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Sohn J, Li L, Zhang L, Settem PR, Honma K, Sharma A, Falkner KL, Novak JM, Sun Y, Kirkwood KL. Porphyromonas gingivalis
indirectly elicits intestinal inflammation by altering the gut microbiota and disrupting epithelial barrier function through IL9‐producing CD4
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T cells. Mol Oral Microbiol 2021; 37:42-52. [DOI: 10.1111/omi.12359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/29/2021] [Accepted: 12/22/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Jiho Sohn
- Genetics, Genomics, and Bioinformatics Program State University of New York at Buffalo University at Buffalo NY USA
- Department of Medicine State University of New York at Buffalo University at Buffalo NY USA
- Department of Oral Biology State University of New York at Buffalo University at Buffalo NY USA
| | - Lu Li
- Department of Oral Biology State University of New York at Buffalo University at Buffalo NY USA
| | - Lixia Zhang
- Department of Oral Biology State University of New York at Buffalo University at Buffalo NY USA
| | - Prasad R. Settem
- Department of Medicine State University of New York at Buffalo University at Buffalo NY USA
| | - Kiyonobu Honma
- Department of Oral Biology State University of New York at Buffalo University at Buffalo NY USA
| | - Ashu Sharma
- Department of Oral Biology State University of New York at Buffalo University at Buffalo NY USA
| | - Karen L. Falkner
- Department of Oral Biology State University of New York at Buffalo University at Buffalo NY USA
| | - Jan M. Novak
- Department of Medicine State University of New York at Buffalo University at Buffalo NY USA
| | - Yijun Sun
- Department of Microbiology and Immunology State University of New York at Buffalo University at Buffalo NY USA
| | - Keith L. Kirkwood
- Department of Medicine State University of New York at Buffalo University at Buffalo NY USA
- Department of Head & Neck/Plastic & Reconstructive Surgery Roswell Park Comprehensive Cancer Center Buffalo NY USA
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Pontefract A, Zhu TF, Walker VK, Hepburn H, Lui C, Zuber MT, Ruvkun G, Carr CE. Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars. Front Microbiol 2017; 8:1819. [PMID: 29018418 PMCID: PMC5623196 DOI: 10.3389/fmicb.2017.01819] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/06/2017] [Indexed: 11/13/2022] Open
Abstract
Life can persist under severe osmotic stress and low water activity in hypersaline environments. On Mars, evidence for the past presence of saline bodies of water is prevalent and resulted in the widespread deposition of sulfate and chloride salts. Here we investigate Spotted Lake (British Columbia, Canada), a hypersaline lake with extreme (>3 M) levels of sulfate salts as an exemplar of the conditions thought to be associated with ancient Mars. We provide the first characterization of microbial structure in Spotted Lake sediments through metagenomic sequencing, and report a bacteria-dominated community with abundant Proteobacteria, Firmicutes, and Bacteroidetes, as well as diverse extremophiles. Microbial abundance and functional comparisons reveal similarities to Ace Lake, a meromictic Antarctic lake with anoxic and sulfidic bottom waters. Our analysis suggests that hypersaline-associated species occupy niches characterized foremost by differential abundance of Archaea, uncharacterized Bacteria, and Cyanobacteria. Potential biosignatures in this environment are discussed, specifically the likelihood of a strong sulfur isotopic fractionation record within the sediments due to the presence of sulfate reducing bacteria. With its high sulfate levels and seasonal freeze-thaw cycles, Spotted Lake is an analog for ancient paleolakes on Mars in which sulfate salt deposits may have offered periodically habitable environments, and could have concentrated and preserved organic materials or their biomarkers over geologic time.
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Affiliation(s)
- Alexandra Pontefract
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
| | - Ting F Zhu
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | - Holli Hepburn
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
| | - Clarissa Lui
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Maria T Zuber
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Christopher E Carr
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
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Brown DR, Whitcomb RF, Bradbury JM. Revised minimal standards for description of new species of the class Mollicutes (division Tenericutes). Int J Syst Evol Microbiol 2008; 57:2703-2719. [PMID: 17978244 DOI: 10.1099/ijs.0.64722-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Minimal standards for novel species of the class Mollicutes (trivial term, mollicutes), last published in 1995, require revision. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes proposes herein revised standards that reflect recent advances in molecular systematics and the species concept for prokaryotes. The mandatory requirements are: (i) deposition of the type strain into two recognized culture collections, preferably located in different countries; (ii) deposition of the 16S rRNA gene sequence into a public database, and a phylogenetic analysis of the relationships among the 16S rRNA gene sequences of the novel species and its neighbours; (iii) deposition of antiserum against the type strain into a recognized collection; (iv) demonstration, by using the combination of 16S rRNA gene sequence analyses, serological analyses and supplementary phenotypic data, that the type strain differs significantly from all previously named species; and (v) assignment to an order, a family and a genus in the class, with an appropriate specific epithet. The 16S rRNA gene sequence provides the primary basis for assignment to hierarchical rank, and may also constitute evidence of species novelty, but serological and supplementary phenotypic data must be presented to substantiate this. Serological methods have been documented to be congruent with DNA-DNA hybridization data and with 16S rRNA gene placements. The novel species must be tested serologically to the greatest extent that the investigators deem feasible against all neighbouring species whose 16S rRNA gene sequences show >0.94 similarity. The investigator is responsible for justifying which characters are most meaningful for assignment to the part of the mollicute phylogenetic tree in which a novel species is located, and for providing the means by which novel species can be identified by other investigators. The publication of the description should appear in a journal having wide circulation. If the journal is not the International Journal of Systematic and Evolutionary Microbiology, copies of the publication must be submitted to that journal so that the name may be considered for inclusion in a Validation List as required by the International Code of Bacteriological Nomenclature (the Bacteriological Code). Updated informal descriptions of the class Mollicutes and some of its constituent higher taxa are available as supplementary material in IJSEM Online.
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Affiliation(s)
- Daniel R Brown
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610-0880, USA
| | - Robert F Whitcomb
- Collaborator, Vegetable Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Beltsville, MD 20705, USA
| | - Janet M Bradbury
- Department of Veterinary Pathology, University of Liverpool, Leahurst, Neston, CH64 7TE, UK
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Stakenborg T, Vicca J, Verhelst R, Butaye P, Maes D, Naessens A, Claeys G, De Ganck C, Haesebrouck F, Vaneechoutte M. Evaluation of tRNA gene PCR for identification of mollicutes. J Clin Microbiol 2005; 43:4558-66. [PMID: 16145107 PMCID: PMC1234151 DOI: 10.1128/jcm.43.9.4558-4566.2005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated the applicability of tRNA gene PCR in combination with fluorescent capillary electrophoresis with an ABI310 genetic analyzer (Applied Biosystems, Calif.) for the identification of different mollicute species. A total of 103 strains and DNA extracts of 30 different species belonging to the genera Acholeplasma, Mycoplasma, and Ureaplasma were studied. Reproducible peak profiles were generated for all samples, except for one M. genitalium isolate, the three M. gallisepticum isolates, and 8 of the 24 Ureaplasma cultures, where no amplification could be obtained. Clustering revealed numerous discrepancies compared to the identifications that had been previously obtained by means of biochemical and serological tests. Final identification was obtained by 16S rRNA gene amplification followed by sequence analysis and/or restriction digestion. This confirmed the identification obtained by tRNA gene PCR in all cases. Seven samples yielded an unexpected tRNA gene PCR profile. Sequence analysis of the 16S rRNA genes showed that six of these samples were mixed and that one had a unique sequence that did not match any of the published sequences, pointing to the existence of a not-yet-described species. In conclusion, we found tRNA gene PCR to be a rapid and discriminatory method to correctly identify a large collection of different species of the class of Mollicutes and to recognize not-yet-described groups.
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Affiliation(s)
- Tim Stakenborg
- Veterinary and Agrochemical Research Center, Brussels, Belgium
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Schaeffer WI, Olson LD, Barile MF, Sun FW. Analysis of Mycoplasma hyorhinis DNA in the presence of host cells without growing the mycoplasma axenically. J Bacteriol 1991; 173:1382-7. [PMID: 1671671 PMCID: PMC207274 DOI: 10.1128/jb.173.4.1382-1387.1991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mycoplasma hyorhinis coisolates with the mitochondria of the cells in which it is carried as an infection. Since both mitochondria and mycoplasmas synthesize DNA by using the prokaryotic DNA polymerase gamma, the use of aphidicolin, which inhibits eukaryotic DNA polymerase alpha, allows for selective synthesis of mycoplasmal and mitochondrial DNA. The restriction patterns of mitochondria and mycoplasmas can easily be differentiated from each other in mixtures of both DNAs. Thus, it is possible to study the molecular biology of this noncultivable mycoplasma in situ rather than after growth in artificial media, with its potential genetic consequences during adjustment to axenic growth.
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Affiliation(s)
- W I Schaeffer
- Department of Microbiology and Molecular Genetics, Colleges of Agriculture and Life Sciences, University of Vermont, Burlington 05405
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