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Bérard A, Mauffrey F, Gaïa N, Perez A, Chaabane C, Schrenzel J, Leprince JG, Bouillaguet S, Lazarevic V. Microbiota of Healthy Dental Pulp Under the Omics Loupe. Int J Mol Sci 2025; 26:3232. [PMID: 40244028 PMCID: PMC11989987 DOI: 10.3390/ijms26073232] [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: 02/19/2025] [Revised: 03/21/2025] [Accepted: 03/25/2025] [Indexed: 04/18/2025] Open
Abstract
This study aims to contribute to the understanding of the dental pulp microbiome through metataxonomic analysis of pulp tissues from clinically healthy impacted third molars in 17 patients. Samples from coronal pulp, outer radicular dentin, and negative controls were included. Each sample was spiked with a known bacterial standard. Sequencing of the 16S rRNA V3-V4 region revealed similarity in bacterial taxonomic profiles. The bacterial DNA was detected in all pulp samples, primarily originating from reagent contaminants. Although some oral taxa appeared more abundant in pulp than in dentin or controls, contaminant species overwhelmingly dominated. Most of the extracted DNA was of human origin, rather than bacterial. Our findings question the concept of a core microbiome in healthy pulp and highlight the critical need for rigorous controls in pulpal microbiome studies.
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Affiliation(s)
- Alan Bérard
- Division of Cariology and Endodontology, University Clinics of Dental Medicine (CUMD), University of Geneva, 1211 Geneva, Switzerland; (A.B.); (J.G.L.)
| | - Florian Mauffrey
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, University of Geneva, 1205 Geneva, Switzerland; (F.M.); (N.G.); (C.C.); (J.S.); (V.L.)
| | - Nadia Gaïa
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, University of Geneva, 1205 Geneva, Switzerland; (F.M.); (N.G.); (C.C.); (J.S.); (V.L.)
| | - Alexandre Perez
- Unit of Oral Surgery and Implantology, Division of Oral and Maxillofacial Surgery, Department of Surgery, Geneva University Hospitals, University of Geneva, 1205 Geneva, Switzerland;
| | - Chiraz Chaabane
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, University of Geneva, 1205 Geneva, Switzerland; (F.M.); (N.G.); (C.C.); (J.S.); (V.L.)
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, University of Geneva, 1205 Geneva, Switzerland; (F.M.); (N.G.); (C.C.); (J.S.); (V.L.)
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Julian Grégoire Leprince
- Division of Cariology and Endodontology, University Clinics of Dental Medicine (CUMD), University of Geneva, 1211 Geneva, Switzerland; (A.B.); (J.G.L.)
| | - Serge Bouillaguet
- Division of Cariology and Endodontology, University Clinics of Dental Medicine (CUMD), University of Geneva, 1211 Geneva, Switzerland; (A.B.); (J.G.L.)
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, University of Geneva, 1205 Geneva, Switzerland; (F.M.); (N.G.); (C.C.); (J.S.); (V.L.)
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Le HQ, Chen SS, Duong CC, Nguyen NC, Nguyen TXQ, Chien IC, Hsiao SS. Assessment of temperature dynamics and microbial community responses in aerobic membrane bioreactors from mesophilic to hyper-thermophilic conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:65849-65865. [PMID: 39607663 DOI: 10.1007/s11356-024-35561-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 11/09/2024] [Indexed: 11/29/2024]
Abstract
This study investigates the impact of temperature variations on the performance of an aerobic membrane bioreactor (MBR) as it transitions from mesophilic (30 °C) to hyper-thermophilic (65 °C) conditions. The microbial community structure was analyzed using 16S rRNA gene sequencing to assess how temperature influences microbial diversity and composition. In mesophilic conditions, the system exhibited high alpha diversity with a Shannon index of 5.92 and 224 observed species. As the temperature increased to 45 °C and 65 °C, diversity decreased significantly, with Shannon indices of 2.54 and 2.82, and 96 and 77 observed species, respectively. Additionally, nutrient removal efficiency, particularly for ammonia and phosphorus, declined at higher temperatures. COD removal efficiency reached 96.5% at 30 °C but decreased to 57% at 45 °C before recovering to 94% at 65 °C. Notably, biomass yield at hyper-thermophilic conditions was 37% lower than at mesophilic conditions, with a yield of 0.06 gVSS/gCODremoved. These findings highlight the potential advantages of operating under hyper-thermophilic conditions, including reduced sludge production, lower nutrient requirements, and increased organic loading capacity. The results provide valuable insights into optimizing high-temperature wastewater treatment processes for more efficient and sustainable industrial applications.
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Affiliation(s)
- Huy Quang Le
- Institute of Environmental Engineering and Management, National Taipei University of Technology, No.1, Sec. 3, Zhongxiao E. Rd., Taipei, 10608, Taiwan
- Faculty of Chemistry and Environment, Dalat University, 01 Phu Dong Thien Vuong Street, Da Lat City, 66000, Vietnam
| | - Shiao-Shing Chen
- Institute of Environmental Engineering and Management, National Taipei University of Technology, No.1, Sec. 3, Zhongxiao E. Rd., Taipei, 10608, Taiwan.
| | - Chinh Cong Duong
- Southern Institute of Water Resources Research, 658 Vo Van Kiet Street, District 5, Ho Chi Minh City, 700000, Vietnam
| | - Nguyen Cong Nguyen
- Faculty of Chemistry and Environment, Dalat University, 01 Phu Dong Thien Vuong Street, Da Lat City, 66000, Vietnam
| | - Thi Xuan Quynh Nguyen
- Institute of Environmental Engineering and Management, National Taipei University of Technology, No.1, Sec. 3, Zhongxiao E. Rd., Taipei, 10608, Taiwan
| | - I-Chieh Chien
- Department of Water Resources and Environmental Engineering, Tamkang University, New Taipei City, 251301, Taiwan
| | - Shiang-Sheng Hsiao
- Institute of Environmental Engineering and Management, National Taipei University of Technology, No.1, Sec. 3, Zhongxiao E. Rd., Taipei, 10608, Taiwan
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Lu H, Chen L. Ideonella margarita sp. nov., Ideonella lacteola sp. nov., Pseudaquabacterium inlustre sp. nov. and Pseudaquabacterium rugosum sp. nov., isolated from streams in China and re-examining the taxonomic status of all the genera within the family Sphaerotilaceae. Int J Syst Evol Microbiol 2024; 74. [PMID: 39196633 DOI: 10.1099/ijsem.0.006495] [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] [Indexed: 08/29/2024] Open
Abstract
Four Gram-stain-negative, aerobic, rod-shaped and motile strains (LYT19WT, DXS22WT, DXS29WT and BYS139WT) were isolated from streams in China. All four strains showed highest 16S rRNA gene sequence similarities to the species of genus Ideonella. The calculated average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values among strains LYT19WT, DXS22WT, DXS29WT, BYS139WT and other closely related strains were less than 79.5, 22.5 and 74.0%, respectively, indicating that each of the four strains should represent an independent novel species. The further reconstructed phylogenomic tree showed that strains LYT19WT and DXS29WT clustered closely with Ideonella strains, but strains DXS22WT and BYS139WT formed an independent clade with Aquabacterium terrae and Aquabacterium pictum. Comparing with other Aquabacterium species, A. terrae and A. pictum harboured distinct physiological and genetic characteristics, so it was reasonable to propose a novel genus Pseudaquabacterium to accommodate A. terrae, A. pictum, DXS22WT and BYS139WT. The major fatty acids of the four strains contained C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and one unidentified aminophospholipid. Combining above descriptions, strains LYT19WT and DXS29WT should represent two novel species of the genus Ideonella, for which the names Ideonella margarita sp. nov. (type strain LYT19WT=GDMCC 1.3205T=KCTC 92545T) and Ideonella lacteola sp. nov. (type strain DXS29WT=GDMCC 1.3207T=KCTC 92547T) are proposed, respectively. Strains DXS22WT and BYS139WT should represent two novel species of the new genus Pseudaquabacterium, for which the names Pseudaquabacterium inlustre sp. nov. (type strain DXS22WT=GDMCC 1.3206T=KCTC 92546T) and Pseudaquabacterium rugosum sp. nov. (type strain BYS139WT=GDMCC 1.3208T=KCTC 92548T) are proposed, respectively.
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Affiliation(s)
- Huibin Lu
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
| | - Li Chen
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
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Musilova J, Kourilova X, Hermankova K, Bezdicek M, Ieremenko A, Dvorak P, Obruca S, Sedlar K. Genomic and phenotypic comparison of polyhydroxyalkanoates producing strains of genus Caldimonas/ Schlegelella. Comput Struct Biotechnol J 2023; 21:5372-5381. [PMID: 37965057 PMCID: PMC10641440 DOI: 10.1016/j.csbj.2023.10.051] [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: 09/27/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs) have emerged as an environmentally friendly alternative to conventional polyesters. In this study, we present a comprehensive analysis of the genomic and phenotypic characteristics of three non-model thermophilic bacteria known for their ability to produce PHAs: Schlegelella aquatica LMG 23380T, Caldimonas thermodepolymerans DSM 15264, and C. thermodepolymerans LMG 21645 and the results were compared with the type strain C. thermodepolymerans DSM 15344T. We have assembled the first complete genomes of these three bacteria and performed the structural and functional annotation. This analysis has provided valuable insights into the biosynthesis of PHAs and has allowed us to propose a comprehensive scheme of carbohydrate metabolism in the studied bacteria. Through phylogenomic analysis, we have confirmed the synonymity between Caldimonas and Schlegelella genera, and further demonstrated that S. aquatica and S. koreensis, currently classified as orphan species, belong to the Caldimonas genus.
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Affiliation(s)
- Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Xenie Kourilova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Kristyna Hermankova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Matej Bezdicek
- Department of Internal Medicine – Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Anastasiia Ieremenko
- Department of Experimental Biology (Section of Microbiology, Microbial Bioengineering Laboratory), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavel Dvorak
- Department of Experimental Biology (Section of Microbiology, Microbial Bioengineering Laboratory), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Stanislav Obruca
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
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Obruča S, Dvořák P, Sedláček P, Koller M, Sedlář K, Pernicová I, Šafránek D. Polyhydroxyalkanoates synthesis by halophiles and thermophiles: towards sustainable production of microbial bioplastics. Biotechnol Adv 2022; 58:107906. [DOI: 10.1016/j.biotechadv.2022.107906] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 01/10/2023]
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Schlegelella koreensis sp. nov., isolated from evaporator core of automobile air conditioning system. Arch Microbiol 2021; 203:2373-2378. [PMID: 33661313 DOI: 10.1007/s00203-021-02206-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/18/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
A white-coloured, aerobic, and rod-shaped bacterium, designated strain ID0723T was isolated from evaporator core of automobile air conditioning system. The strain was Gram-stain-negative, catalase positive, oxidase negative, and grew at pH 5.5-9.5, at temperature 18-37 °C, and at 0-2.0% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence data revealed that the strain ID0723T was affiliated to the genus Schlegelella, with the closest phylogenetic member being Schlegelella brevitalea DSM 7029 T (98.1% sequence similarity). The chemotaxonomic features of strain ID0723T were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as the main polar lipids; Q-8 as an only ubiquinone; and summed feature 3 (C16:1ω7c and/or C16: 1ω6c), C16:0, and summed feature 8 (C18:1ω7c/or C18:1ω6c) as the major fatty acids. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization values between strain ID0723T and S. brevitalea DSM 7029 T were 74.8% and 20.0%, respectively, which were below the cut-off values of 95% and 70%, respectively. The DNA G + C content was 69.9 mol%. The polyphasic taxonomic data clearly indicated that strain ID0723T represents a novel species in the genus Schlegelella for which the name Schlegelella koreensis sp. nov. is proposed, with the type strain ID0723T (= KCTC 72731 T = NBRC 114611 T).
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Discovering symbiosis in the supralittoral: bacterial metabarcoding analysis from the hepatopancreas of Orchestia and Tylos (Crustacea). Symbiosis 2021. [DOI: 10.1007/s13199-021-00749-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Medina-Pascual MJ, Monzón S, Villalón P, Cuesta I, González-Romo F, Valdezate S. Saezia sanguinis gen. nov., sp. nov., a Betaproteobacteria member of order Burkholderiales, isolated from human blood. Int J Syst Evol Microbiol 2020; 70:2016-2025. [PMID: 32003711 DOI: 10.1099/ijsem.0.004010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of an unknown bacterial strain designated CNM695-12, isolated from the blood of an immunocompromised subject, was investigated via phenotypic, chemotaxonomic, genotypic and genomic analyses. Bacterial cells were determined to be Gram-stain-negative bacilli, aerobic, non-motile and non-spore-forming. The strain showed catalase activity but no oxidase activity. Optimal growth occurred at 37 °C, pH 7 and with 0-1 % NaCl. C16 : 0, summed feature 8 (comprising C18 : 1ω7c /C18:1 ω6c), and C18 : 1ω9c were the most abundant fatty acids, and ubiquinone 8 was the major respiratory quinone. The polar lipids present included phosphatidylglycerol, phosphatidylethanolamine and other aminophospholipids. The 16S rRNA gene sequence showed approximately 93.5 % similarity to those of different species with validly published names within the order Burkholderiales (e.g. Leptothrix mobilis Feox-1T, Aquabacterium commune B8T , Aquabacterium citratiphilum B4T and Schlegelella thermodepolymerans K14T). Phylogenetic analyses based on 16S rRNA gene sequences and concatenated alignments including the sequences for 107 essential proteins, revealed the strain to form a novel lineage close to members of the family Comamonadaceae. The highest average nucleotide identity and average amino acid identity values were obtained with Schlegelella thermodepolymerans K14T (69.6 and 55.7 % respectively). The genome, with a size of 3.35 Mb, had a DNA G+C content of 52.4 mol% and encoded 3056 predicted genes, 3 rRNA, 1 transfer-messengerRNA and 51 tRNA. Strain CNM695-12 thus represents a novel species belonging to a novel genus within the order Burkholderiales, for which the name Saezia sanguinis gen. nov., sp. nov. is proposed. The type strain is CNM695-12T (=DSM 104959T=CECT 9208T).
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Affiliation(s)
- María J Medina-Pascual
- Laboratorio de Referencia e Investigación en Taxonomía. Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Sara Monzón
- Unidad de Bioinformática (BU-ISCIII). Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Pilar Villalón
- Laboratorio de Referencia e Investigación en Taxonomía. Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Isabel Cuesta
- Unidad de Bioinformática (BU-ISCIII). Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Sylvia Valdezate
- Laboratorio de Referencia e Investigación en Taxonomía. Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Tang B, Yu Y, Liang J, Zhang Y, Bian X, Zhi X, Ding X. Reclassification of ' Polyangium brachysporum' DSM 7029 as Schlegelella brevitalea sp. nov. Int J Syst Evol Microbiol 2019; 69:2877-2883. [PMID: 31274403 DOI: 10.1099/ijsem.0.003571] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Strain DSM 7029, isolated from a soil sample in Greece, can produce antitumour glidobactins, and has been found, as a heterologous host, to produce useful nonribosomal peptide synthetase-polyketide synthase hybrid molecules known as epothilones. This strain was originally named 'Polyangium brachysporum' of the family Polyangiaceae and the order Myxococcales. However, phylogenetic analysis of the 16S rRNA gene sequence of strain DSM 7029 indicated that it was clustered with members of Schlegelella. Significant growth occurred at 25-42 °C, pH 5.0-10.0 and in the presence of 0-0.2 % (w/v) NaCl. The predominant ubiquinone was Q-8. The major fatty acids were C16 : 1ω7c/C16 : 1ω6c, C16 : 0 and C18 : 1ω7c. The G+C content of genomic DNA was 67.51 mol%. The strain was clearly distinguishable from other neighbouring Schlegelella members and genera Caldimonas and Zhizhongheella, using phylogenetic analysis, fatty acid composition data and a range of physiological and biochemical characteristics and genome analysis. Therefore, strain DSM 7029 represents a novel species of the genus Schlegelella, for which the name Schlegelella brevitalea sp. nov. is proposed.
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Affiliation(s)
- Biao Tang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China.,Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Yucong Yu
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Junheng Liang
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, PR China
| | - Xiaoying Bian
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266235, PR China
| | - Xiaoyang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Xiaoming Ding
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200438, PR China
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Chopyk J, Chattopadhyay S, Kulkarni P, Claye E, Babik KR, Reid MC, Smyth EM, Hittle LE, Paulson JN, Cruz-Cano R, Pop M, Buehler SS, Clark PI, Sapkota AR, Mongodin EF. Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens. MICROBIOME 2017; 5:22. [PMID: 28202080 PMCID: PMC5312438 DOI: 10.1186/s40168-017-0235-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 01/24/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. To address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a commercially-mentholated product. Total genomic DNA was extracted using a multi-step enzymatic and mechanical lysis protocol followed by PCR amplification of the V3-V4 hypervariable regions of the 16S rRNA gene from five cigarette products (18 cigarettes per product for a total of 90 samples): Camel Crush, user-mentholated Camel Crush, Camel Kings, custom-mentholated Camel Kings, and Newport Menthols. Sequencing was performed on the Illumina MiSeq platform and sequences were processed using the Quantitative Insights Into Microbial Ecology (QIIME) software package. RESULTS In all products, Pseudomonas was the most abundant genera and included Pseudomonas oryzihabitans and Pseudomonas putida, regardless of mentholation status. However, further comparative analysis of the five products revealed significant differences in the bacterial compositions across products. Bacterial community richness was higher among non-mentholated products compared to those that were mentholated, particularly those that were custom-mentholated. In addition, mentholation appeared to be correlated with a reduction in potential human bacterial pathogens and an increase in bacterial species resistant to harsh environmental conditions. CONCLUSIONS Taken together, these data provide preliminary evidence that the mentholation of commercially available cigarettes can impact the bacterial community of these products.
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Affiliation(s)
- Jessica Chopyk
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD USA
| | - Suhana Chattopadhyay
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD USA
| | - Prachi Kulkarni
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD USA
| | - Emma Claye
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD USA
| | - Kelsey R. Babik
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD USA
| | - Molly C. Reid
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD USA
| | - Eoghan M. Smyth
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD USA
- School of Medicine, Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, 801 West Baltimore Street, Office #622, Baltimore, MD 21201 USA
| | - Lauren E. Hittle
- School of Medicine, Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, 801 West Baltimore Street, Office #622, Baltimore, MD 21201 USA
| | - Joseph N. Paulson
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | - Raul Cruz-Cano
- Department of Epidemiology and Biostatistics, University of Maryland School of Public Health, College Park, MD USA
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | | | - Pamela I. Clark
- Department of Behavioral and Community Health, University of Maryland School of Public Health, College Park, MD USA
| | - Amy R. Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD USA
| | - Emmanuel F. Mongodin
- School of Medicine, Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, 801 West Baltimore Street, Office #622, Baltimore, MD 21201 USA
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Bacterial Diversity Associated with the Coccolithophorid Algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii. BIOMED RESEARCH INTERNATIONAL 2015; 2015:194540. [PMID: 26273594 PMCID: PMC4529885 DOI: 10.1155/2015/194540] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/30/2015] [Indexed: 02/01/2023]
Abstract
Coccolithophores are unicellular calcifying marine phytoplankton that can form large and conspicuous blooms in the oceans and make significant contributions to oceanic carbon cycling and atmospheric CO2 regulation. Despite their importance, the bacterial diversity associated with these algae has not been explored for ecological or biotechnological reasons. Bacterial membership of Emiliania huxleyi and Coccolithus pelagicus f. braarudii cultures was assessed using cultivation and cultivation-independent methods. The communities were species rich compared to other phytoplankton cultures. Community analysis identified specific taxa which cooccur in all cultures (Marinobacter and Marivita). Hydrocarbon-degrading bacteria were found in all cultures. The presence of Acidobacteria, Acidimicrobidae, Schlegelella, and Thermomonas was unprecedented but were potentially explained by calcification associated with coccolith production. One strain of Acidobacteria was cultivated and is closely related to a marine Acidobacteria isolated from a sponge. From this assessment of the bacterial diversity of coccolithophores, a number of biotechnological opportunities are evident, from bioprospecting for novel taxa such as Acidobacteria to helping understand the relationship between obligate hydrocarbonoclastic bacteria occurrence with phytoplankton and to revealing bacterial taxa that have a specific association with algae and may be suitable candidates as a means to improve the efficiency of mass algal cultivation.
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12
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Dong L, Ming H, Liu L, Zhou EM, Yin YR, Duan YY, Nie GX, Feng HG, Li WJ. Zhizhongheella caldifontis gen. nov., sp. nov., a novel member of the family Comamonadaceae. Antonie van Leeuwenhoek 2014; 105:755-61. [PMID: 24515725 DOI: 10.1007/s10482-014-0131-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/29/2014] [Indexed: 10/25/2022]
Abstract
An alkalitolerant, thermotolerant, strictly aerobic and Gram-staining negative bacterial strain, designated YIM 78140(T), was isolated from a water sample in Hehua hot spring, Tengchong, Yunnan province, south-west China. The colonies were light brown, convex and circular. Phylogenetic analysis of the 16S rRNA gene sequence of strain YIM 78140(T) indicated that it was clustered with members of β-Proteobacteria (with the similarity from 96.9 to 93.6 %). Good growth occurred at 40-50 °C, pH 8.0-9.0 and in the presence of 0-3 % (w/v) NaCl. The predominant ubiquinones were Q-8 and Q-9. The major fatty acids were C16:0, C17:0 cyclo, C18:1 ω7c and summed feature 3. The G+C content of genomic DNA was 70.8 mol%. The results of physiological and biochemical characteristics, phylogenetic analysis allowed the phenotypic and genotypic differentiation of strain YIM 78140(T) from its closest phylogenetic neighbours. Therefore, the strain YIM 78140(T) represents a novel genus of the family Comamonadaceae, for which the name Zhizhongheella caldifontis gen. nov., sp. nov. is proposed. The type strain is YIM 78140(T) (= BCRC 80649(T) = KCTC 32557(T)).
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Affiliation(s)
- Lei Dong
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
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Witzig M, Boguhn J, Kleinsteuber S, Fetzer I, Rodehutscord M. Effect of the corn silage to grass silage ratio and feed particle size of diets for ruminants on the ruminal Bacteroides-Prevotella community in vitro. Anaerobe 2010; 16:412-9. [PMID: 20493960 DOI: 10.1016/j.anaerobe.2010.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 05/04/2010] [Accepted: 05/05/2010] [Indexed: 11/15/2022]
Abstract
This study examined whether different corn silage to grass silage ratios in ruminant rations and different grinding levels of the feed affect the composition of the ruminal Bacteroides-Prevotella community in vitro. Three diets, composed of 10% soybean meal as well as of different corn silage and grass silage proportions, were ground through 1mm or 4mm screened sieves and incubated in a semi-continuous rumen simulation system. On day 14 of the incubation microbes were harvested by centrifugation from the liquid effluent of fermenter vessels. Microbial DNA was extracted for single strand conformation polymorphism (SSCP) analysis of 16S rRNA genes followed by sequencing of single SSCP bands. Fluorescence in situ hybridization (FISH) and real-time quantitative (q) PCR were used to quantify differences in the relative abundance of Bacteroides-Prevotella and Prevotella bryantii. SSCP profiles revealed a significant influence of the forage source as well as of the feed particle size on the community structure of the Bacteroides-Prevotella group. Different, phylogenetically distinct, so far uncultured Prevotella species were detected by sequence analysis of several treatment-dependent occurring SSCP bands indicating different nutritional requirements of these organisms for growth. No quantitative differences in the occurrence of Bacteroides-Prevotella-related species were detected between diets by FISH with probe BAC303. However, real-time qPCR data revealed a higher abundance of P. bryantii with increasing grass silage to corn silage ratio, thus again indicating changes within the community composition of the Bacteroides-Prevotella group. As P. bryantii possesses high proteolytic activity its higher abundance may have been caused by the higher contents of crude protein in the grass silage containing diets. To conclude, results of this study show an influence of the forage source on the ruminal community of Bacteroides-Prevotella. Furthermore, they suggest an effect of the feed particle size on this bacterial group.
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Affiliation(s)
- M Witzig
- Universität Hohenheim, Institut für Tierernährung, Emil-Wolff-Strasse 10, Stuttgart, Germany.
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