1
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Li P, Zhang Y, Chen D, Lin H. Investigation of a novel biofilm model close to the original oral microbiome. Appl Microbiol Biotechnol 2024; 108:330. [PMID: 38730049 PMCID: PMC11087337 DOI: 10.1007/s00253-024-13149-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 01/13/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024]
Abstract
A more optimized culture medium used in vitro to mimic the bacterial composition of original oral flora as similar as possible remains difficult at present, and the goal of this study is to develop a novel oral biofilm medium to restore the original oral microbiome. Firstly, we conducted a systematic literature review by searching PubMed and summarized the current reported culture media in vitro. Seven culture media were found. We used mixed saliva as the origin of oral species to compare the effects of the above media in culturing oral multispecies biofilms. Results indicated that among the seven media brain heart infusion containing 1% sucrose (BHIs) medium, PG medium, artificial saliva (AS) medium, and SHI medium could obviously gain large oral biofilm in vitro. The nutrients contained in different culture media may be suitable for the growth of different oral bacteria; therefore, we optimized several novel media accordingly. Notably, results of crystal violet staining showed that the biofilm cultured in our modified artificial saliva (MAS) medium had the highest amount of biofilm biomass. 16S rRNA gene sequencing showed that the operational taxonomic units (OTUs) and Shannon index of biofilm cultured in MAS medium were also the highest among all the tested media. More importantly, the 16S rRNA gene sequencing analysis indicated that the biofilm cultured in MAS medium was closer to the original saliva species. Besides, biofilm cultured by MAS was denser and produced more exopolysaccharides. MAS supported stable biofilm formation on different substrata. In conclusion, this study demonstrated a novel MAS medium that could culture oral biofilm in vitro closer to the original oral microbiome, showing a good application prospect. KEY POINTS: • We compare the effects of different media in culturing oral biofilms • A novel modified artificial saliva (MAS) medium was obtained in our study • The MAS medium could culture biofilm that was closer to oral microbiome.
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Affiliation(s)
- Pengpeng Li
- Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China
| | - Yuwen Zhang
- Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China
| | - Dongru Chen
- Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China.
| | - Huancai Lin
- Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China.
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2
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Thompson TP, Gilmore BF. Exploring halophilic environments as a source of new antibiotics. Crit Rev Microbiol 2024; 50:341-370. [PMID: 37079280 DOI: 10.1080/1040841x.2023.2197491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/25/2023] [Indexed: 04/21/2023]
Abstract
Microbial natural products from microbes in extreme environments, including haloarchaea, and halophilic bacteria, possess a huge capacity to produce novel antibiotics. Additionally, enhanced isolation techniques and improved tools for genomic mining have expanded the efficiencies in the antibiotic discovery process. This review article provides a detailed overview of known antimicrobial compounds produced by halophiles from all three domains of life. We summarize that while halophilic bacteria, in particular actinomycetes, contribute the vast majority of these compounds the importance of understudied halophiles from other domains of life requires additional consideration. Finally, we conclude by discussing upcoming technologies- enhanced isolation and metagenomic screening, as tools that will be required to overcome the barriers to antimicrobial drug discovery. This review highlights the potential of these microbes from extreme environments, and their importance to the wider scientific community, with the hope of provoking discussion and collaborations within halophile biodiscovery. Importantly, we emphasize the importance of bioprospecting from communities of lesser-studied halophilic and halotolerant microorganisms as sources of novel therapeutically relevant chemical diversity to combat the high rediscovery rates. The complexity of halophiles will necessitate a multitude of scientific disciplines to unravel their potential and therefore this review reflects these research communities.
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Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
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3
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Gao H, Liu Q, Wang X, Li T, Li H, Li G, Tan L, Chen Y. Deciphering the role of female reproductive tract microbiome in reproductive health: a review. Front Cell Infect Microbiol 2024; 14:1351540. [PMID: 38562966 PMCID: PMC10982509 DOI: 10.3389/fcimb.2024.1351540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Relevant studies increasingly indicate that female reproductive health is confronted with substantial challenges. Emerging research has revealed that the microbiome interacts with the anatomy, histology, and immunity of the female reproductive tract, which are the cornerstone of maintaining female reproductive health and preventing adverse pregnancy outcomes. Currently, the precise mechanisms underlying their interaction and impact on physiological functions of the reproductive tract remain elusive, constituting a prominent area of investigation within the field of female reproductive tract microecology. From this new perspective, we explore the mechanisms of interactions between the microbiome and the anatomy, histology, and immunity of the female reproductive tract, factors that affect the composition of the microbiome in the female reproductive tract, as well as personalized medicine approaches in managing female reproductive tract health based on the microbiome. This study highlights the pivotal role of the female reproductive tract microbiome in maintaining reproductive health and influencing the occurrence of reproductive tract diseases. These findings support the exploration of innovative approaches for the prevention, monitoring and treatment of female reproductive tract diseases based on the microbiome.
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Affiliation(s)
- Hong Gao
- Nursing Department, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
- Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON, Canada
| | - Qiao Liu
- School of Nursing, University of South China, Hengyang, China
| | - Xiaolan Wang
- Center for a Combination of Obstetrics and Gynecology and Reproductive Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Ting Li
- Department of Obstetrics, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Huanhuan Li
- Department of Gynaecology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Genlin Li
- Center for a Combination of Obstetrics and Gynecology and Reproductive Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Lingling Tan
- Nursing Department, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Yahui Chen
- School of Nursing, University of South China, Hengyang, China
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4
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Hammad MI, Conrads G, Abdelbary MMH. Isolation, identification, and significance of salivary Veillonella spp., Prevotella spp., and Prevotella salivae in patients with inflammatory bowel disease. Front Cell Infect Microbiol 2023; 13:1278582. [PMID: 38053528 PMCID: PMC10694262 DOI: 10.3389/fcimb.2023.1278582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/30/2023] [Indexed: 12/07/2023] Open
Abstract
The global prevalence of inflammatory bowel disease (IBD) is on the rise, prompting significant attention from researchers worldwide. IBD entails chronic inflammatory disorders of the intestinal tract, characterized by alternating flares and remissions. Through high-throughput sequencing, numerous studies have unveiled a potential microbial signature for IBD patients showing intestinal enrichment of oral-associated bacteria. Simultaneously, the oral microbiome can be perturbed by intestinal inflammation. Our prior investigation, based on 16S rRNA amplicon sequencing, underscored elevated abundance of Veillonella spp. and Prevotella spp. in the salivary microbiomes of IBD patients. Noteworthy, Prevotella salivae emerged as a distinct species significantly associated with IBD. P. salivae is an under-recognized pathogen that was found to play a role in both oral and systemic diseases. In this study, we delve deeper into the salivary microbiomes of both IBD patients and healthy controls. Employing diverse cultivation techniques and real-time quantitative polymerase chain reactions (RT-qPCR), we gauged the prevalence and abundance of Veillonella spp., Prevotella spp., and P. salivae. Our isolation efforts yielded 407 and 168 strains of Veillonella spp., as well as 173 and 90 strains of Prevotella spp., from the saliva samples of IBD patients and healthy controls, respectively. Veillonella-vancomycin agar emerged as the discerning choice for optimal Veillonella spp. cultivation, while Schaedler kanamycin-vancomycin agar proved to be the most suitable medium for cultivating Prevotella spp. strains. Comparing our RT-qPCR findings to the previous 16S rRNA amplicon sequencing data, the results corroborated the higher abundance of Veillonella spp., Prevotella spp., and P. salivae in the saliva of IBD patients compared to healthy controls. However, it's worth noting that in contrast to RT-qPCR, the 16S rRNA amplicon sequencing data revealed greater absolute abundance of all three bacterial groups in both IBD patients and controls.
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Affiliation(s)
- Moshira I. Hammad
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule University Hospital, Aachen, Germany
| | - Georg Conrads
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule University Hospital, Aachen, Germany
| | - Mohamed M. H. Abdelbary
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, Rheinisch-Westfälische Technische Hochschule University Hospital, Aachen, Germany
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany
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5
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Xiao X, Liu S, Deng H, Song Y, Zhang L, Song Z. Advances in the oral microbiota and rapid detection of oral infectious diseases. Front Microbiol 2023; 14:1121737. [PMID: 36814562 PMCID: PMC9939651 DOI: 10.3389/fmicb.2023.1121737] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023] Open
Abstract
Several studies have shown that the dysregulation of the oral microbiota plays a crucial role in human health conditions, such as dental caries, periodontal disease, oral cancer, other oral infectious diseases, cardiovascular diseases, diabetes, bacteremia, and low birth weight. The use of traditional detection methods in conjunction with rapidly advancing molecular techniques in the diagnosis of harmful oral microorganisms has expanded our understanding of the diversity, location, and function of the microbiota associated with health and disease. This review aimed to highlight the latest knowledge in this field, including microbial colonization; the most modern detection methods; and interactions in disease progression. The next decade may achieve the rapid diagnosis and precise treatment of harmful oral microorganisms.
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Affiliation(s)
- Xuan Xiao
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Shangfeng Liu
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Hua Deng
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yuhan Song
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China
| | - Liang Zhang
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China,Liang Zhang,
| | - Zhifeng Song
- Department of Oral Mucosa, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Shanghai Stomatological Hospital, Fudan University, Shanghai, China,*Correspondence: Zhifeng Song,
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6
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Shin J, Kim G, Park J, Lee M, Park Y. Long-term label-free assessments of individual bacteria using three-dimensional quantitative phase imaging and hydrogel-based immobilization. Sci Rep 2023; 13:46. [PMID: 36593327 PMCID: PMC9806822 DOI: 10.1038/s41598-022-27158-y] [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: 09/13/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Three-dimensional (3D) quantitative phase imaging (QPI) enables long-term label-free tomographic imaging and quantitative analysis of live individual bacteria. However, the Brownian motion or motility of bacteria in a liquid medium produces motion artifacts during 3D measurements and hinders precise cell imaging and analysis. Meanwhile, existing cell immobilization methods produce noisy backgrounds and even alter cellular physiology. Here, we introduce a protocol that utilizes hydrogels for high-quality 3D QPI of live bacteria maintaining bacterial physiology. We demonstrate long-term high-resolution quantitative imaging and analysis of individual bacteria, including measuring the biophysical parameters of bacteria and responses to antibiotic treatments.
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Affiliation(s)
- Jeongwon Shin
- grid.37172.300000 0001 2292 0500Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea
| | - Geon Kim
- grid.37172.300000 0001 2292 0500Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea ,grid.37172.300000 0001 2292 0500KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea
| | - Jinho Park
- grid.37172.300000 0001 2292 0500Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea
| | - Moosung Lee
- grid.37172.300000 0001 2292 0500Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea ,grid.37172.300000 0001 2292 0500KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea
| | - YongKeun Park
- grid.37172.300000 0001 2292 0500Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea ,grid.37172.300000 0001 2292 0500KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141 South Korea ,Tomocube Inc., Daejeon, 34051 South Korea
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7
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Murugkar P, Dimise E, Stewart E, Viala SN, Clardy J, Dewhirst FE, Lewis K. Identification of a growth factor required for culturing specific fastidious oral bacteria. J Oral Microbiol 2023; 15:2143651. [DOI: 10.1080/20002297.2022.2143651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Pallavi Murugkar
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave 02115, Boston, MA, USA
| | - Eric Dimise
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School 02115, Boston, MA, USA
| | - Eric Stewart
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave 02115, Boston, MA, USA
| | - Stéphane N. Viala
- Department of Microbiology, the Forsyth Institute, Cambridge, MA, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School 02115, Boston, MA, USA
| | - Floyd E. Dewhirst
- Department of Microbiology, the Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave 02115, Boston, MA, USA
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8
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Khoo C, Duysburgh C, Marzorati M, Van den Abbeele P, Zhang D. A Freeze-Dried Cranberry Powder Consistently Enhances SCFA Production and Lowers Abundance of Opportunistic Pathogens In Vitro. BIOTECH 2022; 11:biotech11020014. [PMID: 35822787 PMCID: PMC9264401 DOI: 10.3390/biotech11020014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/19/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
The American cranberry, Vaccinium macrocarpon, contains fibers and (poly)phenols that could exert health-promoting effects through modulation of gut microbiota. This study aimed to investigate how a freeze-dried whole cranberry powder (FCP) modulated metabolite production and microbial composition using both a 48-h incubation strategy and a long-term human gut simulator study with the M-SHIME (Mucosal Simulator of the Human Intestinal Microbial Ecosystem). FCP was repeatedly administered over three weeks. The studies included five and three study subjects, respectively. In both models, FCP significantly increased levels of health-related short-chain fatty acids (SCFA: acetate, propionate and butyrate), while decreased levels of branched-chain fatty acids (markers of proteolytic fermentation). Interestingly, FCP consistently increased luminal Bacteroidetes abundances in the proximal colon of the M-SHIME (+17.5 ± 9.3%) at the expense of Proteobacteria (−10.2 ± 1.5%). At family level, this was due to the stimulation of Bacteroidaceae and Prevotellaceae and a decrease of Pseudomonodaceae and Enterobacteriaceae. Despite of interpersonal differences, FCP also increased the abundance of families of known butyrate producers. Overall, FCP displayed an interesting prebiotic potential in vitro given its selective utilization by host microorganisms and potential health-related effects on inhibition of pathogens and selective stimulation of beneficial metabolites.
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Affiliation(s)
- Christina Khoo
- Ocean Spray Cranberries, Inc., Bridge Street 152, Middleborough, MA 02349, USA
- Correspondence:
| | - Cindy Duysburgh
- ProDigest BV, Technologiepark-Zwijnaarde 73, 9052 Ghent, Belgium; (C.D.); (M.M.)
| | - Massimo Marzorati
- ProDigest BV, Technologiepark-Zwijnaarde 73, 9052 Ghent, Belgium; (C.D.); (M.M.)
- Center of Microbial Ecology and Technology (CMET), Ghent University, 9000 Ghent, Belgium
| | - Pieter Van den Abbeele
- ProDigest BV, Technologiepark-Zwijnaarde 73, 9052 Ghent, Belgium; (C.D.); (M.M.)
- Cryptobiotix SA, Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium;
| | - Derek Zhang
- Ocean Spray Cranberries, Inc., Bridge Street 152, Middleborough, MA 02349, USA
- IQVIA, Emperor Boulevard 4820, Durham, NC 27703, USA;
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9
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Yang M, Li J, Lv XM, Dai LR, Wu KJ, Tu B, Lawson PA, Tang YQ, Cheng L. Thermosynergistes pyruvativorans gen. nov., sp. nov., an anaerobic, pyruvate-degrading bacterium from Shengli oilfield, and proposal of Thermosynergistaceae fam. nov. in the phylum Synergistetes. Int J Syst Evol Microbiol 2021; 71. [PMID: 34582328 DOI: 10.1099/ijsem.0.005031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, thermophilic, Gram-stain-negative bacterium, named as strain S15T, was isolated from oily sludge of Shengli oilfield in PR China. Cells of strain S15T were straight or slightly curved rods with 0.4-0.8 µm width × 1.4-3 µm length and occurred mostly in pairs or short chains. Endospore-formation was not observed. The strain grew optimally at 55 °C (range from 30-65 °C), pH 6.5 (pH 6.0-8.5) and 0-30 g l-1 NaCl (optimum with 10 g l-1 NaCl). Yeast extract was an essential growth factor for strain S15T. The major cellular fatty acid was iso-C15 : 0 (58.2 %), and the main polar lipids were amino phospholipid (APL), glycolipids (GLs) and phosphatidylethanolamine (PE). The G+C content of DNA of strain S15T was 52.2 mol%. Strain S15T shared 89.8 % 16S rRNA gene similarity with the most related organism Acetomicrobium hydrogeniformans DSM 22491T in the phylum Synergistetes. The paired genomic average amino acid identity (AAI) and percentage of conserved proteins (POCP) values showed relatedness of less than 58.0 and 39.7 % with type strains of the species in the phylum Synergistetes. On the basis of phenotypic, phylogenetic and phylogenomic evidences, strain S15T constitutes a novel species in a novel genus, for the name Thermosynergistes pyruvativorans gen. nov., sp. nov. is proposed. The type strain is S15T (=CCAM 583T=JCM 33159T). Thermosynergistaceae fam. nov. is also proposed.
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Affiliation(s)
- Min Yang
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China.,Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Xiao-Meng Lv
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China.,Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Li-Rong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Ke-Jia Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bo Tu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Yue-Qin Tang
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
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10
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Kusugal P, Bhat KG, Ingalagi P, Patil S, Pattar G. Coculture method for in vitro cultivation of uncultured oral bacteria. J Oral Maxillofac Pathol 2021; 25:266-271. [PMID: 34703120 PMCID: PMC8491346 DOI: 10.4103/0973-029x.325125] [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: 07/28/2020] [Revised: 02/03/2021] [Accepted: 05/18/2021] [Indexed: 12/02/2022] Open
Abstract
PURPOSE The purpose of the study is to culture uncultured oral bacteria with helper strains using the coculture method from the subgingival plaque samples of chronic periodontitis patients. MATERIALS AND METHODS The samples were processed and inoculated on a blood agar medium enriched with hemin and Vitamin K. A helper strain Propionibacterium acnes (ATCC 6919) was cross-streaked across the inoculums to facilitate coculture. The plates were then incubated for 7 days with subsequent subculturing and further incubation. RESULTS Satellite colonies around helper strain showed one colony type of Porphyromonas gingivalis, one was of nonpigmented Prevotella, three were of Fusobacterium nucleatum and five isolates remained unidentified. CONCLUSIONS Coculture could be used effectively as one of the methods in the isolation and in vitro cultivation of oral bacteria. Incubation using the anaerobic jar technique was found to be economical and efficient for the growth of anaerobic oral bacteria.
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Affiliation(s)
- Preethi Kusugal
- Department of Prosthodontics and Crown and Bridge, Maratha Mandal's Nathajirao G Halgekar Institute of Dental Sciences and Research Centre, Belagavi, Karnataka, India
| | - Kishore G Bhat
- Central Research Laboratory, Maratha Mandal's Nathajirao G Halgekar Institute of Dental Sciences and Research Centre, Belagavi, Karnataka, India
| | - Preeti Ingalagi
- Department of Medical Microbiology, Maratha Mandal's Nathajirao G Halgekar Institute of Dental Sciences and Research Centre, Belagavi, Karnataka, India
| | - Sanjivani Patil
- Central Research Laboratory, Maratha Mandal's Nathajirao G Halgekar Institute of Dental Sciences and Research Centre, Belagavi, Karnataka, India
| | - Geeta Pattar
- Central Research Laboratory, Maratha Mandal's Nathajirao G Halgekar Institute of Dental Sciences and Research Centre, Belagavi, Karnataka, India
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11
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Farrer AG, Wright SL, Skelly E, Eisenhofer R, Dobney K, Weyrich LS. Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus. Sci Rep 2021; 11:7456. [PMID: 33811235 PMCID: PMC8018977 DOI: 10.1038/s41598-021-86100-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/26/2021] [Indexed: 02/01/2023] Open
Abstract
Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.
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Affiliation(s)
- Andrew G. Farrer
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia
| | - Sterling L. Wright
- grid.29857.310000 0001 2097 4281The Department of Anthropology, The Pennsylvania State University, University Park, PA USA
| | - Emily Skelly
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia
| | - Raphael Eisenhofer
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia ,grid.1010.00000 0004 1936 7304Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia Australia
| | - Keith Dobney
- grid.1013.30000 0004 1936 834XDepartment of Archaeology, University of Sydney, Sydney, NSW Australia
| | - Laura S. Weyrich
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia ,grid.29857.310000 0001 2097 4281The Department of Anthropology, The Pennsylvania State University, University Park, PA USA ,grid.1010.00000 0004 1936 7304Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia Australia ,grid.29857.310000 0001 2097 4281The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA USA
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12
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Kageyama Y, Shimokawa Y, Kawauchi K, Morimoto M, Aida K, Akiyama T, Nakamura T. Dysbiosis of Oral Microbiota Associated with Palmoplantar Pustulosis. Dermatology 2020; 237:347-356. [PMID: 33279897 DOI: 10.1159/000511622] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/08/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Dysbiosis of oral microbiota is implicated not only in oral inflammatory lesions, but also in a variety of extraoral diseases. The etiology of palmoplantar pustulosis (PPP) remains unclear; however, it has been suggested that chronic inflammation caused by periodontopathic bacterial infection may play a role. OBJECTIVES/METHODS To determine whether patients with PPP have altered diversity and composition of oral microbiota, we conducted the 16S rDNA analysis using saliva samples collected from 21 outpatients with PPP and 10 healthy individuals. RESULTS We found that the proportion of bacteria in the phylum Proteobacteria was significantly lower in PPP patients (p = 0.025). At the genus level, patients with PPP had a significantly lower abundance of Neisseria (p = 0.014), which best accounted for the observed decrease in Proteobacteria. We also identified multiple minor genera and species that were represented at a significantly higher level in the PPP group, several of which have been associated with periodontal diseases. CONCLUSION Our results suggest a possible link between PPP and dysbiosis of oral microbiota, particularly the lower abundance of Neisseria, the most predominant genus of Proteobacteria in healthy oral microbiota. Probiotics that improves oral dysbiosis may be beneficial for patients with PPP as an adjunctive therapy.
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Affiliation(s)
- Yasunari Kageyama
- Takanawa Clinic, Minato-ku, Tokyo, Japan.,Tokai University Hospital, Isehara-shi, Kanagawa, Japan
| | | | | | | | | | - Tetsu Akiyama
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Tsutomu Nakamura
- Laboratory of Molecular and Genetic Information, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan,
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13
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McCracken BA, Nathalia Garcia M. Phylum Synergistetes in the oral cavity: A possible contributor to periodontal disease. Anaerobe 2020; 68:102250. [PMID: 32791127 DOI: 10.1016/j.anaerobe.2020.102250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022]
Abstract
Microbial contributions to periodontal disease have been under renewed scrutiny with the advent of newer technologies to identify their presence and gene expression at the molecular level. Members of the phylum Synergistetes are some of the more recent bacteria to be associated with periodontal disease. Bacteria classified in this phylum can be found in a wide variety of habitats including both inside and outside of a mammalian host. Members of this phylum have been identified as part of the human microbiome. Indeed, many of the identified phylotypes have yet to be cultivated. Here we consider contributions of three named and formally described species to the oral microbial community and to pathogenesis of periodontal disease.
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Affiliation(s)
- Barbara Anne McCracken
- Section of Microbiology, Department of Growth, Development And Structure, 2800 College Ave., Alton, IL, 62002, USA.
| | - M Nathalia Garcia
- Southern Illinois University School of Dental Medicine, Alton, IL, 62002, USA
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14
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Nibali L, Sousa V, Davrandi M, Spratt D, Alyahya Q, Dopico J, Donos N. Differences in the periodontal microbiome of successfully treated and persistent aggressive periodontitis. J Clin Periodontol 2020; 47:980-990. [PMID: 32557763 DOI: 10.1111/jcpe.13330] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 05/23/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]
Abstract
AIMS The primary aim of this investigation was to analyse the periodontal microbiome in patients with aggressive periodontitis (AgP) following treatment. METHODS Sixty-six AgP patients were recalled on average 7 years after completion of active periodontal treatment and had subgingival plaque samples collected and processed for 16S rRNA gene sequencing analyses. RESULTS Of 66 participants, 52 showed persistent periodontal disease, while 13 participants were considered as "successfully treated AgP" (no probing pocket depths >4 mm) and 1 was fully edentulous. Genera associated with persistent generalized disease included Actinomyces, Alloprevotella, Capnocytophaga, Filifactor, Fretibacterium, Fusobacterium, Leptotrichia, Mogibacterium, Saccharibacteria [G-1], Selenomonas and Treponema. "Successfully treated" patients harboured higher proportions of Haemophilus, Rothia, and Lautropia and of Corynebacterium, Streptococcus and Peptidiphaga genera. Overall, patients with persistent generalized AgP (GAgP) revealed higher alpha diversity compared to persistent localized AgP (LAgP) and stable patients (p < .001). Beta diversity analyses revealed significant differences only between stable and persistent GAgP groups (p = .004). CONCLUSION Patients with persistent AgP showed a more dysbiotic subgingival biofilm than those who have been successfully treated. It remains to be established whether such differences were predisposing to disease activity or were a result of a dysbiotic change associated with disease recurrence in the presence of sub-standard supportive periodontal therapy or other patient-related factors.
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Affiliation(s)
- Luigi Nibali
- Periodontology Unit, Centre for Host Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK.,Centre for Oral Immunobiology & Regenerative Medicine & Centre for Oral Clinical Research, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Vanessa Sousa
- Centre for Oral Immunobiology & Regenerative Medicine & Centre for Oral Clinical Research, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Mehmet Davrandi
- Microbial Diseases Department, University College London Eastman Dental Institute, London, UK
| | - David Spratt
- Microbial Diseases Department, University College London Eastman Dental Institute, London, UK
| | - Qumasha Alyahya
- Periodontology Unit, University College London Eastman Dental Institute, London, UK
| | - Jose Dopico
- Periodontics Department, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Nikos Donos
- Centre for Oral Immunobiology & Regenerative Medicine & Centre for Oral Clinical Research, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
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15
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Tripathi VC, Satish S, Horam S, Raj S, lal A, Arockiaraj J, Pasupuleti M, Dikshit DK. Natural products from polar organisms: Structural diversity, bioactivities and potential pharmaceutical applications. POLAR SCIENCE 2018; 18:147-166. [DOI: 10.1016/j.polar.2018.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2023]
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16
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Liu LS, Gkranias N, Farias B, Spratt D, Donos N. Differences in the subgingival microbial population of chronic periodontitis in subjects with and without type 2 diabetes mellitus-a systematic review. Clin Oral Investig 2018; 22:2743-2762. [PMID: 30306333 DOI: 10.1007/s00784-018-2660-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/25/2018] [Indexed: 12/16/2022]
Abstract
OBJECTIVES The purpose of this systematic review was to evaluate the available evidence in the literature in regard to the subgingival microbial population of chronic periodontitis in subjects with type 2 diabetes mellitus (T2DM+PD) compared to non-diabetic subjects (NDM+PD). MATERIALS AND METHODS A literature search was conducted at Ovid MEDLINE and EMBASE database from 1980 to 2016, supplemented by hand searching as needed. Studies presenting with at least one of the primary outcomes (presence of any subgingival microorganisms, proportion and/or the amount of any subgingival plaque bacteria in T2DM+PD versus NDM+PD) were included. Screening, data extraction and quality assessment were conducted independently and in duplicate. RESULTS From 611 citations, 19 full-text papers were screened and 11 articles were included for critical appraisal by both reviewers. Some evidence of a difference in the microbial profile between chronic PD subjects with and without T2DM was identified. The strength of evidence is strongest in Tannerella forthysia (T .forsythia) which was reported to be less frequent in the diabetic (T2DM+PD) group in five of the studies, followed by a weaker strength of evidence for other periodontal pathogens such as Porphyromonas gingivalis (P. gingivalis) and Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans), which were also found less frequent in the diabetic (T2DM+PD) group . CONCLUSION Only few studies have compared T2DM+PD with NDM+PD. It is therefore strongly recommended that further studies which include four distinct groups of participants (NDM+PD, T2DM+PD, NDM+NPD, T2DM+NPD) instead of using intra-subject comparisons between healthy and diseased sites of the same subjects. CLINICAL RELEVANCE Differences in bacterial populations of T2DM+PD in comparison to NDM+PD subjects may indicate the need of different protocols for the treatment of the diabetic patients with periodontal disease.
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Affiliation(s)
- Linda Sun Liu
- Periodontology Unit, UCL Eastman Dental Institute, London, UK
| | - Nikolaos Gkranias
- Centre for Oral Clinical Research, Institute of Dentistry, Barts & The London School of Medicine & Dentistry, Queen Mary University of London (QMUL), Turner Street, London, UK
| | - Bruna Farias
- Postgraduate Department, Federal University of Pernambuco, Recife, Brazil
| | - Dave Spratt
- Microbiology Department, UCL Eastman Dental Institute, London, UK
| | - Nikolaos Donos
- Centre for Oral Clinical Research, Institute of Dentistry, Barts & The London School of Medicine & Dentistry, Queen Mary University of London (QMUL), Turner Street, London, UK.
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17
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Liu L, Firrman J, Tanes C, Bittinger K, Thomas-Gahring A, Wu GD, Van den Abbeele P, Tomasula PM. Establishing a mucosal gut microbial community in vitro using an artificial simulator. PLoS One 2018; 13:e0197692. [PMID: 30016326 PMCID: PMC6050037 DOI: 10.1371/journal.pone.0197692] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/07/2018] [Indexed: 11/19/2022] Open
Abstract
The Twin Simulator of the Human Intestinal Microbial Ecosystem (TWINSHIME®) was initially developed to study the luminal gut microbiota of the ascending (AC), transverse (TC), and descending (DC) colon regions. Given the unique composition and potential importance of the mucosal microbiota for human health, the TWINSHIME was recently adapted to simulate the mucosal microbiota as well as the luminal community. It has been previously demonstrated that the luminal community in the TWINSHIME reaches a steady state within two weeks post inoculation, and is able to differentiate into region specific communities. However, less is known regarding the mucosal community structure and dynamics. During the current study, the luminal and mucosal communities in each region of the TWINSHIME were evaluated over the course of six weeks. Based on 16S rRNA gene sequencing and short chain fatty acid analysis, it was determined that both the luminal and mucosal communities reached stability 10–20 days after inoculation, and remained stable until the end of the experiment. Bioinformatics analysis revealed the formation of unique community structures between the mucosal and luminal phases in all three colon regions, yet these communities were similar to the inoculum. Specific colonizers of the mucus mainly belonged to the Firmicutes phylum and included Lachnospiraceae (AC/TC/DC), Ruminococcaceae and Eubacteriaceae (AC), Lactobacillaceae (AC/TC), Clostridiaceae and Erysipelotrichaceae (TC/DC). In contrast, Bacteroidaceae were enriched in the gut lumen of all three colon regions. The unique profile of short chain fatty acid (SCFA) production further demonstrated system stability, but also proved to be an area of marked differences between the in vitro system and in vivo reports. Results of this study demonstrate that it is possible to replicate the community structure and composition of the gut microbiota in vitro. Through implementation of this system, the human gut microbiota can be studied in a dynamic and continuous fashion.
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Affiliation(s)
- LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
- * E-mail:
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Audrey Thomas-Gahring
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Gary D. Wu
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Peggy M. Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
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18
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Insights into the human oral microbiome. Arch Microbiol 2018; 200:525-540. [PMID: 29572583 DOI: 10.1007/s00203-018-1505-3] [Citation(s) in RCA: 258] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 12/20/2022]
Abstract
Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.
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19
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Díaz-Cárdenas C, López G, Alzate-Ocampo JD, González LN, Shapiro N, Woyke T, Kyrpides NC, Restrepo S, Baena S. Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565 T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring. Stand Genomic Sci 2017; 12:86. [PMID: 29276571 PMCID: PMC5738826 DOI: 10.1186/s40793-017-0303-x] [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: 07/31/2017] [Accepted: 12/05/2017] [Indexed: 11/10/2022] Open
Abstract
A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T (DSM 21565T= KCTC 5659T) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82T. The genome consisted of 2.68 Mbp with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82T genome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes could be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.
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Affiliation(s)
- Carolina Díaz-Cárdenas
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
| | - Gina López
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
| | | | - Laura N González
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá, DC Colombia
| | - Nicole Shapiro
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Silvia Restrepo
- Biological Sciences Department, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá, DC Colombia
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá, DC Colombia
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20
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Abstract
BACKGROUND The majority of environmental bacteria and around a third of oral bacteria remain uncultivated. Furthermore, several bacterial phyla have no cultivable members and are recognised only by detection of their DNA by molecular methods. Possible explanations for the resistance of certain bacteria to cultivation in purity in vitro include: unmet fastidious growth requirements; inhibition by environmental conditions or chemical factors produced by neighbouring bacteria in mixed cultures; or conversely, dependence on interactions with other bacteria in the natural environment, without which they cannot survive in isolation. Auxotrophic bacteria, with small genomes lacking in the necessary genetic material to encode for essential nutrients, frequently rely on close symbiotic relationships with other bacteria for survival, and may therefore be recalcitrant to cultivation in purity. HIGHLIGHT Since in-vitro culture is essential for the comprehensive characterisation of bacteria, particularly with regard to virulence and antimicrobial resistance, the cultivation of uncultivated organisms has been a primary focus of several research laboratories. Many targeted and open-ended strategies have been devised and successfully used. Examples include: the targeted detection of specific bacteria in mixed plate cultures using colony hybridisation; growth in simulated natural environments or in co-culture with 'helper' strains; and modified media preparation techniques or development of customised media eg. supplementation of media with potential growth-stimulatory factors such as siderophores. CONCLUSION Despite significant advances in recent years in methodologies for the cultivation of previously uncultivated bacteria, a substantial proportion remain to be cultured and efforts to devise high-throughput strategies should be a high priority.
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Affiliation(s)
- Sonia R Vartoukian
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
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21
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Krishnan K, Chen T, Paster BJ. A practical guide to the oral microbiome and its relation to health and disease. Oral Dis 2016; 23:276-286. [PMID: 27219464 DOI: 10.1111/odi.12509] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 12/14/2022]
Abstract
The oral microbiome is incredibly complex with the average adult harboring about 50-100 billion bacteria in the oral cavity, which represent about 200 predominant bacterial species. Collectively, there are approximately 700 predominant taxa of which less than one-third still have not yet been grown in vitro. Compared to other body sites, the oral microbiome is unique and readily accessible. There is extensive literature available describing the oral microbiome and discussing the roles that bacteria may play in oral health and disease. However, the purpose of this review is not to rehash these detailed studies but rather to educate the reader with understanding the essence of the oral microbiome, namely that there are abundant bacteria in numbers and types, that there are molecular methods to rapidly determine bacterial associations, that there is site specificity for colonization of the host, that there are specific associations with oral health and disease, that oral bacteria may serve as biomarkers for non-oral diseases, and that oral microbial profiles may have potential use to assess disease risk.
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Affiliation(s)
- K Krishnan
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,New England BioLabs, Ipswich, MA, USA
| | - T Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - B J Paster
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, MA, USA
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22
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A Flow Cytometry Method for Rapidly Assessing Mycobacterium tuberculosis Responses to Antibiotics with Different Modes of Action. Antimicrob Agents Chemother 2016; 60:3869-83. [PMID: 26902767 PMCID: PMC4914659 DOI: 10.1128/aac.02712-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/13/2016] [Indexed: 12/22/2022] Open
Abstract
Current methods for assessing the drug susceptibility of Mycobacterium tuberculosis are lengthy and do not capture information about viable organisms that are not immediately culturable under standard laboratory conditions as a result of antibiotic exposure. We have developed a rapid dual-fluorescence flow cytometry method using markers for cell viability and death. We show that the fluorescent marker calcein violet with an acetoxy-methyl ester group (CV-AM) can differentiate between populations of M. tuberculosis growing at different rates, while Sytox green (SG) can differentiate between live and dead mycobacteria. M. tuberculosis was exposed to isoniazid or rifampin at different concentrations over time and either dual stained with CV-AM and SG and analyzed by flow cytometry or plated to determine the viability of the cells. Although similar trends in the loss of viability were observed when the results of flow cytometry and the plate counting methods were compared, there was a lack of correlation between these two approaches, as the flow cytometry analysis potentially captured information about cell populations that were unable to grow under standard conditions. The flow cytometry approach had an additional advantage in that it could provide insights into the mode of action of the drug: antibiotics targeting the cell wall gave a flow cytometry profile distinct from those inhibiting intracellular processes. This rapid drug susceptibility testing method could identify more effective antimycobacterials, provide information about their potential mode of action, and accelerate their progress to the clinic.
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23
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Vartoukian SR, Moazzez RV, Paster BJ, Dewhirst FE, Wade WG. First Cultivation of Health-Associated Tannerella sp. HOT-286 (BU063). J Dent Res 2016; 95:1308-13. [PMID: 27193146 DOI: 10.1177/0022034516651078] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Despite significant advances in recent years in culture-independent molecular microbiology methods, the detailed study of individual bacterial species still relies on having pure cultures in the laboratory. Yet, more than a third of the approximately 700 bacterial taxa found in the human oral cavity are as yet uncultivated in vitro. One such taxon, Tannerella sp. HOT-286 (phylotype BU063), is the focus of much interest since it is associated with periodontal health, while Tannerella forsythia, its closest phylogenetic neighbor, is strongly associated with periodontal disease. HOT-286, however, has remained uncultivated despite the efforts of several research groups, spanning over a decade. The aim of this study was to cultivate Tannerella sp. HOT-286. A heavily diluted sample of subgingival plaque was inoculated onto culture plates supplemented with siderophores (pyoverdines-Fe complex or desferricoprogen) or a neat plaque suspension. After 8 d of anaerobic incubation, microcolonies and colonies showing satellitism were passaged onto fresh culture plates cross-streaked with potential helper strains or onto cellulose-acetate membranes placed over lawn cultures of helper strains. Subcultured colonies were identified by 16S rRNA gene sequencing, and purity was confirmed by sequencing 20 clones per library prepared from a single colony. Three colonies of interest (derived from pyoverdines- and plaque-supplemented plates) were identified as Tannerella sp. HOT-286. The isolates were found to be incapable of independent growth, requiring helpers such as Propionibacterium acnes and Prevotella intermedia for stimulation, with best growth on membranes over "helper" lawns. A representative isolate was subjected to phenotypic characterization and found to produce a range of glycosidic and proteolytic enzymes. Further comparison of this novel "periodontal health-associated" taxon with T. forsythia will be valuable in investigating virulence factors of the latter and possible health benefits of the former.
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Affiliation(s)
- S R Vartoukian
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - R V Moazzez
- King's College London Dental Institute, London, UK
| | - B J Paster
- The Forsyth Institute, Cambridge, MA, USA Harvard School of Dental Medicine, Boston, MA, USA
| | - F E Dewhirst
- The Forsyth Institute, Cambridge, MA, USA Harvard School of Dental Medicine, Boston, MA, USA
| | - W G Wade
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK The Forsyth Institute, Cambridge, MA, USA
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24
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Abstract
Reconstruction of phylogenetic trees based on 16S rRNA gene sequencing reveals abundant microbial diversity that has not been cultured in the laboratory. Many attribute this so-called 'great plate count anomaly' to traditional microbial cultivation techniques, which largely facilitate the growth of a single species. Yet, it is widely recognized that bacteria in nature exist in complex communities. One technique to increase the pool of cultivated bacterial species is to co-culture multiple species in a simulated natural environment. Here, we present nanoporous microscale microbial incubators (NMMI) that enable high-throughput screening and real-time observation of multi-species co-culture. The key innovation in NMMI is that they facilitate inter-species communication while maintaining physical isolation between species, which is ideal for genomic analysis. Co-culture of a quorum sensing pair demonstrates that the NMMI can be used to culture multiple species in chemical communication while monitoring the growth dynamics of individual species.
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Affiliation(s)
- Zhifei Ge
- Department of Mechanical Engineering, Massachusetts Institute of Technology, USA.
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, USA
| | - Cullen R Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, USA.
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25
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Vartoukian SR, Adamowska A, Lawlor M, Moazzez R, Dewhirst FE, Wade WG. In Vitro Cultivation of 'Unculturable' Oral Bacteria, Facilitated by Community Culture and Media Supplementation with Siderophores. PLoS One 2016; 11:e0146926. [PMID: 26764907 PMCID: PMC4713201 DOI: 10.1371/journal.pone.0146926] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/23/2015] [Indexed: 11/18/2022] Open
Abstract
Over a third of oral bacteria are as-yet-uncultivated in-vitro. Siderophores have been previously shown to enable in-vitro growth of previously uncultivated bacteria. The objective of this study was to cultivate novel oral bacteria in siderophore-supplemented culture media. Various compounds with siderophore activity, including pyoverdines-Fe-complex, desferricoprogen and salicylic acid, were found to stimulate the growth of difficult-to-culture strains Prevotella sp. HOT-376 and Fretibacterium fastidiosum. Furthermore, pyrosequencing analysis demonstrated increased proportions of the as-yet-uncultivated phylotypes Dialister sp. HOT-119 and Megasphaera sp. HOT-123 on mixed culture plates supplemented with siderophores. Therefore a culture model was developed, which incorporated 15 μg siderophore (pyoverdines-Fe-complex or desferricoprogen) or 150 μl neat subgingival-plaque suspension into a central well on agar plates that were inoculated with heavily-diluted subgingival-plaque samples from subjects with periodontitis. Colonies showing satellitism were passaged onto fresh plates in co-culture with selected helper strains. Five novel strains, representatives of three previously-uncultivated taxa (Anaerolineae bacterium HOT-439, the first oral taxon from the Chloroflexi phylum to have been cultivated; Bacteroidetes bacterium HOT-365; and Peptostreptococcaceae bacterium HOT-091) were successfully isolated. All novel isolates required helper strains for growth, implying dependence on a biofilm lifestyle. Their characterisation will further our understanding of the human oral microbiome.
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Affiliation(s)
- Sonia R. Vartoukian
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Aleksandra Adamowska
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Megan Lawlor
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Rebecca Moazzez
- King’s College London Dental Institute, London, United Kingdom
| | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, United States of America
- Harvard School of Dental Medicine, Boston, United States of America
| | - William G. Wade
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- * E-mail:
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Abstract
The oral bacterial microbiome encompasses approximately 700 commonly occurring phylotypes, approximately half of which can be present at any time in any individual. These bacteria are largely indigenous to the oral cavity; this limited habitat range suggests that interactions between the various phylotypes, and between the phylotypes and their environment, are crucial for their existence. Molecular cataloging has confirmed many basic observations on the composition of the oral microbiome that were formulated well before ribosomal RNA-based systematics, but the power and the scope of molecular taxonomy have resulted in the discovery of new phylotypes and, more importantly, have made possible a level of bacterial community analysis that was unachievable with classical methods. Bacterial community structure varies with location within the mouth, and changes in community structure are related to disease initiation and disease progression. Factors that influence the formation and the evolution of communities include selective adherence to epithelial or tooth surfaces, specific cell-to-cell binding as a driver of early community composition, and interorganismal interaction leading to alteration of the local environment, which represents the first step on the road to oral disease. A comprehensive understanding of how these factors interact to drive changes in the composition of the oral microbial community can lead to new strategies for the inhibition of periodontal diseases and dental caries.
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In vitro culture of previously uncultured oral bacterial phylotypes. Appl Environ Microbiol 2015; 81:8307-14. [PMID: 26407883 DOI: 10.1128/aem.02156-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/17/2015] [Indexed: 11/20/2022] Open
Abstract
Around a third of oral bacteria cannot be grown using conventional bacteriological culture media. Community profiling targeting 16S rRNA and shotgun metagenomics methods have proved valuable in revealing the complexity of the oral bacterial community. Studies investigating the role of oral bacteria in health and disease require phenotypic characterizations that are possible only with live cultures. The aim of this study was to develop novel culture media and use an in vitro biofilm model to culture previously uncultured oral bacteria. Subgingival plaque samples collected from subjects with periodontitis were cultured on complex mucin-containing agar plates supplemented with proteose peptone (PPA), beef extract (BEA), or Gelysate (GA) as well as on fastidious anaerobe agar plus 5% horse blood (FAA). In vitro biofilms inoculated with the subgingival plaque samples and proteose peptone broth (PPB) as the growth medium were established using the Calgary biofilm device. Specific PCR primers were designed and validated for the previously uncultivated oral taxa Bacteroidetes bacteria HOT 365 and HOT 281, Lachnospiraceae bacteria HOT 100 and HOT 500, and Clostridiales bacterium HOT 093. All agar media were able to support the growth of 10 reference strains of oral bacteria. One previously uncultivated phylotype, Actinomyces sp. HOT 525, was cultivated on FAA. Of 93 previously uncultivated phylotypes found in the inocula, 26 were detected in in vitro-cultivated biofilms. Lachnospiraceae bacterium HOT 500 was successfully cultured from biofilm material harvested from PPA plates in coculture with Parvimonas micra or Veillonella dispar/parvula after colony hybridization-directed enrichment. The establishment of in vitro biofilms from oral inocula enables the cultivation of previously uncultured oral bacteria and provides source material for isolation in coculture.
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Jumas-Bilak E, Bouvet P, Allen-Vercoe E, Aujoulat F, Lawson PA, Jean-Pierre H, Marchandin H. Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates. Int J Syst Evol Microbiol 2015; 65:3965-3970. [PMID: 26320053 DOI: 10.1099/ijsem.0.000520] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5-91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).
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Affiliation(s)
- Estelle Jumas-Bilak
- Université de Montpellier, Unité Mixte de Recherche 5569 - Hydrosciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, Unité de Bactériologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France.,Centre Hospitalier Universitaire de Montpellier, Laboratoire d'Hygiène Hospitalière, 778 rue de la croix verte, 34295 Montpellier Cedex 5, France
| | - Philippe Bouvet
- Institut Pasteur, Centre National de Référence des Bactéries Anaérobies et du Botulisme, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Emma Allen-Vercoe
- Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Fabien Aujoulat
- Université de Montpellier, Unité Mixte de Recherche 5569 - Hydrosciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, Unité de Bactériologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Hélène Jean-Pierre
- Université de Montpellier, Unité Mixte de Recherche 5569 - Hydrosciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, Unité de Bactériologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France.,Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Hélène Marchandin
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,Université de Montpellier, Unité Mixte de Recherche 5569 - Hydrosciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, Unité de Bactériologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
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Black Queen evolution: the role of leakiness in structuring microbial communities. Trends Genet 2015; 31:475-82. [DOI: 10.1016/j.tig.2015.05.004] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 11/21/2022]
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30
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Cloacibacillus sp., a Potential Human Pathogen Associated with Bacteremia in Quebec and New Brunswick. J Clin Microbiol 2015. [PMID: 26224843 DOI: 10.1128/jcm.01137-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteremia due to Cloacibacillus species is poorly described. We present three cases involving either Cloacibacillus evryensis or Cloacibacillus porcorum. The isolates were identified by 16S rRNA gene sequencing and were susceptible to antibiotics commonly used for anaerobic infections. The clinical significance of these organisms as potential emerging pathogens is discussed.
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31
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Interactions of Salmonella enterica subspecies enterica serovar Typhimurium with gut bacteria. Anaerobe 2015; 33:90-7. [DOI: 10.1016/j.anaerobe.2015.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 11/19/2022]
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Ross MC, Muzny DM, McCormick JB, Gibbs RA, Fisher-Hoch SP, Petrosino JF. 16S gut community of the Cameron County Hispanic Cohort. MICROBIOME 2015; 3:7. [PMID: 25763184 PMCID: PMC4355967 DOI: 10.1186/s40168-015-0072-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/03/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Obesity and type 2 diabetes (T2D) are major public health concerns worldwide, and their prevalence has only increased in recent years. Mexican Americans are disproportionately afflicted by obesity and T2D, and rates are even higher in the United States-Mexico border region. To determine the factors associated with the increased risk of T2D, obesity, and other diseases in this population, the Cameron County Hispanic Cohort was established in 2004. RESULTS In this study, we characterized the 16S gut community of a subset of 63 subjects from this unique cohort. We found that these communities, when compared to Human Microbiome Project subjects, exhibit community shifts often observed in obese and T2D individuals in published studies. We also examined microbial network relationships between operational taxonomic units (OTUs) in the Cameron County Hispanic Cohort (CCHC) and three additional datasets. We identified a group of seven genera that form a tightly interconnected network present in all four tested datasets, dominated by butyrate producers, which are often increased in obese individuals while being depleted in T2D patients. CONCLUSIONS Through a combination of increased disease prevalence and relatively high gut microbial homogeneity in the subset of CCHC members we examined, we believe that the CCHC may represent an ideal community to dissect mechanisms underlying the role of the gut microbiome in human health and disease. The lack of CCHC subject gut community segregation based on all tested metadata suggests that the community structure we observe in the CCHC likely occurs early in life, and endures. This persistent 'disease'-related gut microbial community in CCHC subjects may enhance existing genetic or lifestyle predispositions to the prevalent diseases of the CCHC, leading to increased attack rates of obesity, T2D, non-alcoholic fatty liver disease, and others.
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Affiliation(s)
- Matthew C Ross
- />Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX USA
- />Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Donna M Muzny
- />Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | - Richard A Gibbs
- />Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | - Joseph F Petrosino
- />Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX USA
- />Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
- />Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
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33
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Vengerfeldt V, Špilka K, Saag M, Preem JK, Oopkaup K, Truu J, Mändar R. Highly diverse microbiota in dental root canals in cases of apical periodontitis (data of illumina sequencing). J Endod 2014; 40:1778-83. [PMID: 25227214 DOI: 10.1016/j.joen.2014.06.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/06/2014] [Accepted: 06/10/2014] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Chronic apical periodontitis (CAP) is a frequent condition that has a considerable effect on a patient's quality of life. We aimed to reveal root canal microbial communities in antibiotic-naive patients by applying Illumina sequencing (Illumina Inc, San Diego, CA). METHODS Samples were collected under strict aseptic conditions from 12 teeth (5 with primary CAP, 3 with secondary CAP, and 4 with a periapical abscess [PA]) and characterized by profiling the microbial community on the basis of the V6 hypervariable region of the 16S ribosomal RNA gene by using Illumina HiSeq2000 sequencing combinatorial sequence-tagged polymerase chain reaction products. RESULTS Root canal specimens displayed highly polymicrobial communities in all 3 patient groups. One sample contained 5-8 (mean = 6.5) phyla of bacteria. The most numerous were Firmicutes and Bacteroidetes, but Actinobacteria, Fusobacteria, Proteobacteria, Spirochaetes, Tenericutes, and Synergistetes were also present in most of the patients. One sample contained 30-70 different operational taxonomic units; the mean (± standard deviation) was lower in the primary CAP group (36 ± 4) than in the PA (45 ± 4) and secondary CAP (43 ± 13) groups (P < .05). The communities were individually different, but anaerobic bacteria predominated as the rule. Enterococcus faecalis was found only in patients with secondary CAP. One PA sample displayed a significantly high proportion (47%) of Proteobacteria, mainly at the expense of Janthinobacterium lividum. CONCLUSIONS This study provided an in-depth characterization of the microbiota of periapical tissues, revealing highly polymicrobial communities and minor differences between the study groups. A full understanding of the etiology of periodontal disease will only be possible through further in-depth systems-level analyses of the host-microbiome interaction.
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Affiliation(s)
| | - Katerina Špilka
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Mare Saag
- Department of Stomatology, University of Tartu, Tartu, Estonia
| | - Jens-Konrad Preem
- Department of Geography, Faculty of Science and Technology, University of Tartu, Tartu, Estonia; Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
| | - Kristjan Oopkaup
- Department of Geography, Faculty of Science and Technology, University of Tartu, Tartu, Estonia; Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
| | - Jaak Truu
- Department of Geography, Faculty of Science and Technology, University of Tartu, Tartu, Estonia; Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
| | - Reet Mändar
- Department of Microbiology, Faculty of Medicine, University of Tartu, Tartu, Estonia; Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.
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Axenic culture of a candidate division TM7 bacterium from the human oral cavity and biofilm interactions with other oral bacteria. Appl Environ Microbiol 2014; 80:6480-9. [PMID: 25107981 DOI: 10.1128/aem.01827-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The diversity of bacterial species in the human oral cavity is well recognized, but a high proportion of them are presently uncultivable. Candidate division TM7 bacteria are almost always detected in metagenomic studies but have not yet been cultivated. In this paper, we identified candidate division TM7 bacterial phylotypes in mature plaque samples from around orthodontic bonds in subjects undergoing orthodontic treatment. Successive rounds of enrichment in laboratory media led to the isolation of a pure culture of one of these candidate division TM7 phylotypes. The bacteria formed filaments of 20 to 200 μm in length within agar plate colonies and in monospecies biofilms on salivary pellicle and exhibited some unusual morphological characteristics by transmission electron microscopy, including a trilaminated cell surface layer and dense cytoplasmic deposits. Proteomic analyses of cell wall protein extracts identified abundant polypeptides predicted from the TM7 partial genomic sequence. Pleiomorphic phenotypes were observed when the candidate division TM7 bacterium was grown in dual-species biofilms with representatives of six different oral bacterial genera. The TM7 bacterium formed long filaments in dual-species biofilm communities with Actinomyces oris or Fusobacterium nucleatum. However, the TM7 isolate grew as short rods or cocci in dual-species biofilms with Porphyromonas gingivalis, Prevotella intermedia, Parvimonas micra, or Streptococcus gordonii, forming notably robust biofilms with the latter two species. The ability to cultivate TM7 axenically should majorly advance understanding of the physiology, genetics, and virulence properties of this novel candidate division oral bacterium.
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35
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Teles R, Teles F, Frias-Lopez J, Paster B, Haffajee A. Lessons learned and unlearned in periodontal microbiology. Periodontol 2000 2014; 62:95-162. [PMID: 23574465 PMCID: PMC3912758 DOI: 10.1111/prd.12010] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Periodontal diseases are initiated by bacterial species living in polymicrobial biofilms at or below the gingival margin and progress largely as a result of the inflammation elicited by specific subgingival species. In the past few decades, efforts to understand the periodontal microbiota have led to an exponential increase in information about biofilms associated with periodontal health and disease. In fact, the oral microbiota is one of the best-characterized microbiomes that colonize the human body. Despite this increased knowledge, one has to ask if our fundamental concepts of the etiology and pathogenesis of periodontal diseases have really changed. In this article we will review how our comprehension of the structure and function of the subgingival microbiota has evolved over the years in search of lessons learned and unlearned in periodontal microbiology. More specifically, this review focuses on: (i) how the data obtained through molecular techniques have impacted our knowledge of the etiology of periodontal infections; (ii) the potential role of viruses in the etiopathogenesis of periodontal diseases; (iii) how concepts of microbial ecology have expanded our understanding of host-microbe interactions that might lead to periodontal diseases; (iv) the role of inflammation in the pathogenesis of periodontal diseases; and (v) the impact of these evolving concepts on therapeutic and preventive strategies to periodontal infections. We will conclude by reviewing how novel systems-biology approaches promise to unravel new details of the pathogenesis of periodontal diseases and hopefully lead to a better understanding of their mechanisms.
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36
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Edlund A, Yang Y, Hall AP, Guo L, Lux R, He X, Nelson KE, Nealson KH, Yooseph S, Shi W, McLean JS. An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome. MICROBIOME 2013; 1:25. [PMID: 24451062 PMCID: PMC3971625 DOI: 10.1186/2049-2618-1-25] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/17/2013] [Indexed: 05/11/2023]
Abstract
BACKGROUND Our knowledge of microbial diversity in the human oral cavity has vastly expanded during the last two decades of research. However, much of what is known about the behavior of oral species to date derives from pure culture approaches and the studies combining several cultivated species, which likely does not fully reflect their function in complex microbial communities. It has been shown in studies with a limited number of cultivated species that early oral biofilm development occurs in a successional manner and that continuous low pH can lead to an enrichment of aciduric species. Observations that in vitro grown plaque biofilm microcosms can maintain similar pH profiles in response to carbohydrate addition as plaque in vivo suggests a complex microbial community can be established in the laboratory. In light of this, our primary goal was to develop a robust in vitro biofilm-model system from a pooled saliva inoculum in order to study the stability, reproducibility, and development of the oral microbiome, and its dynamic response to environmental changes from the community to the molecular level. RESULTS Comparative metagenomic analyses confirmed a high similarity of metabolic potential in biofilms to recently available oral metagenomes from healthy subjects as part of the Human Microbiome Project. A time-series metagenomic analysis of the taxonomic community composition in biofilms revealed that the proportions of major species at 3 hours of growth are maintained during 48 hours of biofilm development. By employing deep pyrosequencing of the 16S rRNA gene to investigate this biofilm model with regards to bacterial taxonomic diversity, we show a high reproducibility of the taxonomic carriage and proportions between: 1) individual biofilm samples; 2) biofilm batches grown at different dates; 3) DNA extraction techniques and 4) research laboratories. CONCLUSIONS Our study demonstrates that we now have the capability to grow stable oral microbial in vitro biofilms containing more than one hundred operational taxonomic units (OTU) which represent 60-80% of the original inoculum OTU richness. Previously uncultivated Human Oral Taxa (HOT) were identified in the biofilms and contributed to approximately one-third of the totally captured 16S rRNA gene diversity. To our knowledge, this represents the highest oral bacterial diversity reported for an in vitro model system so far. This robust model will help investigate currently uncultivated species and the known virulence properties for many oral pathogens not solely restricted to pure culture systems, but within multi-species biofilms.
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Affiliation(s)
- Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
- UCLA School of Dentistry, 10833 Le Conte Avenue, CHS Box 951668, Los Angeles, CA 90095, USA
| | - Youngik Yang
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
| | - Adam P Hall
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
| | - Lihong Guo
- UCLA School of Dentistry, 10833 Le Conte Avenue, CHS Box 951668, Los Angeles, CA 90095, USA
| | - Renate Lux
- UCLA School of Dentistry, 10833 Le Conte Avenue, CHS Box 951668, Los Angeles, CA 90095, USA
| | - Xuesong He
- UCLA School of Dentistry, 10833 Le Conte Avenue, CHS Box 951668, Los Angeles, CA 90095, USA
| | - Karen E Nelson
- Department of Human Genomic Medicine, J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Kenneth H Nealson
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
- Department of Earth Sciences, USC, ZHS 117, Los Angeles, CA 90089, USA
| | - Shibu Yooseph
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
| | - Wenyuan Shi
- UCLA School of Dentistry, 10833 Le Conte Avenue, CHS Box 951668, Los Angeles, CA 90095, USA
| | - Jeffrey S McLean
- Microbial and Environmental Genomics, J. Craig Venter Institute, 10355 Science Center Drive, CA 921 21 San Diego, USA
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Honda T, Fujita T, Tonouchi A. Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field. Int J Syst Evol Microbiol 2013; 63:3679-3686. [DOI: 10.1099/ijs.0.052225-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic bacterium that could ferment amino acids and organic acids was isolated from an anaerobic, propionate-oxidizing enrichment culture originating from soil of a rice field in Japan. Cells of the isolate, designated strain 4F6ET, were Gram-staining-negative, oxidase- and catalase-negative, non-spore-forming, vibrio-shaped, motile rods (0.8×2.0–2.5 µm) with two or three lateral flagella. Growth occurred at 20–42 °C (optimum at 37–40 °C), at pH 6.4–8.4 (optimum at pH 7.3) and at 0–1.5 % (w/v) NaCl (optimum at 0–0.5 %). Good growth occurred on glycine, serine, cysteine, pyruvate and citrate, whereas poor growth was observed on threonine, glutamine, l-malate, α-ketoglutarate, peptone and Casamino acids. In co-culture with the hydrogen-utilizing methanogen
Methanobacterium formicicum
JCM 10132T, strain 4F6ET oxidized alanine, valine, leucine, isoleucine, methionine, aspartate, glutamate, histidine, asparagine and fumarate. Yeast extract was required for growth. The G+C content of genomic DNA was 61.9 mol%. A phylogenetic analysis based on comparison of the 16S rRNA gene sequence showed that the type strains of
Fretibacterium fastidiosum
,
Aminobacterium colombiense
and
Aminobacterium mobile
, members of the family
Synergistaceae
, were the closest relatives of strain 4F6ET, with low sequence similarities (89.3, 89.5 and 86.2 %, respectively). Strain 4F6ET contained iso-C13 : 0 (24.43 %), iso-C15 : 0 (16.47 %) and C19 : 1ω11c/C19 : 1ω9c (16.32 %) as the major fatty acids, which differed from those of
F. fastidiosum
,
Aminobacterium colombiense
and
Aminobacterium mobile
. On the basis of phenotypic, chemotaxonomic and phylogenetic differences between strain 4F6ET and the type strains of
F. fastidiosum
and
Aminobacterium
species, we propose that strain 4F6ET represents a novel genus and species, Aminivibrio pyruvatiphilus gen. nov., sp. nov. The type strain of Aminivibrio pyruvatiphilus is strain 4F6ET ( = JCM 18417T = DSM 25964T).
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Affiliation(s)
- Takuya Honda
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Takashi Fujita
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
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Rôças IN, Neves MAS, Provenzano JC, Siqueira JF. Susceptibility of as-yet-uncultivated and difficult-to-culture bacteria to chemomechanical procedures. J Endod 2013; 40:33-7. [PMID: 24331987 DOI: 10.1016/j.joen.2013.07.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/28/2013] [Accepted: 07/30/2013] [Indexed: 02/04/2023]
Abstract
INTRODUCTION A significant portion of the bacteria taking part of the microbiome associated with apical periodontitis still remain to be cultivated and phenotypically characterized. This molecular study evaluated the prevalence of selected as-yet-uncultivated and difficult-to-culture bacterial taxa in infected root canals and their susceptibility to chemomechanical procedures. METHODS Root canals of single-rooted teeth with apical periodontitis were prepared using rotary nickel-titanium instruments and 2.5% sodium hypochlorite as the irrigant. DNA extracts from samples taken before (S1) and after (S2) chemomechanical preparation were surveyed for the presence of 7 as-yet-uncultivated phylotypes and 1 difficult-to-culture species using end-point polymerase chain reaction. Samples were also subjected to quantitative analysis of total bacteria and levels of the 2 most prevalent taxa. RESULTS Bacteroidaceae sp. HOT-272 (24%) and Fretibacterium fastidiosum (20%) were the most prevalent taxa in S1. Their mean counts in S1 were 8.25 × 10(3) and 2.13 × 10(3) rRNA gene copies, corresponding to 0.18% and 0.55% of the total bacteria. Chemomechanical debridement promoted a highly statistically significant reduction in total bacterial counts (P < .001), but 64% of the canals were still positive for bacterial presence. Of the target taxa, only Bacteroidaceae sp. HOT-272 and F. fastidiosum were detected in S2 (each one in 1 sample). The reduction in counts of both taxa was also highly significant (P < .001). CONCLUSIONS Findings confirmed that several as-yet-uncultivated and difficult-to-grow bacterial taxa can participate in the microbiome associated with apical periodontitis. Two of them were found in relatively high prevalence but rarely as a dominant species. Chemomechanical procedures were highly effective in completely eliminating these taxa or at least substantially reducing their numbers.
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Affiliation(s)
- Isabela N Rôças
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mônica A S Neves
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José C Provenzano
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José F Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Estácio de Sá University, Rio de Janeiro, Rio de Janeiro, Brazil.
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Siqueira JF, Rôças IN. As-yet-uncultivated oral bacteria: breadth and association with oral and extra-oral diseases. J Oral Microbiol 2013; 5:21077. [PMID: 23717756 PMCID: PMC3664057 DOI: 10.3402/jom.v5i0.21077] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 12/19/2022] Open
Abstract
It has been shown that 40–60% of the bacteria found in different healthy and diseased oral sites still remain to be grown in vitro, phenotypically characterized, and formally named as species. The possibility exists that these as-yet-uncultivated bacteria play important ecological roles in oral bacterial communities and may participate in the pathogenesis of several oral infectious diseases. There is also a potential for these as-yet-uncultivated oral bacteria to take part in extra-oral infections. For a comprehensive characterization of physiological and pathogenic properties as well as antimicrobial susceptibility of individual bacterial species, strains need to be grown in pure culture. Advances in culturing techniques have allowed the cultivation of several oral bacterial taxa only previously known by a 16S rRNA gene sequence signature, and novel species have been proposed. There is a growing need for developing improved methods to cultivate and characterize the as-yet-uncultivated portion of the oral microbiome so as to unravel its role in health and disease.
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Affiliation(s)
- José F Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, Estácio de Sá University, Rio de Janeiro, Brazil
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Vartoukian SR, Downes J, Palmer RM, Wade WG. Fretibacterium fastidiosum gen. nov., sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2013; 63:458-463. [DOI: 10.1099/ijs.0.041038-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SGP1T, a strain belonging to a lineage of the phylum
Synergistetes
with no previously cultivated representatives was subjected to a comprehensive range of phenotypic and genotypic tests. For good growth the strain was dependent on co-culture with, or extracts from, selected other oral bacteria. Cells of strain SGP1T were asaccharolytic and major amounts of acetic acid and moderate amounts of propionic acid were produced as end products of metabolism in peptone-yeast extract-glucose broth supplemented with a filtered cell sonicate of
Fusobacterium nucleatum subsp. nucleatum
ATCC 25586T (25 %, v/v). Hydrogen sulphide was produced and gelatin was weakly hydrolysed. The major cellular fatty acids were C14 : 0, C18 : 0 and C16 : 0. The DNA G+C content of strain SGP1T was 63 mol%. Phylogenetic analysis of the full-length 16S rRNA gene showed that strain SGP1T represented a novel group within the phylum
Synergistetes
. A novel species in a new genus, Fretibacterium fastidiosum gen. nov., sp. nov., is proposed. The type strain of Fretibacterium fastidiosum is SGP1T ( = DSM 25557T = JCM 16858T).
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Affiliation(s)
- Sonia R. Vartoukian
- King’s College London Dental Institute at Guy’s, King’s College and St Thomas’ Hospitals, Microbiology Unit, London SE1 9RT, UK
| | - Julia Downes
- King’s College London Dental Institute at Guy’s, King’s College and St Thomas’ Hospitals, Microbiology Unit, London SE1 9RT, UK
| | - Richard M. Palmer
- King’s College London Dental Institute at Guy’s, King’s College and St Thomas’ Hospitals, Microbiology Unit, London SE1 9RT, UK
| | - William G. Wade
- King’s College London Dental Institute at Guy’s, King’s College and St Thomas’ Hospitals, Microbiology Unit, London SE1 9RT, UK
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Looft T, Levine UY, Stanton TB. Cloacibacillus porcorum sp. nov., a mucin-degrading bacterium from the swine intestinal tract and emended description of the genus Cloacibacillus. Int J Syst Evol Microbiol 2012; 63:1960-1966. [PMID: 23041639 PMCID: PMC3709534 DOI: 10.1099/ijs.0.044719-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, mesophilic, amino-acid-fermenting bacterium, designated strain CL-84T, was isolated from the swine intestinal tract on mucin-based media. Cells were curved rods (0.8–1.2×3.5–5.0 µm), stained Gram-negative and were non-motile with no evidence of spores. Strain CL-84T produced acetate, propionate, formate and butyrate as the end products of metabolism when grown on serine. Optimum growth occurred at 39 °C and pH 6.5. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 and C16 : 0, distinguishing strain CL-84T from closely related species. The DNA G+C content of strain CL-84T was 55.1 mol%. 16S rRNA gene sequence analysis showed that strain CL-84T shared 90–95 % similarity with characterized genera within the phylum Synergistetes, family Synergistaceae. Phylogenetic analysis showed that strain CL-84T was related to, but distinct from, Cloacibacillus evryensis. Based on these findings, we propose that strain CL-84T represents a novel species of the genus Cloacibacillus. We further propose the name Cloacibacillus porcorum sp. nov. be designated for this species. The type strain is CL-84T ( = DSM 25858T = CCUG 62631T). An emended description of the genus Cloacibacillus is provided.
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Affiliation(s)
- T Looft
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - U Y Levine
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - T B Stanton
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA
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You M, Mo S, Watt RM, Leung WK. Prevalence and diversity of Synergistetes taxa in periodontal health and disease. J Periodontal Res 2012; 48:159-68. [PMID: 22881378 DOI: 10.1111/j.1600-0765.2012.01516.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2012] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVE Members of the phylum Synergistetes have previously been identified within periodontitis subgingival plaque and are considered putative periodontopathogens. This study compared the diversity of subginigval Synergistetes in a cohort of subjects with periodontitis (n = 10) vs. periodontitis-free controls (n = 10). MATERIAL AND METHODS Pooled subgingival plaque samples from all deep periodontal pockets or all sulci were collected from the periodontitis and periodontitis-free subjects, respectively. Bacterial 16S rRNA genes were PCR-amplified from purified subgingival plaque DNA using a Synergistetes 'selective' primer set. PCR products were cloned and sequenced to analyze the prevalence and diversity of Synergistetes operational taxonomic units (OTUs) present in plaque samples of both subject groups. RESULTS A total of 1030 non-chimeric 16S rRNA clones were obtained, of which 162 corresponded to members of the phylum Synergistetes. A significantly larger number of Synergistetes clones were obtained from periodontitis subgingival plaque than from periodontitis-free controls (25.4% vs. 5.9%, p < 0.001). All Synergistetes clones corresponded to cluster A oral Synergistetes, and fell into 31 OTUs (99% sequence identity cut-off). Twenty-nine Synergistetes OTUs were detected in the periodontitis group while eight were detected in the periodontitis-free group (p < 0.001). Five Synergistetes OTUs; including one OTU corresponding to the recently-characterized species Fretibacterium fastidiosum, were more prevalent in the periodontitis subjects (p < 0.05). CONCLUSION OTUs belonging to oral Synergistetes cluster A were more readily detectable and were more diverse in subgingival plaque from periodontitis subjects compared with periodontitis-free controls. Specific Synergistetes OTUs appear to be associated with periodontitis.
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Affiliation(s)
- M You
- Oral Diagnosis and Polyclinics, Prince Philip Dental Hospital, The University of Hong Kong, Hong Kong SAR, China
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Molecular signatures for the phylum Synergistetes and some of its subclades. Antonie Van Leeuwenhoek 2012; 102:517-40. [DOI: 10.1007/s10482-012-9759-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
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Abstract
The bacteria that can be grown in the laboratory are only a small fraction of the total diversity that exists in nature. At all levels of bacterial phylogeny, uncultured clades that do not grow on standard media are playing critical roles in cycling carbon, nitrogen, and other elements, synthesizing novel natural products, and impacting the surrounding organisms and environment. While molecular techniques, such as metagenomic sequencing, can provide some information independent of our ability to culture these organisms, it is essentially impossible to learn new gene and pathway functions from pure sequence data. A true understanding of the physiology of these bacteria and their roles in ecology, host health, and natural product production requires their cultivation in the laboratory. Recent advances in growing these species include coculture with other bacteria, recreating the environment in the laboratory, and combining these approaches with microcultivation technology to increase throughput and access rare species. These studies are unraveling the molecular mechanisms of unculturability and are identifying growth factors that promote the growth of previously unculturable organisms. This minireview summarizes the recent discoveries in this area and discusses the potential future of the field.
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Ribeiro AC, Matarazzo F, Faveri M, Zezell DM, Mayer MPA. Exploring bacterial diversity of endodontic microbiota by cloning and sequencing 16S rRNA. J Endod 2011; 37:922-6. [PMID: 21689545 DOI: 10.1016/j.joen.2011.04.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 04/08/2011] [Accepted: 04/10/2011] [Indexed: 11/27/2022]
Abstract
INTRODUCTION The characterization of microbial communities infecting the endodontic system in each clinical condition may help on the establishment of a correct prognosis and distinct strategies of treatment. The purpose of this study was to determine the bacterial diversity in primary endodontic infections by 16S ribosomal-RNA (rRNA) sequence analysis. METHODS Samples from root canals of untreated asymptomatic teeth (n = 12) exhibiting periapical lesions were obtained, 16S rRNA bacterial genomic libraries were constructed and sequenced, and bacterial diversity was estimated. RESULTS A total of 489 clones were analyzed (mean, 40.7 ± 8.0 clones per sample). Seventy phylotypes were identified of which six were novel phylotypes belonging to the family Ruminococcaceae. The mean number of taxa per canal was 10.0, ranging from 3 to 21 per sample; 65.7% of the cloned sequences represented phylotypes for which no cultivated isolates have been reported. The most prevalent taxa were Atopobium rimae (50.0%), Dialister invisus, Prevotella oris, Pseudoramibacter alactolyticus, and Tannerella forsythia (33.3%). CONCLUSIONS Although several key species predominate in endodontic samples of asymptomatic cases with periapical lesions, the primary endodontic infection is characterized by a wide bacterial diversity, which is mostly represented by members of the phylum Firmicutes belonging to the class Clostridia followed by the phylum Bacteroidetes.
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Affiliation(s)
- Adriana C Ribeiro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Wade WG. Has the use of molecular methods for the characterization of the human oral microbiome changed our understanding of the role of bacteria in the pathogenesis of periodontal disease? J Clin Periodontol 2011; 38 Suppl 11:7-16. [PMID: 21323699 DOI: 10.1111/j.1600-051x.2010.01679.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Only around half of oral bacteria can be grown in the laboratory using conventional culture methods. Molecular methods based on 16S rRNA gene sequence are now available and are being used to characterize the periodontal microbiota in its entirety. AIM This review describes the cultural characterization of the oral and periodontal microbiotas and explores the influence of the additional data now available from culture-independent molecular analyses on current thinking on the role of bacteria in periodontitis. RESULTS Culture-independent molecular analysis of the periodontal microbiota has shown it to be far more diverse than previously thought. A number of species including some that have yet to be cultured are as strongly associated with disease as those organisms traditionally regarded as periodontal pathogens. Sequencing of bacterial genomes has revealed a high degree of intra-specific genetic diversity. CONCLUSIONS The use of molecular methods for the characterization of the periodontal microbiome has greatly expanded the range of bacterial species known to colonize this habitat. Understanding the interactions between the human host and its commensal bacterial community at the functional level is a priority.
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Kador M, Horn MA, Dettner K. Novel oligonucleotide probes for in situ detection of pederin-producing endosymbionts of Paederus riparius rove beetles (Coleoptera: Staphylinidae). FEMS Microbiol Lett 2011; 319:73-81. [PMID: 21426381 DOI: 10.1111/j.1574-6968.2011.02270.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial endosymbionts from female Paederus rove beetles are hitherto uncultured, phylogenetically related to Pseudomonas sp., and produce the polyketide pederin, which exhibits strong cytotoxic effects and antitumoral activities. The location of such endosymbionts inside beetles and on beetles' eggs is hypothesized based on indirect evidence rather than elucidated. Thus, an endosymbiont-specific and a competitor oligonucleotide probe (Cy3-labelled PAE444 and unlabelled cPAE444, respectively) were designed and utilized for FISH with semi-thin sections of Paederus riparius eggs. Cy3-PAE444-positive cells were densely packed and covered the whole eggshell. Hundred percent of EUB338-Mix-positive total bacterial cells were PAE444 positive, indicating a biofilm dominated by Paederus endosymbionts. Analysis of different egg deposition stadiums by electron microscopy and pks (polyketide synthase gene, a structural gene associated with pederin biosynthesis)-PCR supported results obtained by FISH and revealed that the endosymbiont-containing layer is applied to the eggshell inside the efferent duct. These findings suggest that P. riparius endosymbionts are located inside unknown structures of the female genitalia, which allow for a well-regulated release of endosymbionts during oviposition. The novel oligonucleotide probes developed in this study will facilitate (1) the identification of symbiont-containing structures within genitalia of their beetle hosts and (2) directed cultivation approaches in the future.
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Affiliation(s)
- Matthias Kador
- Animal Ecology II, University of Bayreuth, Bayreuth, Germany Ecological Microbiology, University of Bayreuth, Bayreuth, Germany.
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Abstract
The human mouth is host to a diverse collection of microorganisms including bacteria, viruses, fungi and protozoa. Recent advances using molecular methods for the analysis of complex bacterial communities have demonstrated the richness of the oral bacterial biota and the presence of numerous previously undescribed lineages. Dental plaque forms in a structured way with pioneer species able to colonise pellicle-coated enamel followed by secondary plaque formers such as Fusobacterium nucleatum that have the capability of coaggregating with a range of other genera and species. The mature plaque biofilm has many features of multicellular organisms with the constituent organisms cooperating to make nutrients available and resist environmental stresses, and communicating to regulate their overall numbers. Control of the oral microbiota to prevent disease has conventionally been by mechanical means augmented with toothpastes and mouthrinses, but improved knowledge of oral microbial ecology is allowing the development of pre and pro-biotic approaches. Other possibilities include interference with the plaque formation process and the perturbation of bacterial communication networks.
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Abstract
The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.
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