral microbiome and potentially favor the growth of selected probiotic bacteria when in combination. The findings extend previous knowledge on the combined effects of HAMLET and antibiotics against target pathogens to include potential modulatory effects on polymicrobial biofilms of human origin.
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Affiliation(s)
- Navdeep Kaur Brar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Sudhanshu Shekhar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Roger Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Anders P. Hakansson
- Institute of Experimental Infection Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
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2
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Brar NK, Dhariwal A, Åmdal HA, Junges R, Salvadori G, Baker JL, Edlund A, Petersen FC. Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome. NPJ Biofilms Microbiomes 2024; 10:37. [PMID: 38565843 PMCID: PMC10987642 DOI: 10.1038/s41522-024-00507-7] [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: 08/28/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Prolonged exposure to antibiotics at low concentration can promote processes associated with bacterial biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the total abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. The ecological impact on the microbiome and resistome was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.
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Affiliation(s)
- N K Brar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - A Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - H A Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - R Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - G Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - J L Baker
- Department of Oral Rehabilitation & Biosciences, Oregon Health & Science University, Portland, OR, USA
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA, USA
| | - A Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA, USA
| | - F C Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway.
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3
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Winter H, Wagner R, Ehlbeck J, Urich T, Schnabel U. Deep Impact: Shifts of Native Cultivable Microbial Communities on Fresh Lettuce after Treatment with Plasma-Treated Water. Foods 2024; 13:282. [PMID: 38254583 PMCID: PMC10815073 DOI: 10.3390/foods13020282] [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: 11/23/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Foods consumed raw, such as lettuce, can host food-borne human-pathogenic bacteria. In the worst-case, these diseases cause to death. To limit illness and industrial losses, one innovative sanitation method is non-thermal plasma, which offers an extremely efficient reduction of living microbial biomass. Unfortunately, the total viable count (TVC), one of the most common methods for quantifying antimicrobial effects, provides no detailed insights into the composition of the surviving microbial community after treatment. To address this information gap, different special agars were used to investigate the reduction efficiency of plasma-treated water (PTW) on different native cultivable microorganisms. All tested cultivable microbial groups were reduced using PTW. Gram-negative bacteria showed a reduction of 3.81 log10, and Gram-positive bacteria showed a reduction of 3.49 log10. Fungi were reduced by 3.89 log10. These results were further validated using a live/dead assay. MALDI-ToF (matrix-assisted laser-desorption-ionization time-of-flight)-based determination was used for a diversified overview. The results demonstrated that Gram-negative bacteria were strongly reduced. Interestingly, Gram-positive bacteria and fungi were reduced by nearly equal amounts, but could still recover from PTW treatment. MALDI-ToF mainly identified Pseudomonas spp. and groups of Bacillus on the tested lettuce. These results indicate that the PTW treatment could efficiently achieve a ubiquitous, spectrum-wide reduction of microbial life.
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Affiliation(s)
- Hauke Winter
- Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Strasse 2, 17489 Greifswald, Germany; (H.W.); (R.W.); (J.E.)
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany;
| | - Robert Wagner
- Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Strasse 2, 17489 Greifswald, Germany; (H.W.); (R.W.); (J.E.)
| | - Jörg Ehlbeck
- Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Strasse 2, 17489 Greifswald, Germany; (H.W.); (R.W.); (J.E.)
| | - Tim Urich
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany;
| | - Uta Schnabel
- Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Strasse 2, 17489 Greifswald, Germany; (H.W.); (R.W.); (J.E.)
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Cleaver L, Garnett JA. How to study biofilms: technological advancements in clinical biofilm research. Front Cell Infect Microbiol 2023; 13:1335389. [PMID: 38156318 PMCID: PMC10753778 DOI: 10.3389/fcimb.2023.1335389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/30/2023] [Indexed: 12/30/2023] Open
Abstract
Biofilm formation is an important survival strategy commonly used by bacteria and fungi, which are embedded in a protective extracellular matrix of organic polymers. They are ubiquitous in nature, including humans and other animals, and they can be surface- and non-surface-associated, making them capable of growing in and on many different parts of the body. Biofilms are also complex, forming polymicrobial communities that are difficult to eradicate due to their unique growth dynamics, and clinical infections associated with biofilms are a huge burden in the healthcare setting, as they are often difficult to diagnose and to treat. Our understanding of biofilm formation and development is a fast-paced and important research focus. This review aims to describe the advancements in clinical biofilm research, including both in vitro and in vivo biofilm models, imaging techniques and techniques to analyse the biological functions of the biofilm.
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Affiliation(s)
- Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, United Kingdom
| | - James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, United Kingdom
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5
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Yuan L, Dai H, He G, Yang Z, Jiao X. Invited review: Current perspectives for analyzing the dairy biofilms by integrated multiomics. J Dairy Sci 2023; 106:8181-8192. [PMID: 37641326 DOI: 10.3168/jds.2023-23306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/26/2023] [Indexed: 08/31/2023]
Abstract
Biofilms formed by pathogenic or spoilage microorganisms have become serious issues in the dairy industry, as this mode of life renders such microorganisms highly resistant to cleaning-in-place (CIP) procedures, disinfectants, desiccation, and other control strategies. The advent of omics techniques, especially the integration of different omics tools, has greatly improved our understanding of the features of microbial biofilms, and provided in-depth knowledge on developing effective methods that are directly against deleterious biofilms. This review provides novel insights into the single use of each omics tool and the application of multiomics tools to unravel the mechanisms of biofilm formation, specific molecular phenotypes exhibited by biofilms, and biofilm control strategies. Challenges and future perspective on the integration of omics tools for biofilm studies are also addressed.
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Affiliation(s)
- Lei Yuan
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, 225127 China; Jiangsu Key Laboratory of Zoonoses, Yangzhou, Jiangsu, 225009 China; Key Laboratory of Dairy Science (Northeast Agricultural University), Ministry of Education, Harbin 150030, China
| | - Hongchao Dai
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, 225127 China
| | - Guoqing He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, 310058 China
| | - Zhenquan Yang
- School of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, 225127 China.
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonoses, Yangzhou, Jiangsu, 225009 China.
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King AM, Zhang Z, Glassey E, Siuti P, Clardy J, Voigt CA. Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra. Nat Microbiol 2023; 8:2420-2434. [PMID: 37973865 DOI: 10.1038/s41564-023-01524-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Human-associated bacteria secrete modified peptides to control host physiology and remodel the microbiota species composition. Here we scanned 2,229 Human Microbiome Project genomes of species colonizing skin, gastrointestinal tract, urogenital tract, mouth and trachea for gene clusters encoding RiPPs (ribosomally synthesized and post-translationally modified peptides). We found 218 lanthipeptides and 25 lasso peptides, 70 of which were synthesized and expressed in E. coli and 23 could be purified and functionally characterized. They were tested for activity against bacteria associated with healthy human flora and pathogens. New antibiotics were identified against strains implicated in skin, nasal and vaginal dysbiosis as well as from oral strains selectively targeting those in the gut. Extended- and narrow-spectrum antibiotics were found against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. Mining natural products produced by human-associated microbes will enable the elucidation of ecological relationships and may be a rich resource for antimicrobial discovery.
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Affiliation(s)
- Andrew M King
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhengan Zhang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emerson Glassey
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Piro Siuti
- Synthetic Biology Group, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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7
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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.
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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
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Baker JL. Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research. FEMS Microbiol Rev 2023; 47:fuad051. [PMID: 37667515 PMCID: PMC10503653 DOI: 10.1093/femsre/fuad051] [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: 01/31/2023] [Revised: 08/02/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.
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Affiliation(s)
- Jonathon L Baker
- Department of Oral Rehabilitation & Biosciences, School of Dentistry, Oregon Health & Science University, 3181 Sam Jackson Park Road, Portland, OR 97202, United States
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA 92093, United States
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9
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Taj B, Adeolu M, Xiong X, Ang J, Nursimulu N, Parkinson J. MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities. MICROBIOME 2023; 11:143. [PMID: 37370188 DOI: 10.1186/s40168-023-01562-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 04/28/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND Whole microbiome RNASeq (metatranscriptomics) has emerged as a powerful technology to functionally interrogate microbial communities. A key challenge is how best to process, analyze, and interpret these complex datasets. In a typical application, a single metatranscriptomic dataset may comprise from tens to hundreds of millions of sequence reads. These reads must first be processed and filtered for low quality and potential contaminants, before being annotated with taxonomic and functional labels and subsequently collated to generate global bacterial gene expression profiles. RESULTS Here, we present MetaPro, a flexible, massively scalable metatranscriptomic data analysis pipeline that is cross-platform compatible through its implementation within a Docker framework. MetaPro starts with raw sequence read input (single-end or paired-end reads) and processes them through a tiered series of filtering, assembly, and annotation steps. In addition to yielding a final list of bacterial genes and their relative expression, MetaPro delivers a taxonomic breakdown based on the consensus of complementary prediction algorithms, together with a focused breakdown of enzymes, readily visualized through the Cytoscape network visualization tool. We benchmark the performance of MetaPro against two current state-of-the-art pipelines and demonstrate improved performance and functionality. CONCLUSIONS MetaPro represents an effective integrated solution for the processing and analysis of metatranscriptomic datasets. Its modular architecture allows new algorithms to be deployed as they are developed, ensuring its longevity. To aid user uptake of the pipeline, MetaPro, together with an established tutorial that has been developed for educational purposes, is made freely available at https://github.com/ParkinsonLab/MetaPro . The software is freely available under the GNU general public license v3. Video Abstract.
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Affiliation(s)
- Billy Taj
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Mobolaji Adeolu
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Xuejian Xiong
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Jordan Ang
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ON, L5L 1C6, Canada
| | - Nirvana Nursimulu
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3G4, Canada
| | - John Parkinson
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3G4, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 3G4, Canada.
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10
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Dow L, Gallart M, Ramarajan M, Law SR, Thatcher LF. Streptomyces and their specialised metabolites for phytopathogen control - comparative in vitro and in planta metabolic approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1151912. [PMID: 37389291 PMCID: PMC10301723 DOI: 10.3389/fpls.2023.1151912] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023]
Abstract
In the search for new crop protection microbial biocontrol agents, isolates from the genus Streptomyces are commonly found with promising attributes. Streptomyces are natural soil dwellers and have evolved as plant symbionts producing specialised metabolites with antibiotic and antifungal activities. Streptomyces biocontrol strains can effectively suppress plant pathogens via direct antimicrobial activity, but also induce plant resistance through indirect biosynthetic pathways. The investigation of factors stimulating the production and release of Streptomyces bioactive compounds is commonly conducted in vitro, between Streptomyces sp. and a plant pathogen. However, recent research is starting to shed light on the behaviour of these biocontrol agents in planta, where the biotic and abiotic conditions share little similarity to those of controlled laboratory conditions. With a focus on specialised metabolites, this review details (i) the various methods by which Streptomyces biocontrol agents employ specialised metabolites as an additional line of defence against plant pathogens, (ii) the signals shared in the tripartite system of plant, pathogen and biocontrol agent, and (iii) an outlook on new approaches to expedite the identification and ecological understanding of these metabolites under a crop protection lens.
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Affiliation(s)
- Lachlan Dow
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Microbiomes for One Systems Health Future Science Platform, Acton, ACT, Australia
| | - Marta Gallart
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Advanced Engineering Biology Future Science Platform, Acton, ACT, Australia
| | - Margaret Ramarajan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
| | - Simon R. Law
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Microbiomes for One Systems Health Future Science Platform, Acton, ACT, Australia
| | - Louise F. Thatcher
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Microbiomes for One Systems Health Future Science Platform, Acton, ACT, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Advanced Engineering Biology Future Science Platform, Acton, ACT, Australia
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Kwoji ID, Aiyegoro OA, Okpeku M, Adeleke MA. 'Multi-omics' data integration: applications in probiotics studies. NPJ Sci Food 2023; 7:25. [PMID: 37277356 DOI: 10.1038/s41538-023-00199-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
The concept of probiotics is witnessing increasing attention due to its benefits in influencing the host microbiome and the modulation of host immunity through the strengthening of the gut barrier and stimulation of antibodies. These benefits, combined with the need for improved nutraceuticals, have resulted in the extensive characterization of probiotics leading to an outburst of data generated using several 'omics' technologies. The recent development in system biology approaches to microbial science is paving the way for integrating data generated from different omics techniques for understanding the flow of molecular information from one 'omics' level to the other with clear information on regulatory features and phenotypes. The limitations and tendencies of a 'single omics' application to ignore the influence of other molecular processes justify the need for 'multi-omics' application in probiotics selections and understanding its action on the host. Different omics techniques, including genomics, transcriptomics, proteomics, metabolomics and lipidomics, used for studying probiotics and their influence on the host and the microbiome are discussed in this review. Furthermore, the rationale for 'multi-omics' and multi-omics data integration platforms supporting probiotics and microbiome analyses was also elucidated. This review showed that multi-omics application is useful in selecting probiotics and understanding their functions on the host microbiome. Hence, recommend a multi-omics approach for holistically understanding probiotics and the microbiome.
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Affiliation(s)
- Iliya Dauda Kwoji
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Olayinka Ayobami Aiyegoro
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, Northwest, South Africa
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Matthew Adekunle Adeleke
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa.
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12
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Yin W, Zhang Z, Shuai X, Zhou X, Yin D. Caffeic Acid Phenethyl Ester (CAPE) Inhibits Cross-Kingdom Biofilm Formation of Streptococcus mutans and Candida albicans. Microbiol Spectr 2022; 10:e0157822. [PMID: 35980199 PMCID: PMC9602599 DOI: 10.1128/spectrum.01578-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/02/2022] [Indexed: 12/31/2022] Open
Abstract
Streptococcus mutans and Candida albicans exhibit strong cariogenicity through cross-kingdom biofilm formation during the pathogenesis of dental caries. Caffeic acid phenethyl ester (CAPE), a natural compound, has potential antimicrobial effects on each species individually, but there are no reports of its effect on this dual-species biofilm. This study aimed to explore the effects of CAPE on cariogenic biofilm formation by S. mutans and C. albicans and the related mechanisms. The effect of CAPE on planktonic cell growth was investigated, and crystal violet staining, the anthrone-sulfuric acid assay and confocal laser scanning microscopy were used to evaluate biofilm formation. The structures of the formed biofilms were observed using scanning electron microscopy. To explain the antimicrobial effect of CAPE, quantitative real-time PCR (qRT-PCR) was applied to monitor the relative expression levels of cariogenic genes. Finally, the biocompatibility of CAPE in human oral keratinocytes (HOKs) was evaluated using the CCK-8 assay. The results showed that CAPE suppressed the growth, biofilm formation and extracellular polysaccharides (EPS) synthesis of C. albicans and S. mutans in the coculture system of the two species. The expression of the gtf gene was also suppressed by CAPE. The efficacy of CAPE was concentration dependent, and the compound exhibited acceptable biocompatibility. Our research lays the foundation for further study of the application of the natural compound CAPE as a potential antimicrobial agent to control dental caries-associated cross-kingdom biofilms. IMPORTANCE Severe dental caries is a multimicrobial infectious disease that is strongly induced by the cross-kingdom biofilm formed by S. mutans and C. albicans. This study aimed to investigate the potential of caffeic acid phenethyl ester (CAPE) as a natural product in the prevention of severe caries. This study clarified the inhibitory effect of CAPE on cariogenic biofilm formation and the control of cariogenic genes. It deepens our understanding of the synergistic cariogenic effect of S. mutans and C. albicans and provides a new perspective for the prevention and control of dental caries with CAPE. These findings may contribute to the development of CAPE as a promising antimicrobial agent targeting this caries-related cross-kingdom biofilm.
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Affiliation(s)
- Wumeng Yin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Zhong Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Xinxing Shuai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Derong Yin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
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13
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OUIDIR T, GABRIEL B, CHABANE YNAIT. Overview of multi-species biofilms in different ecosystems: wastewater treatment, soil and oral cavity. J Biotechnol 2022; 350:67-74. [DOI: 10.1016/j.jbiotec.2022.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023]
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14
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Wang D, Nambu T, Tanimoto H, Iwata N, Yoshikawa K, Okinaga T, Yamamoto K. Interdental Plaque Microbial Community Changes under In Vitro Violet LED Irradiation. Antibiotics (Basel) 2021; 10:antibiotics10111348. [PMID: 34827286 PMCID: PMC8614803 DOI: 10.3390/antibiotics10111348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/23/2022] Open
Abstract
Oral microbiome dysbiosis has important links to human health and disease. Although photodynamic therapy influences microbiome diversity, the specific effect of violet light irradiation remains largely unknown. In this study, we analyzed the effect of violet light-emitting diode (LED) irradiation on interdental plaque microbiota. Interdental plaque was collected from 12 human subjects, exposed to violet LED irradiation, and cultured in a specialized growth medium. Next-generation sequencing of the 16S ribosomal RNA genes revealed that α-diversity decreased, whereas β-diversity exhibited a continuous change with violet LED irradiation doses. In addition, we identified several operational taxonomic units that exhibited significant shifts during violet LED irradiation. Specifically, violet LED irradiation led to a significant reduction in the relative abundance of Fusobacterium species, but a significant increase in several species of oral bacteria, such as Veillonella and Campylobacter. Our study provides an overview of oral plaque microbiota changes under violet LED irradiation, and highlights the potential of this method for adjusting the balance of the oral microbiome without inducing antibiotic resistance.
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Affiliation(s)
- Dan Wang
- Department of Operative Dentistry, Graduate School of Dentistry, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan;
| | - Takayuki Nambu
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan
- Correspondence: (T.N.); (T.O.)
| | - Hiroaki Tanimoto
- Department of Operative Dentistry, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan; (H.T.); (N.I.); (K.Y.); (K.Y.)
| | - Naohiro Iwata
- Department of Operative Dentistry, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan; (H.T.); (N.I.); (K.Y.); (K.Y.)
| | - Kazushi Yoshikawa
- Department of Operative Dentistry, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan; (H.T.); (N.I.); (K.Y.); (K.Y.)
| | - Toshinori Okinaga
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan
- Correspondence: (T.N.); (T.O.)
| | - Kazuyo Yamamoto
- Department of Operative Dentistry, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan; (H.T.); (N.I.); (K.Y.); (K.Y.)
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15
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Belasic TZ, Pejova B, Curkovic HO, Kamenar E, Cetenovic B, Spalj S. Influence of intraoral application of antiseptics and fluorides during orthodontic treatment on corrosion and mechanical characteristics of nickel-titanium alloy in orthodontic appliances. Angle Orthod 2021; 91:528-537. [PMID: 33566077 DOI: 10.2319/052620-480.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 11/01/2020] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES To explore whether the commercial agents recommended for controlling dental biofilm formation had a significant effect in vivo on mechanical and corrosion properties of nickel-titanium (NiTi) alloy. MATERIALS AND METHODS NiTi archwires (dimensions 0.508 × 0.508 mm) were collected from 36 orthodontic patients aged 13-42 years after a 3-month intraoral exposure. Three experimental groups were formed: (1) subjects conducting regular oral hygiene, (2) subjects who used fluorides for intensive prophylaxis for the first month, and (3) subjects who used chlorhexidine in the same manner. Corrosion behavior, surface characteristics, stiffness, hardness, and friction were analyzed. RESULTS Exposure to intraoral conditions significantly reduced the stiffness and hardness of the NiTi alloy (P ≤ .015). Fluoride tended to reduce stiffness and hardness more than did saliva or antiseptic, but not significantly. Roughness and friction were not significantly influenced by oral exposure. Intraoral aging predominantly produced general corrosion independent of the adjuvant prophylactic agent, although localized corrosion may also have occurred. CONCLUSIONS Fluorides and the antiseptic chlorhexidine do not increase corrosion more than saliva itself, nor do they further modify the mechanical properties of the NiTi alloy.
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16
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Lin CW, Chen YT, Ho HH, Hsieh PS, Kuo YW, Lin JH, Liu CR, Huang YF, Chen CW, Hsu CH, Lin WY, Yang SF. Lozenges with probiotic strains enhance oral immune response and health. Oral Dis 2021; 28:1723-1732. [PMID: 33749084 DOI: 10.1111/odi.13854] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/22/2021] [Accepted: 03/15/2021] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Probiotics participate in regulating oral microbiota and reducing the prevalence of oral diseases; however, clinical research on probiotics is insufficient. Therefore, in this study, we performed in vitro screening of potential oral protective probiotic strains and then evaluated the clinical efficacy of the selected strains on maintaining oral health. MATERIALS AND METHODS Fifty healthy individuals were recruited and randomly assigned into the placebo group and probiotics group, which included three strains of probiotics, Lactobacillus salivarius subs. salicinius AP-32, Lactobacillus paracasei ET-66, and Lactobacillus plantarum LPL28. Each group was blindly administered placebo or probiotics for four weeks. RESULTS Next-generation sequencing results showed that the oral microbiota of Lactobacillus salivarius in the oral cavity were significantly increased in subjects supplemented with mixed probiotic lozenges. The anti-bacterial activities of viable probiotics were observed within two weeks. Both IgA levels and Lactobacillus and Bifidobacterium abundances in the oral cavity were significantly increased in the experimental groups, along with a reduced formation of plaque. Most participants reported that their oral health conditions and intestinal symptoms had improved. CONCLUSIONS Overall, our clinical study suggests that oral probiotic lozenges may enhance oral immunity, modulate oral microbiota, and improve oral health.
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Affiliation(s)
- Chiao-Wen Lin
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yi-Tzu Chen
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan.,School of Dentistry, Chung Shan Medical University, Taichung, Taiwan
| | - Hsieh-Hsun Ho
- Research and Development Department, Bioflag Biotech Co., Ltd, Tainan, Taiwan
| | - Pei-Shan Hsieh
- Research and Development Department, Bioflag Biotech Co., Ltd, Tainan, Taiwan
| | - Yi-Wei Kuo
- Research and Development Department, Bioflag Biotech Co., Ltd, Tainan, Taiwan
| | - Jia-Hung Lin
- Research and Development Department, Bioflag Biotech Co., Ltd, Tainan, Taiwan
| | - Cheng-Ruei Liu
- Research and Development Department, Bioflag Biotech Co., Ltd, Tainan, Taiwan
| | - Yu-Fen Huang
- Research and Development Department, Bioflag Biotech Co., Ltd, Tainan, Taiwan
| | - Ching-Wei Chen
- Research and Development Department, Bioflag Biotech Co., Ltd, Tainan, Taiwan
| | - Chen-Hung Hsu
- Research and Development Department, Bioflag Biotech Co., Ltd, Tainan, Taiwan
| | - Wen-Yang Lin
- Research and Development Department, Bioflag Biotech Co., Ltd, Tainan, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
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17
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Sadiq FA, Burmølle M, Heyndrickx M, Flint S, Lu W, Chen W, Zhao J, Zhang H. Community-wide changes reflecting bacterial interspecific interactions in multispecies biofilms. Crit Rev Microbiol 2021; 47:338-358. [PMID: 33651958 DOI: 10.1080/1040841x.2021.1887079] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Existence of most bacterial species, in natural, industrial, and clinical settings in the form of surface-adhered communities or biofilms has been well acknowledged for decades. Research predominantly focusses on single-species biofilms as these are relatively easy to study. However, microbiologists are now interested in studying multispecies biofilms and revealing interspecific interactions in these communities because of the existence of a plethora of different bacterial species together in almost all natural settings. Multispecies biofilms-led emergent properties are triggered by bacterial social interactions which have huge implication for research and practical knowledge useful for the control and manipulation of these microbial communities. Here, we discuss some important bacterial interactions that take place in multispecies biofilm communities and provide insights into community-wide changes that indicate bacterial interactions and elucidate underlying mechanisms.
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Affiliation(s)
- Faizan Ahmed Sadiq
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium.,Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Steve Flint
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
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18
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Rodrigues R, Chung AP, Mortensen MS, Fernandes MH, Monteiro AB, Furfuro R, Silva CC, Manso MC, Sørensen SJ, Morais PV. Temporal oral microbiome changes with brushing in children with cleft lip and palate. Heliyon 2021; 7:e06513. [PMID: 33817376 PMCID: PMC8005767 DOI: 10.1016/j.heliyon.2021.e06513] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/21/2020] [Accepted: 03/10/2021] [Indexed: 11/25/2022] Open
Abstract
This cohort study aimed to characterize the oral microbiome of children with CLP, from two different age groups, and evaluate the effect of supervised or unsupervised toothbrushing on the microbiome of the cleft over time. Swab samples were collected from the cleft area at three different time points (A; no brushing, B; after 15 days and C; after 30 days) and were analyzed using next-generation sequencing to determine the microbial composition and diversity in these time points. Overall, brushing significantly decreased the abundance of the genera Alloprevotella and Leptotrichia in the two age groups examined, and for Alloprevotella this decrease was more evident for children (2-6 years old). In the preteen group (7-12 years old), a significant relative increase of the genus Rothia was observed after brushing. In this study, the systematic brushing over a period of thirty days also resulted in differences at the intra-individual bacterial richness.
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Affiliation(s)
- Rita Rodrigues
- Faculty of Dentistry, University of Porto, R. Dr. Manuel Pereira da Silva, 93, 4200-393, Porto, Portugal
- Faculty of Health Sciences, University Fernando Pessoa, Praça 9 de Abril, 349, 4249-004, Porto, Portugal
| | - Ana P. Chung
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Martin S. Mortensen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Maria H. Fernandes
- Associated Laboratory for Green Chemistry (LAQV/REQUIMTE), University of Porto, 4051-401, Porto, Portugal
| | | | - Rowney Furfuro
- Compor Clinic, R. Aval de Cima 34, 4200-105, Porto, Portugal
| | - Cátia C. Silva
- Faculty of Health Sciences, University Fernando Pessoa, Praça 9 de Abril, 349, 4249-004, Porto, Portugal
| | - Maria C. Manso
- Associated Laboratory for Green Chemistry (LAQV/REQUIMTE), University of Porto, 4051-401, Porto, Portugal
- Faculty of Health Sciences, University Fernando Pessoa, Fernando Pessoa Energy, Environment and Health Research Unit (FP-ENAS), Praça de 9 de Abril, 349, 4249-004, Porto, Portugal
| | - Søren J. Sørensen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Paula V. Morais
- University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
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19
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Bacterial Adhesion of Streptococcus mutans to Dental Material Surfaces. Molecules 2021; 26:molecules26041152. [PMID: 33670043 PMCID: PMC7926644 DOI: 10.3390/molecules26041152] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/13/2023] Open
Abstract
The aim of this study was to investigate and understand bacterial adhesion to different dental material surfaces like amalgam, Chromasit, an Co-Cr alloy, an IPS InLine ceramic, yttrium stabilized tetragonal polycrystalline zirconia (TPZ), a resin-based composite, an Au-Pt alloy, and a tooth. For all materials, the surface roughness was assessed by profilometry, the surface hydrophobicity was determined by tensiometry, and the zeta potential was measured by electrokinetic phenomena. The arithmetic average roughness was the lowest for the TPZ ceramic (Ra = 0.23 µm ± 0.02 µm), while the highest value was observed for the Au-Pt alloy (Ra = 0.356 µm ± 0.075 µm). The hydrophobicity was the lowest on the TPZ ceramic and the highest on the Co-Cr alloy. All measured streaming potentials were negative. The most important cause of tooth caries is the bacterium Streptococcus mutans, which was chosen for this study. The bacterial adhesion to all material surfaces was determined by scanning electron microscopy. We showed that the lowest bacterial extent was on the amalgam, whereas the greatest extent was on tooth surfaces. In general, measurements showed that surface properties like roughness, hydrophobicity and charge have a significant influence on bacterial adhesion extent. Therefore, dental material development should focus on improving surface characteristics to reduce the risk of secondary caries.
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20
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Lamont EI, Gadkari A, Kerns KA, To TT, Daubert D, Kotsakis G, Bor B, He X, McLean JS. Modified SHI medium supports growth of a disease-state subgingival polymicrobial community in vitro. Mol Oral Microbiol 2020; 36:37-49. [PMID: 33174294 PMCID: PMC7984074 DOI: 10.1111/omi.12323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023]
Abstract
Developing a laboratory model of oral polymicrobial communities is essential for in vitro studies of the transition from healthy to diseased oral plaque. SHI medium is an enriched growth medium capable of supporting in vitro biofilms with similar diversity to healthy supragingival inocula; however, this medium does not maintain the diversity of gram‐negative bacteria more associated with subgingival plaque. Here, we systematically modified SHI medium components to investigate the impacts of varying nutrients and develop a medium capable of supporting a specific disease‐state subgingival community. A diseased subgingival plaque sample was inoculated in SHI medium with increasing concentrations of sucrose (0%, 0.1%, 0.5%), fetal bovine serum (FBS) (0%, 10%, 20%, 30%, 50%), and mucin (0.1, 2.5, 8.0 g/L) and grown for 48 hrs, then the 16S rRNA profiles of the resulting biofilms were examined. In total, these conditions were able to capture 89 of the 119 species and 43 of the 51 genera found in the subgingival inoculum. Interestingly, biofilms grown in high sucrose media, although dominated by acidogenic Firmicutes with a low final pH, contained several uncultured taxa from the genus Treponema, information that may aid culturing these periodontitis‐associated fastidious organisms. Biofilms grown in a modified medium (here named subSHI‐v1 medium) with 0.1% sucrose and 10% FBS had a high diversity closest to the inoculum and maintained greater proportions of many gram‐negative species of interest from the subgingival periodontal pocket (including members of the genera Prevotella and Treponema, and the Candidate Phyla Radiation phylum Saccharibacteria), and therefore best represented the disease community.
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Affiliation(s)
- Eleanor I Lamont
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | - Archita Gadkari
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | | | - Thao T To
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | - Diane Daubert
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | - Georgios Kotsakis
- Department of Periodontics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA, USA
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21
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Seneviratne CJ, Suriyanarayanan T, Widyarman AS, Lee LS, Lau M, Ching J, Delaney C, Ramage G. Multi-omics tools for studying microbial biofilms: current perspectives and future directions. Crit Rev Microbiol 2020; 46:759-778. [PMID: 33030973 DOI: 10.1080/1040841x.2020.1828817] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The advent of omics technologies has greatly improved our understanding of microbial biology, particularly in the last two decades. The field of microbial biofilms is, however, relatively new, consolidated in the 1980s. The morphogenic switching by microbes from planktonic to biofilm phenotype confers numerous survival advantages such as resistance to desiccation, antibiotics, biocides, ultraviolet radiation, and host immune responses, thereby complicating treatment strategies for pathogenic microorganisms. Hence, understanding the mechanisms governing the biofilm phenotype can result in efficient treatment strategies directed specifically against molecular markers mediating this process. The application of omics technologies for studying microbial biofilms is relatively less explored and holds great promise in furthering our understanding of biofilm biology. In this review, we provide an overview of the application of omics tools such as transcriptomics, proteomics, and metabolomics as well as multi-omics approaches for studying microbial biofilms in the current literature. We also highlight how the use of omics tools directed at various stages of the biological information flow, from genes to metabolites, can be integrated via multi-omics platforms to provide a holistic view of biofilm biology. Following this, we propose a future artificial intelligence-based multi-omics platform that can predict the pathways associated with different biofilm phenotypes.
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Affiliation(s)
- Chaminda J Seneviratne
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore.,Duke NUS Medical School, Singapore, Singapore
| | - Tanujaa Suriyanarayanan
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore.,Duke NUS Medical School, Singapore, Singapore
| | - Armelia Sari Widyarman
- Department of Microbiology, Faculty of Dentistry, Trisakti University, Grogol, West Jakarta, Indonesia
| | - Lye Siang Lee
- Duke-NUS Medical School, Metabolomics Lab, Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Matthew Lau
- Singapore Oral Microbiomics Initiative (SOMI), National Dental Research Institute Singapore, National Dental Centre, Singapore, Singapore
| | - Jianhong Ching
- Duke-NUS Medical School, Metabolomics Lab, Cardiovascular and Metabolic Disorders, Singapore, Singapore
| | - Christopher Delaney
- School of Medicine, Dentistry & Nursing, Glasgow Dental Hospital & School, University of Glasgow, Glasgow, UK
| | - Gordon Ramage
- School of Medicine, Dentistry & Nursing, Glasgow Dental Hospital & School, University of Glasgow, Glasgow, UK
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22
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Veses V, González-Torres P, Carbonetto B, Del Mar Jovani-Sancho M, González-Martínez R, Cortell-Ballester I, Sheth CC. Dental black plaque: metagenomic characterization and comparative analysis with white-plaque. Sci Rep 2020; 10:15962. [PMID: 32994464 PMCID: PMC7525459 DOI: 10.1038/s41598-020-72460-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/02/2020] [Indexed: 11/18/2022] Open
Abstract
Extrinsic black dental staining is an external dental discoloration of bacterial origin, considered a special form of dental plaque. Currently, there is no definitive therapeutic option for eliminating black stain. This study employed 16S rRNA metagenomics to analyze black stain and white-plaque samples from 27 adult volunteers. Study objectives were to: describe the microbial diversity of adult black stain samples; characterize their taxonomic profile; compare the microbiomes of black stain versus white-plaque from adult volunteers and propose a functional map of the black stain microbiome using PICRUSt2. The black stain microbiome was poorer in species diversity as compared to white-plaque. The five most abundant genera in black stain were Capnocytophaga, Leptotrichia, Fusobacterium, Corynebacterium and Streptococcus. Functional analysis of microbial species revealed conserved and consistent clustering of functional pathways within and between black stain and white-plaque microbiomes. We describe enrichment of heme biosynthetic pathways in black stain. Our results suggest that the dysbiosis in black stain resembles "orally healthy" communities. The increased abundance of heme biosynthetic pathways suggests that heme-dependent iron sequestration and subsequent metabolism are key for black stain formation. Further research should decipher the regulation of heme biosynthetic genes and characterize the temporal sequence leading to colonization and dysbiosis.
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Affiliation(s)
- Verónica Veses
- Department of Biomedical Sciences, Faculty of Health Sciences, Universidad Cardenal Herrera-CEU, CEU Universities, 46113, Moncada, Valencia, Spain
| | | | | | - Mª Del Mar Jovani-Sancho
- Department of Dentistry, Faculty of Health Sciences, Universidad Cardenal Herrera-CEU, CEU Universities, 46113, Moncada, Valencia, Spain
| | - Raquel González-Martínez
- Department of Dentistry, Faculty of Health Sciences, Universidad Cardenal Herrera-CEU, CEU Universities, 46113, Moncada, Valencia, Spain
| | - Isidoro Cortell-Ballester
- Department of Biomedical Sciences, Faculty of Health Sciences, Universidad Cardenal Herrera-CEU, CEU Universities, 46113, Moncada, Valencia, Spain
| | - Chirag C Sheth
- Department of Medicine, Faculty of Health Sciences, Universidad Cardenal Herrera-CEU-, CEU Universities, 46113, Moncada, Valencia, Spain.
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23
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Zannoni A, Pietra M, Gaspardo A, Accorsi PA, Barone M, Turroni S, Laghi L, Zhu C, Brigidi P, Forni M. Non-invasive Assessment of Fecal Stress Biomarkers in Hunting Dogs During Exercise and at Rest. Front Vet Sci 2020; 7:126. [PMID: 32373631 PMCID: PMC7186473 DOI: 10.3389/fvets.2020.00126] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Intense exercise causes to organisms to have oxidative stress and inflammation at the gastrointestinal (GI) level. The reduction in intestinal blood flow and the exercise-linked thermal damage to the intestinal mucosa can cause intestinal barrier disruption, followed by an inflammatory response. Furthermore, the adaptation to exercise may affect the gut microbiota and the metabolome of the biofluids. The aim of the present research was to evaluate the presence of a GI derangement in hunting dogs through a non-invasive sampling as a consequence of a period of intense exercise in comparison with samples collected at rest. The study included nine dogs that underwent the same training regime for hunting wild boar. In order to counterbalance physiological variations, multiple-day replicates were collected and pooled at each experimental point for each dog. The samples were collected immediately at rest before the training (T0), after 60 days of training (T1), after 60 days of hunting wild boar (T2), and finally, at 60 days of rest after hunting (T3). A number of potential stress markers were evaluated: fecal cortisol metabolites (FCMs) as a major indicator of altered physiological states, immunoglobulin A (IgA) as an indicator of intestinal immune protection, and total antioxidant activity [total antioxidant capacity (TAC)]. Since stool samples contain exfoliated cells, we investigated also the presence of some transcripts involved in GI permeability [occludin (OCLN), protease-activated receptor-2 (PAR-2)] and in the inflammatory mechanism [interleukin (IL)-8, IL-6, IL-1b, tumor necrosis factor alpha (TNFα), calprotectin (CALP), heme oxygenase-1 (HO-1)]. Finally, the metabolome and the microbiota profiles were analyzed. No variation in FCM and IgA content and no differences in OCLN and CALP gene expression between rest and training were observed. On the contrary, an increase in PAR-2 and HO-1 transcripts, a reduction in total antioxidant activity, and a different profile of microbiota and metabolomics data were observed. Collectively, the data in the present study indicated that physical exercise in our model could be considered a mild stressor stimulus.
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Affiliation(s)
- Augusta Zannoni
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy.,Health Sciences and Technologies-Interdepartmental Center for Industrial Research (CIRI-SDV), Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Marco Pietra
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Alba Gaspardo
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Pier Attilio Accorsi
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Monica Barone
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.,Interdepartmental Centre for Agri-Food Industrial Research, University of Bologna, Bologna, Italy
| | - Luca Laghi
- Interdepartmental Centre for Agri-Food Industrial Research, University of Bologna, Bologna, Italy.,Department of Agro-Food Science and Technology, Centre of Foodomics, University of Bologna, Cesena, Italy
| | - Chenglin Zhu
- Department of Agro-Food Science and Technology, Centre of Foodomics, University of Bologna, Cesena, Italy
| | - Patrizia Brigidi
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.,Interdepartmental Centre for Agri-Food Industrial Research, University of Bologna, Bologna, Italy
| | - Monica Forni
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy.,Health Sciences and Technologies-Interdepartmental Center for Industrial Research (CIRI-SDV), Alma Mater Studiorum-University of Bologna, Bologna, Italy
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24
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Solidago virgaurea L. Plant Extract Targeted Against Candida albicans to Reduce Oral Microbial Biomass: a Double Blind Randomized Trial on Healthy Adults. Antibiotics (Basel) 2020; 9:antibiotics9040137. [PMID: 32218125 PMCID: PMC7235725 DOI: 10.3390/antibiotics9040137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023] Open
Abstract
Oral microbiome plays an important part on oral health and endogenous bacteria and fungi should not be eradicated. However, their proliferation must be controlled by oral hygiene care. In vitro, Solidago virgaurea ssp. virgaurea L. (SV) plant extract inhibits the adherence and hyphal formation of a fungus, Candida albicans. It reduces the biomass of Candida-bacterial biofilms but not fungal or bacterial growth. Unlike chemical antiseptics, like triclosan and chlorhexidine for instance, SV is a plant extract easily biodegradable. The purpose of this study was to assess the in vivo effectiveness of SV extract in reducing oral biomass. A randomized, double-blind clinical study, with dental plaque evaluation designed to assess the effectiveness of a fluorinated toothpaste containing SV (Bucovia™, Givaudan, Vernier, Switzerland) was conducted. Sixty-six subjects (SV group n = 33 vs. control n = 33) brushed their teeth twice a day for a 4-week period. Supragingival dental plaque was sampled. Total bacterial load (broad spectral bacterial quantitative Polymerase Chain Reaction (qPCR)), C. albicans and seven bacterial species were quantified by qPCR. In the Intervention group, there was a decrease of Total bacterial load (ΔD0D28 p = 0.005 and ΔD14D28 p = 0.026), Streptococcus mutans (ΔD0D14 p = 0.024) and C. albicans (ΔD0D28 p = 0.022). In the Control group Total bacterial load tended to decrease from baseline to day 28 (ΔD0D28 p = 0.062 and ΔD14D28 p = 0.009). Plaque Index and Gingival Index improved in both groups.
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25
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Diaz P, Valm A. Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties. J Dent Res 2020; 99:18-25. [PMID: 31590609 PMCID: PMC6927214 DOI: 10.1177/0022034519880157] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Oral microbial communities are extraordinarily complex in taxonomic composition and comprise interdependent biological systems. The bacteria, archaea, fungi, and viruses that thrive within these communities engage in extensive cell-cell interactions, which are both beneficial and antagonistic. Direct physical interactions among individual cells mediate large-scale architectural biofilm arrangements and provide spatial proximity for chemical communication and metabolic cooperation. In this review, we summarize recent work in identifying specific molecular components that mediate cell-cell interactions and describe metabolic interactions, such as cross-feeding and exchange of electron acceptors and small molecules, that modify the growth and virulence of individual species. We argue, however, that although pairwise interaction models have provided useful information, complex community-like systems are needed to study the properties of oral communities. The networks of multiple synergistic and antagonistic interactions within oral biofilms give rise to the emergent properties of persistence, stability, and long-range spatial structure, with these properties mediating the dysbiotic transitions from health to oral diseases. A better understanding of the fundamental properties of interspecies networks will lead to the development of effective strategies to manipulate oral communities.
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Affiliation(s)
- P.I. Diaz
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
| | - A.M. Valm
- Department of Biological Sciences, University at Albany, SUNY, Albany, NY, USA,A.M. Valm, Department of Biological Sciences, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
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26
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Røder HL, Olsen NMC, Whiteley M, Burmølle M. Unravelling interspecies interactions across heterogeneities in complex biofilm communities. Environ Microbiol 2019; 22:5-16. [DOI: 10.1111/1462-2920.14834] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 01/29/2023]
Affiliation(s)
- Henriette L. Røder
- Section of Microbiology, Department of BiologyUniversity of Copenhagen Copenhagen Denmark
| | - Nanna M. C. Olsen
- Section of Microbiology, Department of BiologyUniversity of Copenhagen Copenhagen Denmark
| | - Marvin Whiteley
- School of Biological SciencesGeorgia Institute of Technology, Atlanta Georgia USA
- Emory‐Children's Cystic Fibrosis Center, Atlanta Georgia USA
- Center for Microbial Dynamics and InfectionGeorgia Institute of Technology, Atlanta Georgia USA
| | - Mette Burmølle
- Section of Microbiology, Department of BiologyUniversity of Copenhagen Copenhagen Denmark
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27
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Bai F, Cai Z, Yang L. Recent progress in experimental and human disease-associated multi-species biofilms. Comput Struct Biotechnol J 2019; 17:1234-1244. [PMID: 31921390 PMCID: PMC6944735 DOI: 10.1016/j.csbj.2019.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 12/16/2022] Open
Abstract
Human bodies are colonized by trillions of microorganisms, which are often referred to as human microbiota and play important roles in human health. Next generation sequencing studies have established links between the genetic content of human microbiota and various human diseases. However, it remains largely unknown about the spatial organizations and interspecies interactions of individual species within the human microbiota. Bacterial cells tend to form surface-attached biofilms in many natural environments, which enable intercellular communications and interactions in a microbial ecosystem. In this review, we summarize the recent progresses on the experimental and human disease-associated multi-species biofilm studies. We hypothesize that engineering biofilm structures and interspecies interactions might provide a tool for manipulating the composition and function of human microbiota.
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Affiliation(s)
- Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhao Cai
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technology University, Singapore
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, China
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28
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Nambu T, Wang D, Mashimo C, Maruyama H, Kashiwagi K, Yoshikawa K, Yamamoto K, Okinaga T. Nitric Oxide Donor Modulates a Multispecies Oral Bacterial Community-An In Vitro Study. Microorganisms 2019; 7:microorganisms7090353. [PMID: 31540050 PMCID: PMC6780529 DOI: 10.3390/microorganisms7090353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 01/10/2023] Open
Abstract
The deterioration of human oral microbiota is known to not only cause oral diseases but also to affect systemic health. Various environmental factors are thought to influence the disruption and restoration of the oral ecosystem. In this study, we focused on the effect of nitric oxide (NO) produced by denitrification and NO synthase enzymes on dental plaque microbiota. Interdental plaques collected from 10 subjects were exposed to NO donor sodium nitroprusside (SNP) and then cultured in a specialized growth medium. Depending on the concentration of exposed SNP, a decrease in α-diversity and a continuous change in β-diversity in the dental plaque community were shown by sequencing bacterial 16S rRNA genes. We also identified eight operational taxonomic units that were significantly altered by NO exposure. Among them, the exposure of NO donors to Fusobacterium nucleatum cells showed a decrease in survival rate consistent with the results of microbiota analysis. Meanwhile, in addition to NO tolerance, an increase in the tetrazolium salt-reducing activity of Campylobacter concisus cells was confirmed by exposure to SNP. This study provides an overview of how oral plaque microbiota shifts with exposure to NO and may contribute to the development of a method for adjusting the balance of the oral microbiome.
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Affiliation(s)
- Takayuki Nambu
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan.
| | - Dan Wang
- Department of Operative Dentistry, Graduate School of Dentistry, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan.
| | - Chiho Mashimo
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan.
| | - Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan.
| | - Kosuke Kashiwagi
- Department of Fixed Prosthodontics, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan.
| | - Kazushi Yoshikawa
- Department of Operative Dentistry, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan.
| | - Kazuyo Yamamoto
- Department of Operative Dentistry, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan.
| | - Toshinori Okinaga
- Department of Bacteriology, Osaka Dental University, 8-1, Kuzuha-Hanazono, Hirakata, Osaka 573-1121, Japan.
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29
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Mark Welch JL, Dewhirst FE, Borisy GG. Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis. Annu Rev Microbiol 2019; 73:335-358. [PMID: 31180804 PMCID: PMC7153577 DOI: 10.1146/annurev-micro-090817-062503] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Microbial communities are complex and dynamic, composed of hundreds of taxa interacting across multiple spatial scales. Advances in sequencing and imaging technology have led to great strides in understanding both the composition and the spatial organization of these complex communities. In the human mouth, sequencing results indicate that distinct sites host microbial communities that not only are distinguishable but to a meaningful degree are composed of entirely different microbes. Imaging suggests that the spatial organization of these communities is also distinct. Together, the literature supports the idea that most oral microbes are site specialists. A clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general.
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Affiliation(s)
| | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge MA 02142 and Harvard School of Dental Medicine, Boston MA 02115
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