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Shaikh HFM, Oswal PU, Kugaji MS, Katti SS, Bhat KG, Kandaswamy E, Joshi VM. Association of F. alocis and D. pneumosintes with Periodontitis Disease Severity and Red Complex Bacteria. Dent J (Basel) 2024; 12:105. [PMID: 38668017 PMCID: PMC11048763 DOI: 10.3390/dj12040105] [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: 02/22/2024] [Revised: 03/21/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Oral biofilms are considered the principal etiological agent in the development of periodontitis. Novel species that may contribute to periodontitis and dysbiosis have been identified recently. The study aims to evaluate the presence of F. alocis and D. pneumosintes in healthy and diseased patients and their association with clinical parameters and with red complex bacteria. The study included 60 subjects, with 30 patients each in the healthy and periodontitis groups. The clinical parameters were noted, and samples were subjected to DNA extraction followed by a polymerase chain reaction. Statistical analysis was performed using the Graph Pad Prism software. Results: F. alocis and D. pneumosintes were detected at a significantly higher percentage in the periodontitis group compared to the healthy group (p < 0.05). D. pneumosintes was significantly associated with T. forsythia in the periodontitis group (p < 0.05). Both of these organisms were present in sites with higher clinical attachment loss (p < 0.05). This study demonstrated that both F. alocis and D. pneumosintes were detected at a significantly higher percentage in periodontitis subjects and were detected more frequently in sites with a greater clinical attachment loss. It was also evident that both F. alocis and D. pneumosintes can be present independently of other putative periodontal pathogens.
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Affiliation(s)
- Hawaabi F. M. Shaikh
- Department of Periodontology, Maratha Mandal’s Nathajirao G. Halgekar Institute of Dental Sciences & Research Centre, Belagavi 590019, India; (H.F.M.S.); (P.U.O.); (S.S.K.)
| | - Pratima U. Oswal
- Department of Periodontology, Maratha Mandal’s Nathajirao G. Halgekar Institute of Dental Sciences & Research Centre, Belagavi 590019, India; (H.F.M.S.); (P.U.O.); (S.S.K.)
| | - Manohar Suresh Kugaji
- Centre for Advanced Medical Research, BLDE Deemed to be University, Vijayapura 586103, India
| | - Sandeep S. Katti
- Department of Periodontology, Maratha Mandal’s Nathajirao G. Halgekar Institute of Dental Sciences & Research Centre, Belagavi 590019, India; (H.F.M.S.); (P.U.O.); (S.S.K.)
| | | | - Eswar Kandaswamy
- Department of Periodontics, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, LA 70119, USA;
| | - Vinayak M. Joshi
- Department of Periodontics, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, LA 70119, USA;
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Kitagawa H, Tadera K, Omori K, Nomura T, Shigemoto N, Ohge H. A case of bacteremia caused by Dialister micraerophilus with Enterocloster clostridioformis and Eggerthella lenta in a patient with pyometra. BMC Infect Dis 2024; 24:128. [PMID: 38267864 PMCID: PMC10809547 DOI: 10.1186/s12879-024-08999-6] [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: 08/02/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Infection by Dialister micraerophilus, an obligate anaerobic gram-negative bacillus, has rarely been described, and its clinical characteristics remain unclear. CASE PRESENTATION We report a case of bacteremia caused by D. micraerophilus, Enterocloster clostridioformis, and Eggerthella lenta in a 47-year-old woman, associated with pyometra. D. micraerophilus was identified using 16S rRNA gene sequencing and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. D. micraerophilus was detected by polymerase chain reaction using D. micraerophilus-specific primers and E. clostridioformis and E. lenta was isolated from the drainage pus sample obtained from the pyometra uterus. The patient achieved a cure after abscess drainage and 2-week antibiotic treatment. CONCLUSIONS To the best of our knowledge, this is the first report of D. micraerophilus bacteremia. D. micraerophilus may be associated with gynecological infections. Clinicians should consider both oral and gynecological sites when searching to identify the focus of D. micraerophilus infection.
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Affiliation(s)
- Hiroki Kitagawa
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan.
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University , Hiroshima, Japan.
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan.
| | - Kayoko Tadera
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Section of Clinical Laboratory, Division of Clinical Support, Hiroshima University Hospital, Hiroshima, Japan
- Division of Laboratory Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Keitaro Omori
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Toshihito Nomura
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Norifumi Shigemoto
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University , Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Translational Research Center, Hiroshima University, Hiroshima, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
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3
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Vals-Delgado C, Alcala-Diaz JF, Molina-Abril H, Roncero-Ramos I, Caspers MPM, Schuren FHJ, Van den Broek TJ, Luque R, Perez-Martinez P, Katsiki N, Delgado-Lista J, Ordovas JM, van Ommen B, Camargo A, Lopez-Miranda J. An altered microbiota pattern precedes Type 2 diabetes mellitus development: From the CORDIOPREV study. J Adv Res 2022; 35:99-108. [PMID: 35024196 PMCID: PMC8721255 DOI: 10.1016/j.jare.2021.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 12/12/2022] Open
Abstract
Type 2 diabetes (T2DM) increases the risk of recurrence in myocardial infarction patients. A gut microbiota profile is associated to the further T2DM development. Microbiome data improved the prediction of T2DM development when added to clinical parameters. A risk score including the most predictive genera was associated with the probability of T2DM. A high risk score was associated with a higher hepatic insulin resistance and β-cell dysfunction.
Introduction A distinctive gut microbiome have been linked to type 2 diabetes mellitus (T2DM). Objectives We aimed to evaluate whether gut microbiota composition, in addition to clinical biomarkers, could improve the prediction of new incident cases of diabetes in patients with coronary heart disease. Methods All the patients from the CORDIOPREV (Clinical Trials.gov.Identifier: NCT00924937) study without T2DM at baseline were included (n = 462). Overall, 107 patients developed it after a median of 60 months. The gut microbiota composition was determined by 16S rRNA gene sequencing and predictive models were created using hold-out method. Results A gut microbiota profile associated with T2DM development was determined through a microbiome-based predictive model. The addition of microbiome data to clinical parameters (variables included in FINDRISC risk score and the diabetes risk score of the American Diabetes Association, HDL, triglycerides and HbA1c) improved the prediction increasing the area under the curve from 0.632 to 0.946. Furthermore, a microbiome-based risk score including the ten most discriminant genera, was associated with the probability of develop T2DM. Conclusion These results suggest that a microbiota profile is associated to the T2DM development. An integrate predictive model of microbiome and clinical data that can improve the prediction of T2DM is also proposed, if is validated in independent populations to prevent this disease.
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Affiliation(s)
- Cristina Vals-Delgado
- Lipids and Atherosclerosis Unit, Internal Medicine Unit, Reina Sofia University Hospital, Córdoba 14004, Spain.,Maimonides Biomedical Research Institute of Cordoba (IMIBIC)/University of Cordoba/Reina Sofia University Hospital, Córdoba 14004, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Juan F Alcala-Diaz
- Lipids and Atherosclerosis Unit, Internal Medicine Unit, Reina Sofia University Hospital, Córdoba 14004, Spain.,Maimonides Biomedical Research Institute of Cordoba (IMIBIC)/University of Cordoba/Reina Sofia University Hospital, Córdoba 14004, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Helena Molina-Abril
- Department of Applied Mathematics I, University of Seville, Seville 41012, Spain
| | - Irene Roncero-Ramos
- Lipids and Atherosclerosis Unit, Internal Medicine Unit, Reina Sofia University Hospital, Córdoba 14004, Spain.,Maimonides Biomedical Research Institute of Cordoba (IMIBIC)/University of Cordoba/Reina Sofia University Hospital, Córdoba 14004, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Martien P M Caspers
- Netherlands Institute for Applied Science (TNO), Research Group Microbiology & Systems Biology, Zeist NL-3704 HE, the Netherlands
| | - Frank H J Schuren
- Netherlands Institute for Applied Science (TNO), Research Group Microbiology & Systems Biology, Zeist NL-3704 HE, the Netherlands
| | - Tim J Van den Broek
- Netherlands Institute for Applied Science (TNO), Research Group Microbiology & Systems Biology, Zeist NL-3704 HE, the Netherlands
| | - Raul Luque
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Córdoba 14004, Spain
| | - Pablo Perez-Martinez
- Lipids and Atherosclerosis Unit, Internal Medicine Unit, Reina Sofia University Hospital, Córdoba 14004, Spain.,Maimonides Biomedical Research Institute of Cordoba (IMIBIC)/University of Cordoba/Reina Sofia University Hospital, Córdoba 14004, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Niki Katsiki
- First Department of Internal Medicine, Division of Endocrinology-Metabolism, Diabetes Center, AHEPA University Hospital, Thessaloniki 546 21, Greece
| | - Javier Delgado-Lista
- Lipids and Atherosclerosis Unit, Internal Medicine Unit, Reina Sofia University Hospital, Córdoba 14004, Spain.,Maimonides Biomedical Research Institute of Cordoba (IMIBIC)/University of Cordoba/Reina Sofia University Hospital, Córdoba 14004, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Jose M Ordovas
- Nutrition and Genomics Laboratory, J.M.-US Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, United States.,IMDEA Alimentacion, Madrid, Spain
| | - Ben van Ommen
- Netherlands Institute for Applied Science (TNO), Research Group Microbiology & Systems Biology, Zeist NL-3704 HE, the Netherlands
| | - Antonio Camargo
- Lipids and Atherosclerosis Unit, Internal Medicine Unit, Reina Sofia University Hospital, Córdoba 14004, Spain.,Maimonides Biomedical Research Institute of Cordoba (IMIBIC)/University of Cordoba/Reina Sofia University Hospital, Córdoba 14004, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Jose Lopez-Miranda
- Lipids and Atherosclerosis Unit, Internal Medicine Unit, Reina Sofia University Hospital, Córdoba 14004, Spain.,Maimonides Biomedical Research Institute of Cordoba (IMIBIC)/University of Cordoba/Reina Sofia University Hospital, Córdoba 14004, Spain.,CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
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Yang M, Luo P, Zhang F, Xu K, Feng R, Xu P. Large-scale correlation analysis of deep venous thrombosis and gut microbiota. Front Cardiovasc Med 2022; 9:1025918. [PMID: 36419497 PMCID: PMC9677955 DOI: 10.3389/fcvm.2022.1025918] [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: 08/23/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
Objective Although previous studies have shown that gut microbiota may be involved in the occurrence of deep venous thrombosis (DVT), the specific link between the two remains unclear. The present study aimed to explore this question from a genetic perspective. Materials and methods Genome-wide association study (GWAS) summary data of DVT were obtained from the UK Biobank (N = 9,059). GWAS summary data of the gut microbiota were obtained from the Flemish Gut Flora Project (N = 2,223) and two German cohorts (FoCus, N = 950; PopGen, N = 717). All the participants were of European ancestry. Linkage disequilibrium score (LDSC) regression has great potential for analyzing the heritability of disease or character traits. LDSC regression was used to analyze the genetic correlation between DVT and the gut microbiota based on the GWAS summary data obtained from previous studies. Mendelian randomization (MR) was used to analyze the genetic causal relationship between DVT and the gut microbiota. We used the random effects inverse variance weighted, MR Egger, weighted median, simple mode, and weighted mode to perform MR analysis. We performed a sensitivity analysis of the MR analysis results by examining heterogeneity and horizontal pleiotropy. Results Linkage disequilibrium score analysis showed that Streptococcaceae (correlation coefficient = -0.542, SE = 0.237, P = 0.022), Dialister (correlation coefficient = -0.623, SE = 0.316, P = 0.049), Streptococcus (correlation coefficient = -0.576, SE = 0.264, P = 0.029), and Lactobacillales (correlation coefficient = -0.484, SE = 0.237, P = 0.042) had suggestive genetic correlation with DVT. In addition, the MR analysis showed that Streptococcaceae had a positive genetic causal relationship with DVT (P = 0.027, OR = 1.005). There was no heterogeneity or horizontal pleiotropy in the MR analysis (P > 0.05). Conclusion In this study, four gut microbes (Streptococcaceae, Dialister Streptococcus, Lactobacillales) had suggestive genetic correlations with DVT, and Streptococcaceae had a positive causal relationship with DVT. Our findings provide a new research direction for the further study of and prevention of DVT.
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Affiliation(s)
- Mingyi Yang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Pan Luo
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ke Xu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ruoyang Feng
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Peng Xu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Dynamic Changes in Soil Microbial Communities with Glucose Enrichment in Sediment Microbial Fuel Cells. Indian J Microbiol 2021; 61:497-505. [PMID: 34744205 DOI: 10.1007/s12088-021-00959-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/17/2021] [Indexed: 12/21/2022] Open
Abstract
To investigate soil microbial community dynamics in sediment microbial fuel cells (MFCs), this study applied nonhydric (D) and hydric (S) soils to single-chamber and mediator-free MFCs. Glucose was also used to enrich microorganisms in the soils. The voltage outputs of both the D and S sediment MFCs increased over time but differed from each other. The initial open circuit potentials were 345 and 264 mV for the D and S MFCs. The voltage output reached a maximum of 503 and 604 mV for D and S on days 125 and 131, respectively. The maximum power densities of the D and S MFCs were 2.74 and 2.12 mW m-2, analyzed on day 50. Clustering results revealed that the two groups did not cluster after glucose supplementation and 126 days of MFC function. The change in Geobacter abundance was consistent with the voltage output, indicating that these bacteria may act as the main exoelectrogens on the anode. Spearman correlation analysis demonstrated that, in the D soils, Geobacter was positively correlated with Dialister and negatively correlated with Bradyrhizobium, Kaistobacter, Pedomicrobium, and Phascolarctobacterium; in the S soils, Geobacter was positively correlated with Shewanella and negatively correlated with Blautia. The results suggested that different soil sources in the MFCs and the addition of glucose as a nutrient produced diverse microbial communities with varying voltage output efficiencies. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-021-00959-x.
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The Dwindling Microbiota of Aerobic Vaginitis, an Inflammatory State Enriched in Pathobionts with Limited TLR Stimulation. Diagnostics (Basel) 2020; 10:diagnostics10110879. [PMID: 33126716 PMCID: PMC7692151 DOI: 10.3390/diagnostics10110879] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 01/04/2023] Open
Abstract
While bacterial vaginosis (BV) is a well-known type of vaginal dysbiosis, aerobic vaginitis (AV) is an inflammatory condition that remains understudied and under-recognised. It predisposes women to serious complications including urogenital infections and pregnancy problems. Here, we investigated the bacterial community in AV to explore its possible role in AV pathogenesis. We collected vaginal lavage fluid samples of women (n = 58) classified by wet-mount microscopy as suffering from AV or BV and included an asymptomatic reference group without signs of AV or BV. AV samples showed reduced absolute abundances of bacteria in general and specifically of lactobacilli by qPCR, but 16S rRNA gene sequencing and amplicon sequence variant analysis revealed that Lactobacillus remained the dominant taxon in 25% of the AV samples studied. The other AV samples showed high relative abundances of Streptococcus agalactiae and, unexpectedly, the anaerobes Gardnerella vaginalis and Prevotella bivia in more than half of the AV samples studied. Yet, despite increased relative abundance of these potential pathogens or pathobionts in the AV bacterial communities, the AV samples only slightly stimulated Toll-like receptor 4 and showed reduced activation of Toll-like receptor 2/6, receptors of two pathways central to mucosal immunity. Our findings indicate that the reduced total bacterial abundance with associated enrichment in certain pathobionts in AV might be mainly a consequence of the inflammatory conditions and/or altered hormonal regulation rather than bacteria being a major cause of the inflammation.
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Dahmana H, Raoult D, Fenollar F, Mediannikov O. Insecticidal Activity of Bacteria from Larvae Breeding Site with Natural Larvae Mortality: Screening of Separated Supernatant and Pellet Fractions. Pathogens 2020; 9:pathogens9060486. [PMID: 32570965 PMCID: PMC7350308 DOI: 10.3390/pathogens9060486] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 01/15/2023] Open
Abstract
Mosquitoes can transmit to humans devastating and deadly pathogens. As many chemical insecticides are banned due to environmental side effects or are of reduced efficacy due to resistance, biological control, including the use of bacterial strains with insecticidal activity, is of increasing interest and importance. The urgent actual need relies on the discovery of new compounds, preferably of a biological nature. Here, we explored the phenomenon of natural larvae mortality in larval breeding sites to identify potential novel compounds that may be used in biological control. From there, we isolated 14 bacterial strains of the phylum Firmicutes, most of the order Bacillales. Cultures were carried out under controlled conditions and were separated on supernatant and pellet fractions. The two fractions and a 1:1 mixture of the two fractions were tested on L3 and early L4 Aedes albopictus. Two concentrations were tested (2 and 6 mg/L). Larvae mortality was recorded at 24, 48 and 72 h and compared to that induced by the commercialized B. thuringiensis subsp. israelensis. Of the 14 strains isolated, 11 were active against the A. albopictus larvae: 10 of the supernatant fractions and one pellet fraction, and mortality increased with the concentration. For the insecticide activity prediction in three strains of the Bacillus cereus complex, PCR screening of the crystal (Cry) and cytolytic (Cyt) protein families characteristic to B. thuringiensis subsp. israelensis was performed. Most of the genes coding for these proteins' synthesis were not detected. We identified bacterial strains that exhibit higher insecticidal activity compared with a commercial product. Further studies are needed for the characterization of active compounds.
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Affiliation(s)
- Handi Dahmana
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France; (H.D.); (D.R.)
- IHU-Méditerranée Infection, 13005 Marseille, France;
| | - Didier Raoult
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France; (H.D.); (D.R.)
- IHU-Méditerranée Infection, 13005 Marseille, France;
| | - Florence Fenollar
- IHU-Méditerranée Infection, 13005 Marseille, France;
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France
| | - Oleg Mediannikov
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France; (H.D.); (D.R.)
- IHU-Méditerranée Infection, 13005 Marseille, France;
- Correspondence: ; Tel.: +33-(0)4-13-73-24-01; Fax: +33-(0)4-13-73-24-02
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Xu Z, Xie Z, Sun J, Huang S, Chen Y, Li C, Sun X, Xia B, Tian L, Guo C, Li F, Pi G. Gut Microbiome Reveals Specific Dysbiosis in Primary Osteoporosis. Front Cell Infect Microbiol 2020; 10:160. [PMID: 32373553 PMCID: PMC7186314 DOI: 10.3389/fcimb.2020.00160] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/25/2020] [Indexed: 12/14/2022] Open
Abstract
Object: Primary osteoporosis (PO) is the most common bone disease, which is characterized by decreased bone mass, damage of bone tissue microstructure, increased bone fragility, and is prone to fracture. Gut microbiome may be involved in bone metabolism of PO through gut-brain axis regulation of immune system and endocrine system, however, the specific mechanism is still unclear. The purpose of this study was to characterize the gut microbiome of patients with PO and its possible role in the occurrence and development of the disease. Methods: Fecal samples were collected from 48 PO patients and 48 healthy controls (HC). The composition of gut microbiome community was analyzed by 16s rDNA amplification sequencing, and the difference of gut microbiome composition between PO patients and HC individuals was compared. PICRUSt was also used to predict the biological function of gut microbiome in patients with PO, and to explore its possible role in the occurrence and development of this disease. The classification model is constructed by random forest algorithm so as to screen the key biomarkers. Result: The diversity of gut microorganisms in PO patients was significantly higher than that in HC group (p < 0.05) and there was significant difference in microbial composition in PO group. The abundance of Dialister (0.036 vs. 0.004, p < 0.001) and Faecalibacterium (0.331 vs. 0.132, p < 0.001) were significantly enriched which were the key flora related to PO. Although no significant correlation between bone mineral density and the richness of microbial communities are found, PICRUST results show that there are a wide range of potential pathways between gut microbiome and PO patients, including genetic information processing, metabolism, environmental information processing, cellular processes, human diseases, and organic systems. Notably, the discriminant model based on dominant microflora can effectively distinguish PO from HC (AUC = 93.56). Conclusions: The findings show that PO is related to the change of gut microbiome, especially the enriched Dialister and Faecalibacterium genera, which give new clues to understand the disease and provide markers for the diagnosis and new strategies for intervention treatment of the disease.
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Affiliation(s)
- Zhiming Xu
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Zheng Xie
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Jianguang Sun
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Shilei Huang
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yangyang Chen
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Chengxiang Li
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xing Sun
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Bicheng Xia
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Lingyang Tian
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Caijuan Guo
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Feng Li
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Guofu Pi
- Department of Orthopaedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
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Sakamoto M, Ikeyama N, Toyoda A, Murakami T, Mori H, Iino T, Ohkuma M. Dialister hominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2020; 70:589-595. [DOI: 10.1099/ijsem.0.003797] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Ibaraki 305-0074, Japan
| | - Nao Ikeyama
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takao Iino
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Abstract
There is now a wealth of evidence showing that communication between microbiota and the host is critical to sustain the vital functions of the healthy host, and disruptions of this homeostatic coexistence are known to be associated with a range of diseases including obesity and type 2 diabetes. Microbiota-derived metabolites act both as nutrients and as messenger molecules and can signal to distant organs in the body to shape host pathophysiology. In this review, we provide a new perspective on succinate as a gut microbiota-derived metabolite with a key role governing intestinal homeostasis and energy metabolism. Thus, succinate is not merely a major intermediary of the TCA traditionally considered as an extracellular danger signal in the host, but also a by-product of some bacteria and a primary cross-feeding metabolite between gut resident microbes. In addition to maintain a healthy microbiome, specific functions of microbiota-derived succinate in peripheral tissues regulating host nutrient metabolism should not be rule out. Indeed, recent research point to some probiotic interventions directed to modulate succinate levels in the intestinal lumen, as a new microbiota-based therapies to treat obesity and related co-morbidities. While further research is essential, a large body of evidence point to succinate as a new strategic mediator in the microbiota-host cross-talk, which might provide the basis for new therapeutically approaches in a near future.
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Affiliation(s)
- Sonia Fernández-Veledo
- Departament of Endocrinology and Nutrition and Research Unit, University Hospital of Tarragona Joan XXIII-Institut d'Investigació Sanitària Pere Virgili (IISPV), c/ Dr. Mallafré Guasch, 4, 43007, Tarragona, Spain.
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain.
| | - Joan Vendrell
- Departament of Endocrinology and Nutrition and Research Unit, University Hospital of Tarragona Joan XXIII-Institut d'Investigació Sanitària Pere Virgili (IISPV), c/ Dr. Mallafré Guasch, 4, 43007, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain
- Rovira i Virgili University, Tarragona, Spain
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11
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Anani H, Abdallah RA, Khoder M, Fontanini A, Mailhe M, Ricaboni D, Raoult D, Fournier PE. Colibacter massiliensis gen. nov. sp. nov., a novel Gram-stain-positive anaerobic diplococcal bacterium, isolated from the human left colon. Sci Rep 2019; 9:17199. [PMID: 31748674 PMCID: PMC6868274 DOI: 10.1038/s41598-019-53791-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
The gut microbiota is considered to play a key role in human health. As a consequence, deciphering its microbial diversity is mandatory. A polyphasic taxonogenomic strategy based on the combination of phenotypic and genomic analyses was used to characterize a new bacterium, strain Marseille-P2911. This strain was isolated from a left colon sample of a 60-year old man who underwent a colonoscopy for an etiological investigation of iron-deficiency anemia in Marseille, France. On the basis of 16S rRNA sequence comparison, the closest phylogenetic neighbor was Anaeroglobus geminatus (94.59% 16S rRNA gene sequence similarity) within the family Veillonellaceae. Cells were anaerobic, Gram-stain-positive, non-spore-forming, catalase/oxidase negative cocci grouped in pairs. The bacterium was able to grow at 37 °C after 2 days of incubation. Strain Marseille-P2911 exhibited a genome size of 1,715,864-bp with a 50.2% G + C content, and digital DNA-DNA hybridization (dDDH) and OrthoANI values with A. geminatus of only 19.1 ± 4.5% and 74.42%, respectively. The latter value being lower than the threshold for genus delineation (80.5%), we propose the creation of the new genus Colibacter gen. nov., with strain Marseille-P2911T (=DSM 103304 = CSUR P2911) being the type strain of the new species Colibacter massiliensis gen. nov., sp. nov.
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Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Rita Abou Abdallah
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - May Khoder
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Fontanini
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Morgane Mailhe
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Davide Ricaboni
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France. .,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
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12
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Cobo F, Rodríguez-Granger J, Sampedro A, Navarro-Marí JM. Bartholin's abscess due to Dialister micraerophilus in a woman presenting with repetitive bartholinitis episodes. Med Mal Infect 2018; 48:225-226. [DOI: 10.1016/j.medmal.2017.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/28/2017] [Indexed: 11/17/2022]
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13
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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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14
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Zhang X, Fang Z, Zhang C, Xia H, Jie Z, Han X, Chen Y, Ji L. Effects of Acarbose on the Gut Microbiota of Prediabetic Patients: A Randomized, Double-blind, Controlled Crossover Trial. Diabetes Ther 2017; 8:293-307. [PMID: 28130771 PMCID: PMC5380489 DOI: 10.1007/s13300-017-0226-y] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION The α-glucosidase inhibitor acarbose is an efficacious medicine for the treatment and prevention of type 2 diabetes mellitus (T2DM). However, the response of gut microbiota to acarbose is important, as the microbiota may have a critical role in the development of metabolic diseases, and acarbose is metabolized exclusively within the gastrointestinal tract. We explored the changes in the proportion and diversity of gut microbiota before and after treatment with acarbose in patients with prediabetes. METHODS We designed a randomized, double-blind, controlled crossover trial in which 52 Chinese patients with prediabetes by an oral glucose tolerance test (OGTT) with a BMI of 18-35 kg/m2 were randomly allocated to treatment with acarbose or placebo. Gut microbiota characterizations were determined with 16S rDNA-based high-throughput sequencing. RESULTS Of the 52 participants who entered the study, 40 (76.9%) completed the protocol. On the basis of the operational taxonomic unit (OTU) profiles, a total of 107 OTUs were significantly altered after acarbose treatment, with 76 (71%) assigned to the order of Clostridiales. Ruminococcaceae (15 OTUs) and Lachnospiraceae (22 OTUs) decreased in response to acarbose, and 48 OTUs increased by 12.8-fold, including Lactobacillaceae (8 of 9 belonging to Lactobacillus), Ruminococcaceae (6 of 11 belonging to Faecalibacterium), and Veillonellaceae (8 of 15 belonging to Dialister). At genera level, five flourished after treatment with acarbose, including Lactobacillus and Dialister, while Butyricicoccus, Phascolarctobacterium, and Ruminococcus were inhibited. CONCLUSION This study suggests that the benefits of acarbose for T2DM may correlate with the selective modulation of the gut microbiota. TRIAL REGISTRATION Chinese Clinical Trial Register number, ChiCTR-TTRCC-13004112.
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Affiliation(s)
- Xiuying Zhang
- Department of Endocrinology and Metabolism, Peking University People's Hospital, Peking University Diabetes Centre, Beijing, 100044, China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, 430056, China
| | - Chunfang Zhang
- Department of Clinical Epidemiology, Peking University People's Hospital, Beijing, 100044, China
| | | | - Zhuye Jie
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xueyao Han
- Department of Endocrinology and Metabolism, Peking University People's Hospital, Peking University Diabetes Centre, Beijing, 100044, China
| | - Yingli Chen
- Department of Endocrinology and Metabolism, Peking University People's Hospital, Peking University Diabetes Centre, Beijing, 100044, China
| | - Linong Ji
- Department of Endocrinology and Metabolism, Peking University People's Hospital, Peking University Diabetes Centre, Beijing, 100044, China.
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15
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Wadsworth WD, Argiento R, Guindani M, Galloway-Pena J, Shelburne SA, Vannucci M. An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data. BMC Bioinformatics 2017; 18:94. [PMID: 28178947 PMCID: PMC5299727 DOI: 10.1186/s12859-017-1516-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 01/31/2017] [Indexed: 12/19/2022] Open
Abstract
Background The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer. Integrative approaches which aim at associating the composition of the human microbiome with other available information, such as clinical covariates and environmental predictors, are paramount to develop a more complete understanding of the role of microbiome in disease development. Results In this manuscript, we propose a Bayesian Dirichlet-Multinomial regression model which uses spike-and-slab priors for the selection of significant associations between a set of available covariates and taxa from a microbiome abundance table. The approach allows straightforward incorporation of the covariates through a log-linear regression parametrization of the parameters of the Dirichlet-Multinomial likelihood. Inference is conducted through a Markov Chain Monte Carlo algorithm, and selection of the significant covariates is based upon the assessment of posterior probabilities of inclusions and the thresholding of the Bayesian false discovery rate. We design a simulation study to evaluate the performance of the proposed method, and then apply our model on a publicly available dataset obtained from the Human Microbiome Project which associates taxa abundances with KEGG orthology pathways. The method is implemented in specifically developed R code, which has been made publicly available. Conclusions Our method compares favorably in simulations to several recently proposed approaches for similarly structured data, in terms of increased accuracy and reduced false positive as well as false negative rates. In the application to the data from the Human Microbiome Project, a close evaluation of the biological significance of our findings confirms existing associations in the literature. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1516-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Raffaele Argiento
- ESOMAS Department, University of Torino and Collegio Carlo Alberto, Torino, Italy
| | - Michele Guindani
- Department of Statistics, University of California, Irvine, CA, USA
| | - Jessica Galloway-Pena
- Department of Infectious Disease, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Samuel A Shelburne
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Marina Vannucci
- Department of Statistics, Rice University, Houston, TX, USA.
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16
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Hiranmayi KV, Sirisha K, Ramoji Rao MV, Sudhakar P. Novel Pathogens in Periodontal Microbiology. J Pharm Bioallied Sci 2017; 9:155-163. [PMID: 28979069 PMCID: PMC5621177 DOI: 10.4103/jpbs.jpbs_288_16] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Periodontitis is a polymicrobial disease caused by complex interactions between distinct pathogens in a biofilm resulting in the destruction of periodontal tissues. It seems evident that unknown microorganisms might be involved in onset or progression of periodontitis. For many decades, research in the field of oral microbiology failed to identify certain subgingival microbiota due to technical limitations but, over a period of 12 years using molecular approaches and sequencing techniques, it became feasible to reveal the existence of new periodontal pathogens. Therefore, it is evident that in addition to conventional periodontal pathogens, other microbes might be involved in onset and progression of periodontitis. The novel pathogens enlisted under periodontal phylogeny include Cryptobacterium curtum, Dialister pneumosintes, Filifactor alocis, Mitsuokella dentalis, Slackia exigua, Selenomonas sputigena, Solobacterium moorei, Treponema lecithinolyticum, and Synergistes. The polymicrobial etiology of periodontitis has been elucidated by comprehensive techniques, and studies throwing light on the possible virulence mechanisms possessed by these novel periodontal pathogens are enlisted.
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Affiliation(s)
- K Vidya Hiranmayi
- Post Graduate Student, Department of Periodontics and Implantology, Drs S and NR Siddhartha Institute of Dental Sciences, Krishna District, Andhra Pradesh, India
| | - K Sirisha
- Reader, Department of Periodontics and Implantology, Drs S and NR Siddhartha Institute of Dental Sciences, Krishna District, Andhra Pradesh, India
| | - M V Ramoji Rao
- HOD, Department of Periodontics and Implantology, Drs S and NR Siddhartha Institute of Dental Sciences, Krishna District, Andhra Pradesh, India
| | - P Sudhakar
- Post Graduate Student, Department of Periodontics and Implantology, Drs S and NR Siddhartha Institute of Dental Sciences, Krishna District, Andhra Pradesh, India
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17
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Bostwick DG, Woody J, Hunt C, Budd W. Antimicrobial resistance genes and modelling of treatment failure in bacterial vaginosis: clinical study of 289 symptomatic women. J Med Microbiol 2016; 65:377-386. [PMID: 26887782 DOI: 10.1099/jmm.0.000236] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Clinical management of bacterial vaginosis (BV) is difficult owing to inaccurate diagnostic tests, limited drug choices, and a high rate of recurrence. To our knowledge, there has not been a previous study of antimicrobial resistance (AMR) genes in community practice using next-generation sequencing (NGS). A case-control study (1 : 1 age-matched with and without BV) was undertaken in a series of 326 nongravid women of reproductive age with symptoms of BV to determine the prevalence of AMR genes. NGS was used to describe the complete vaginal microbiota and identify bacterial genes associated with resistance to: macrolides and/or lincosamides - ermA, ermB, ermC, erM, ermTR and mefA; tetracyclines, β-lactams, streptomycin, gentamicin and/or tobramycin - acrA, acrB, mecA, tet, tetA, tolC and aac2; 5-nitroimadazoles - nim and nimB; and triazoles - cdr1 and mdr1. An evidence base was created to inform treatment decisions applicable to individual patients. AMR genes were identified in all drug classes: macrolides, 35.2 %; lincosamides, 35.6 %; tetracyclines, 21.8 %; aminoglycosides (streptomycin, gentamicin and tobramycin), 5.2 % each; 5-nitroimidazoles, 0.3 %; and triazoles, 18.7 %. There was more than a fourfold-higher frequency of AMR genes in pathogens from BV than from non-BV patients for macrolides (58.2 versus 12.3 %, respectively), lincosamides (58.9 versus 12.3 %) and tetracyclines (35.6 versus 8.0 %) (Fisher's exact test; all p < 0.001). For each patient with BV, the spectrum of resistance genes was matched to the pathogens present. AMR genes were present in the majority of vaginal microbiomes of patients with symptoms of BV.
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18
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Medina E, Pérez-Díaz IM, Breidt F, Hayes J, Franco W, Butz N, Azcarate-Peril MA. Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods. J Food Sci 2015; 81:M121-9. [PMID: 26605993 DOI: 10.1111/1750-3841.13158] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/22/2015] [Indexed: 12/01/2022]
Abstract
Fermented cucumber spoilage (FCS) characterized by rising pH and the appearance of manure- and cheese-like aromas is a challenge of significant economical impact for the pickling industry. Previous culture-based studies identified the yeasts Pichia manshurica and Issatchenkia occidentalis, 4 Gram-positive bacteria, Lactobacillus buchneri, Lactobacillus parrafaraginis, Clostridium sp., and Propionibacterium and 1 Gram-negative genus, Pectinatus, as relevant in various stages of FCS given their ability to metabolize lactic acid. It was the objective of this study to augment the current knowledge of FCS using culture-independent methods to microbiologically characterize commercial spoilage samples. Ion Torrent data and 16S rRNA cloning library analyses of samples collected from commercial fermentation tanks confirmed the presence of L. rapi and L. buchneri and revealed the presence of additional species involved in the development of FCS such as Lactobacillus namurensis, Lactobacillus acetotolerans, Lactobacillus panis, Acetobacter peroxydans, Acetobacter aceti, and Acetobacter pasteurianus at pH below 3.4. The culture-independent analyses also revealed the presence of species of Veillonella and Dialister in spoilage samples with pH above 4.0 and confirmed the presence of Pectinatus spp. during lactic acid degradation at the higher pH. Acetobacter spp. were successfully isolated from commercial samples collected from tanks subjected to air purging by plating on Mannitol Yeast Peptone agar. In contrast, Lactobacillus spp. were primarily identified in samples of FCS collected from tanks not subjected to air purging for more than 4 mo. Thus, it is speculated that oxygen availability may be a determining factor in the initiation of spoilage and the leading microbiota.
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Affiliation(s)
- Eduardo Medina
- the Dept. of Food, Bioprocessing, and Nutrition Sciences, North Carolina State Univ, Raleigh, NC, 27695, U.S.A.,the Dept. of Food Biotechnology, Inst. de la Grasa, CSIC, Univ. Campus Pablo de Olavide, Building 46, Seville, 41013, Spain
| | - Ilenys M Pérez-Díaz
- the USDA-Agriculture Research Service, SAA, Food Science Research Unit, 322 Schaub Hall-NCSU, Raleigh, NC, 27695, U.S.A
| | - Fred Breidt
- the USDA-Agriculture Research Service, SAA, Food Science Research Unit, 322 Schaub Hall-NCSU, Raleigh, NC, 27695, U.S.A
| | - Janet Hayes
- the USDA-Agriculture Research Service, SAA, Food Science Research Unit, 322 Schaub Hall-NCSU, Raleigh, NC, 27695, U.S.A
| | - Wendy Franco
- Dept. of Chemical Enngineering and Bioprocesses, Pontificia Universidad Católica de Chile, Ave, Vicuna Mackena 4860, Macul, 7820436, Santiago, Chile
| | - Natasha Butz
- the Microbiome Core Facility, Dept. of Cell Biology and Physiology, School of Medicine, Univ. of North Carolina, Chapell Hill, NC, 27599, U.S.A
| | - María Andrea Azcarate-Peril
- the Microbiome Core Facility, Dept. of Cell Biology and Physiology, School of Medicine, Univ. of North Carolina, Chapell Hill, NC, 27599, U.S.A
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Lactulose increases bacterial diversity and modulates the swine faecal microbiome as revealed by 454-pyrosequencing. Anim Feed Sci Technol 2015. [DOI: 10.1016/j.anifeedsci.2015.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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20
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Wallace RJ, Rooke JA, McKain N, Duthie CA, Hyslop JJ, Ross DW, Waterhouse A, Watson M, Roehe R. The rumen microbial metagenome associated with high methane production in cattle. BMC Genomics 2015; 16:839. [PMID: 26494241 PMCID: PMC4619255 DOI: 10.1186/s12864-015-2032-0] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/08/2015] [Indexed: 02/01/2023] Open
Abstract
Background Methane represents 16 % of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 % of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high- and low-methane-emitting cattle phenotypes. Methods Four pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes databasefor functional analysis. Results Deep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5× more numerous (P = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; P = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed 100 % identity with a publicly available protein sequence. Conclusions The abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals, a finding useful for genetic screening purposes. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis, as similarly postulated for Australian macropods. Large numbers of predicted protein sequences differed between high- and low-methane-emitting cattle. Ninety-nine percent were unknown, indicating a fertile area for future exploitation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2032-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- R John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, AB21 9SB, UK.
| | | | - Nest McKain
- Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, AB21 9SB, UK.
| | | | | | | | | | - Mick Watson
- Edinburgh Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.
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21
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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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22
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Pajarillo EAB, Chae JP, Balolong MP, Kim HB, Park CS, Kang DK. Effects of probiotic Enterococcus faecium NCIMB 11181 administration on swine fecal microbiota diversity and composition using barcoded pyrosequencing. Anim Feed Sci Technol 2015. [DOI: 10.1016/j.anifeedsci.2015.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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23
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Andersen SJ, Candry P, Basadre T, Khor WC, Roume H, Hernandez-Sanabria E, Coma M, Rabaey K. Electrolytic extraction drives volatile fatty acid chain elongation through lactic acid and replaces chemical pH control in thin stillage fermentation. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:221. [PMID: 26697110 PMCID: PMC4687354 DOI: 10.1186/s13068-015-0396-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/30/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Volatile fatty acids (VFA) are building blocks for the chemical industry. Sustainable, biological production is constrained by production and recovery costs, including the need for intensive pH correction. Membrane electrolysis has been developed as an in situ extraction technology tailored to the direct recovery of VFA from fermentation while stabilizing acidogenesis without caustic addition. A current applied across an anion exchange membrane reduces the fermentation broth (catholyte, water reduction: H2O + e(-) → ½ H2 + OH(-)) and drives carboxylate ions into a clean, concentrated VFA stream (anolyte, water oxidation: H2O → 2e(-) + 2 H(+) + O2). RESULTS In this study, we fermented thin stillage to generate a mixed VFA extract without chemical pH control. Membrane electrolysis (0.1 A, 3.22 ± 0.60 V) extracted 28 ± 6 % of carboxylates generated per day (on a carbon basis) and completely replaced caustic control of pH, with no impact on the total carboxylate production amount or rate. Hydrogen generated from the applied current shifted the fermentation outcome from predominantly C2 and C3 VFA (64 ± 3 % of the total VFA present in the control) to majority of C4 to C6 (70 ± 12 % in the experiment), with identical proportions in the VFA acid extract. A strain related to Megasphaera elsdenii (maximum abundance of 57 %), a bacteria capable of producing mid-chain VFA at a high rate, was enriched by the applied current, alongside a stable community of Lactobacillus spp. (10 %), enabling chain elongation of VFA through lactic acid. A conversion of 30 ± 5 % VFA produced per sCOD fed (60 ± 10 % of the reactive fraction) was achieved, with a 50 ± 6 % reduction in suspended solids likely by electro-coagulation. CONCLUSIONS VFA can be extracted directly from a fermentation broth by membrane electrolysis. The electrolytic water reduction products are utilized in the fermentation: OH(-) is used for pH control without added chemicals, and H2 is metabolized by species such as Megasphaera elsdenii to produce greater value, more reduced VFA. Electro-fermentation displays promise for generating added value chemical co-products from biorefinery sidestreams and wastes.
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Affiliation(s)
- Stephen J. Andersen
- />Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Building A, Room A0.092, B-9000 Ghent, Belgium
| | - Pieter Candry
- />Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Building A, Room A0.092, B-9000 Ghent, Belgium
| | - Thais Basadre
- />Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Building A, Room A0.092, B-9000 Ghent, Belgium
| | - Way Cern Khor
- />Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Building A, Room A0.092, B-9000 Ghent, Belgium
| | - Hugo Roume
- />Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Building A, Room A0.092, B-9000 Ghent, Belgium
| | - Emma Hernandez-Sanabria
- />Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Building A, Room A0.092, B-9000 Ghent, Belgium
| | - Marta Coma
- />Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Building A, Room A0.092, B-9000 Ghent, Belgium
- />Centre for Sustainable Chemical Technologies, University of Bath, Claverton Down, Bath, BA2 7AY UK
| | - Korneel Rabaey
- />Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Building A, Room A0.092, B-9000 Ghent, Belgium
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24
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Dudek M, Adams J, Swain M, Hegarty M, Huws S, Gallagher J. Metaphylogenomic and potential functionality of the limpet Patella pellucida's gastrointestinal tract microbiome. Int J Mol Sci 2014; 15:18819-39. [PMID: 25334059 PMCID: PMC4227249 DOI: 10.3390/ijms151018819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/30/2014] [Accepted: 10/11/2014] [Indexed: 11/16/2022] Open
Abstract
This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida. Using a modified indirect DNA extraction protocol and performing metagenomic profiling based on specific prokaryotic marker genes, the abundance of bacterial groups was identified from the analyzed metagenome. The members of three significantly abundant phyla of Proteobacteria, Firmicutes and Bacteroidetes were characterized through the literature and their predicted functions towards the host, as well as potential applications in the industrial environment assessed.
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Affiliation(s)
- Magda Dudek
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
| | - Jessica Adams
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
| | - Martin Swain
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
| | - Matthew Hegarty
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
| | - Sharon Huws
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
| | - Joe Gallagher
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales SY23 3EE, UK.
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25
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Soluble maize fibre affects short-term calcium absorption in adolescent boys and girls: a randomised controlled trial using dual stable isotopic tracers. Br J Nutr 2014; 112:446-56. [PMID: 24848974 DOI: 10.1017/s0007114514000981] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Soluble maize fibre (SCF) has been found to significantly improve bone mineral density and strength in growing rats compared with several other novel prebiotic fibres. The objective of the present study was to investigate the effect of SCF on Ca absorption and retention in pubertal children by studying the potential absorption mechanisms of the intestinal microbiota. A total of twenty-four adolescent boys and girls (12-15 years) participated in two 3-week metabolic balance studies testing 0 g/d SCF (control (CON) treatment) and 12 g/d SCF (SCF treatment) in a random order by inclusion in a low-Ca diet (600 mg/d). Fractional Ca absorption was measured at the end of the two intervention periods using a dual-stable isotope method. Diet composites and faecal and urine samples were collected daily and analysed for Ca content. Ca retention was calculated as dietary Ca intake minus Ca excretion in faeces and urine over the last 2 weeks. Microbial community composition in the faecal samples collected at the beginning and end of each session was determined by 454 pyrosequencing of the PCR-amplified 16S ribosomal RNA gene. Fractional Ca absorption was 12 % higher (41 mg/d) after the SCF treatment compared with that after the CON treatment (0·664 (sd 0·129) and 0·595 (sd 0·142), respectively; P= 0·02), but Ca retention was unaffected. The average proportion of bacteria of the phylum Bacteroidetes was significantly greater in the participants after the SCF treatment than after the CON treatment. These results suggest that moderate daily intake of SCF, a well-tolerated prebiotic fibre, increases short-term Ca absorption in adolescents consuming less than the recommended amounts of Ca.
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Roger F, Lamy B, Jumas-Bilak E, Kodjo A, Marchandin H. Ribosomal multi-operon diversity: an original perspective on the genus Aeromonas. PLoS One 2012; 7:e46268. [PMID: 23032081 PMCID: PMC3459834 DOI: 10.1371/journal.pone.0046268] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 08/28/2012] [Indexed: 12/31/2022] Open
Abstract
16S rRNA gene (rrs) is considered of low taxonomic interest in the genus Aeromonas. Here, 195 Aeromonas strains belonging to populations structured by multilocus phylogeny were studied using an original approach that considered Ribosomal Multi-Operon Diversity. This approach associated pulsed-field gel electrophoresis (PFGE) to assess rrn operon number and distribution across the chromosome and PCR-temporal temperature gel electrophoresis (TTGE) to assess rrs V3 region heterogeneity. Aeromonads harbored 8 to 11 rrn operons, 10 operons being observed in more than 92% of the strains. Intraspecific variability was low or nul except for A. salmonicida and A. aquariorum suggesting that large chromosomic rearrangements might occur in these two species while being extremely rarely encountered in the evolution of other taxa. rrn operon number at 8 as well as PFGE patterns were shown valuable for taxonomic purpose allowing resolution of species complexes. PCR-TTGE revealed a high rate of strains (41.5%) displaying intragenomic rrs heterogeneity. Strains isolated from human samples more frequently displayed intragenomic heterogeneity than strains recovered from non-human and environmental specimens. Intraspecific variability ranged from 0 to 76.5% of the strains. The observation of species-specific TTGE bands, the recovery of identical V3 regions in different species and the variability of intragenomic heterogeneity (1-13 divergent nucleotides) supported the occurrence of mutations and horizontal transfer in aeromonad rrs evolution. Altogether, the presence of a high number of rrn operon, the high proportion of strains harboring divergent rrs V3 region and the previously demonstrated high level of genetic diversity argued in favor of highly adaptative capabilities of aeromonads. Outstanding features observed for A. caviae supported the ongoing process of adaptation to a specialized niche represented by the gut, previously hypothesized. 16S rRNA gene is an informative marker in the genus Aeromonas for both evolutionary and polyphasic taxonomic studies provided that multi-operon fingerprinting approaches are used.
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Affiliation(s)
- Frédéric Roger
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
| | - Brigitte Lamy
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
- Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
- Groupe d’Etude Français des Aeromonas (GFA), Lyon, France
| | - Estelle Jumas-Bilak
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
- Laboratoire d’Hygiène hospitalière, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
| | - Angeli Kodjo
- Groupe d’Etude Français des Aeromonas (GFA), Lyon, France
- CNRS UMR 5557 Ecologie microbienne, VetAgro Sup Campus vétérinaire de Lyon, Université Claude Bernard Lyon 1, Marcy-l’Étoile, France
| | | | - Hélène Marchandin
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
- Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
- * E-mail:
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Identification by 16S rRNA gene sequencing of Negativicoccus succinicivorans recovered from the blood of a patient with hemochromatosis and pancreatitis. J Clin Microbiol 2011; 49:3082-4. [PMID: 21653773 DOI: 10.1128/jcm.01913-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe a case of Negativicoccus succinicivorans bacteremia in an adult man with hemochromatosis and acute pancreatitis. Conventional phenotypic tests and commercial identification systems failed to definitively identify the tiny anaerobic Gram-negative coccus isolated from two sets of blood cultures. The bacterium was identified by 16S rRNA gene sequencing and analysis using the SmartGene Integrated Database Network System software. This is the first published report of the recovery of this organism from a patient with invasive infection.
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Marchandin H, Teyssier C, Campos J, Jean-Pierre H, Roger F, Gay B, Carlier JP, Jumas-Bilak E. Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes. Int J Syst Evol Microbiol 2009; 60:1271-1279. [PMID: 19667386 DOI: 10.1099/ijs.0.013102-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of a hitherto unknown, Gram-negative, tiny, anaerobic coccus were collected from human clinical samples originating from skin and soft tissues. The three isolates displayed at least 99.9 % identity in their 16S rRNA gene sequences and more than 99.8 % identity in their dnaK gene sequences. The isolates were affiliated to the family Veillonellaceae, the coccobacillus Dialister micraerophilus being the most closely related species, but there was no more than 91.1 % identity in the 16S rRNA gene sequence between this species and the three isolates. Phylogeny based on the 16S rRNA gene confirmed that the three strains represent a novel and robust lineage within the current family Veillonellaceae. A similar genomic structure was demonstrated for the three isolates by PFGE-based analysis. Morphology and metabolic end products, as well as genotypic and phylogenetic data supported the proposal of the novel genus Negativicoccus gen. nov., with the novel species Negativicoccus succinicivorans sp. nov. [type strain ADV 07/08/06-B-1388(T) (=AIP 149.07(T)=CIP 109806(T)=DSM 21255(T)=CCUG 56017(T)) as type species]. Phylogenetic analyses based on the 16S rRNA gene sequences of members of the phylum Firmicutes and other phyla indicated that the family Veillonellaceae forms a robust lineage clearly separated from those of the classes 'Bacilli', 'Clostridia', Thermolithobacteria and 'Erysipelotrichi' in the phylum Firmicutes. Therefore, we propose that this family is a class-level taxon in the phylum Firmicutes, for which the name Negativicutes classis nov. is proposed, based on the Gram-negative type of cell wall of its members, with the type order Selenomonadales ord. nov. In this order, a novel family, Acidaminococcaceae fam. nov., is proposed and description of the family Veillonellaceae is emended.
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Affiliation(s)
- Hélène Marchandin
- Centre Hospitalier et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,Université Montpellier 1, EA 3755, Laboratoire de Bactériologie-Virologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34060 Montpellier Cedex 5, France
| | - Corinne Teyssier
- Université Montpellier 1, EA 3755, Laboratoire de Bactériologie-Virologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34060 Montpellier Cedex 5, France
| | - Josiane Campos
- Centre Hospitalier et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Hélène Jean-Pierre
- Centre Hospitalier et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.,Université Montpellier 1, EA 3755, Laboratoire de Bactériologie-Virologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34060 Montpellier Cedex 5, France
| | - Frédéric Roger
- Université Montpellier 1, EA 3755, Laboratoire de Bactériologie-Virologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34060 Montpellier Cedex 5, France
| | - Bernard Gay
- Université Montpellier 1 et Université Montpellier 2, UMR 5236-CPBS CNRS, Centre d'études d'agents pathogènes et Biotechnologies pour la Santé, Institut de Biologie, 4, Boulevard Henri IV, CS 69033, 34965 Montpellier Cedex 2, France
| | - Jean-Philippe Carlier
- Institut Pasteur, Centre National de Référence des Bactéries Anaérobies et du Botulisme, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Estelle Jumas-Bilak
- Université Montpellier 1, EA 3755, Laboratoire de Bactériologie-Virologie, Faculté de Pharmacie, 15, Avenue Charles Flahault, BP 14491, 34060 Montpellier Cedex 5, France
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29
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García-Sánchez JE, José Fresnadillo M, García-Sánchez E. [New anaerobic bacterial species in human infections]. Enferm Infecc Microbiol Clin 2009; 28:173-84. [PMID: 19477040 DOI: 10.1016/j.eimc.2008.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 09/18/2008] [Accepted: 09/19/2008] [Indexed: 10/20/2022]
Abstract
This review offers succinct, precise, and complete information based on the available data concerning new anaerobic bacterial species involved in infectious diseases in humans. All hitherto undescribed species, those not previously implicated in clinical conditions, those with confirmed implication in human disease that have not been characterized, and those that have undergone taxonomic changes are considered to be "new".
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30
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Morotomi M, Nagai F, Sakon H, Tanaka R. Dialister succinatiphilus sp. nov. and Barnesiella intestinihominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2009; 58:2716-20. [PMID: 19060046 DOI: 10.1099/ijs.0.2008/000810-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Two anaerobic, non-spore-forming, bacteria (YIT 11850(T) and YIT 11860(T)) that stained Gram-negative, were isolated from human faeces. Cells of strain YIT 11850(T) were coccobacilli, asaccharolytic and largely unreactive, with only traces of lactate and propionate as metabolic end products; however, strain YIT 11850(T) was able to decarboxylate succinate to propionate. The DNA G+C content of strain YIT 11850(T) was 51.9 mol%. Following 16S rRNA gene sequence analysis, this strain was found to be most closely related to Dialister propionicifaciens, with 95.1 % sequence similarity between the two taxa. Biochemical data supported the affiliation of strain YIT 11850(T) to the genus Dialister. Strain YIT 11850(T) therefore represents a novel species for which the name Dialister succinatiphilus sp. nov. is proposed; the type strain is YIT 11850(T) (=DSM 21274(T)=JCM 15077(T)). Cells of the other isolate, strain YIT 11860(T), were non-motile, rod-shaped, positive for aesculin hydrolysis, negative for indole production, produced succinic and acetic acids as end products of glucose metabolism and possessed a DNA G+C content of 45.5 mol%. On the basis of 16S rRNA gene sequence similarity values, this strain was shown to belong to the family 'Porphyromonadaceae' related to Barnesiella viscericola (96.0 %); similarity values with species within the family 'Porphyromonadaceae' with validly published names were less than 86 %. Biochemical data supported the affiliation of strain YIT 11860(T) to the genus Barnesiella. Strain YIT 11860(T) therefore represents a novel species for which the name Barnesiella intestinihominis sp. nov. is proposed; the type strain is YIT 11860(T) (=DSM 21032(T)=JCM 15079(T)).
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Affiliation(s)
- Masami Morotomi
- Yakult Central Institute for Microbiological Research, Kunitachi, Tokyo, Japan.
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31
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Woo P, Lau S, Teng J, Tse H, Yuen KY. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 2008; 14:908-34. [DOI: 10.1111/j.1469-0691.2008.02070.x] [Citation(s) in RCA: 524] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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32
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Jumas-Bilak E, Carlier JP, Jean-Pierre H, Citron D, Bernard K, Damay A, Gay B, Teyssier C, Campos J, Marchandin H. Jonquetella anthropi gen. nov., sp. nov., the first member of the candidate phylum 'Synergistetes' isolated from man. Int J Syst Evol Microbiol 2008; 57:2743-2748. [PMID: 18048718 DOI: 10.1099/ijs.0.65213-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six clinical isolates of a hitherto unknown, strictly anaerobic, Gram-negative rod showing fastidious growth were subjected to a polyphasic taxonomic study, including phenotypic, genomic and phylogenetic feature analyses. 16S rRNA gene sequenced-based phylogeny revealed that the novel strains represent a homogeneous group distant from any recognized species in the candidate phylum 'Synergistetes'. The novel isolates were most closely related to species of the genus Dethiosulfovibrio, with 88.2-88.7 % 16S rRNA gene sequence similarity. Large-scale chromosome structure and DNA G+C content also differentiated the novel strains from members of the genus Dethiosulfovibrio. The novel strains were asaccharolytic. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic, lactic, succinic and isovaleric acids and the major cellular fatty acids iso-C(15 : 0) and C(16 : 0). Based on the data presented here, a new genus, Jonquetella gen. nov., is proposed with one novel species, Jonquetella anthropi sp. nov. J. anthropi is the first characterized species of the candidate phylum 'Synergistetes' that includes human isolates. The G+C content of the DNA of the type strain of J. anthropi ADV 126(T) (=AIP 136.05(T)=CIP 109408(T)=CCUG 53819(T)) is 59.4 mol%.
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Affiliation(s)
- Estelle Jumas-Bilak
- Université Montpellier 1, EA 3755, Faculté de Pharmacie, Laboratoire de Bactériologie-Virologie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - Jean-Philippe Carlier
- Institut Pasteur, Centre National de Référence des Bactéries Anaérobies et du Botulisme, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Hélène Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Diane Citron
- R. M. Alden Research Laboratory, Santa Monica Blvd, Santa Monica, CA 90404, USA
| | - Kathryn Bernard
- National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington St., Suite H5040, Winnipeg, MB R3E 3R2, Canada
| | - Audrey Damay
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Bernard Gay
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Corinne Teyssier
- Université Montpellier 1, EA 3755, Faculté de Pharmacie, Laboratoire de Bactériologie-Virologie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - Josiane Campos
- 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 Montpellier 1, EA 3755, Faculté de Pharmacie, Laboratoire de Bactériologie-Virologie, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
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33
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Alauzet C, Mory F, Carlier JP, Marchandin H, Jumas-Bilak E, Lozniewski A. Prevotella nanceiensis sp. nov., isolated from human clinical samples. Int J Syst Evol Microbiol 2008; 57:2216-2220. [PMID: 17911286 DOI: 10.1099/ijs.0.65173-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of anaerobic, non-pigmented, Gram-negative bacilli isolated from various human clinical samples were characterized in terms of phenotypic and genotypic tests, including sequence analysis of 16S rRNA and rpoB genes. The strains were most closely related to the type strains of Prevotella marshii and Prevotella shahii on the basis of both 16S rRNA (89.8 and 89.0 % identity, respectively) and rpoB gene sequences (83.1 and 82.8 % identity, respectively). Phylogenetic analysis showed that the isolates constituted a robust homogeneous group distinct from known species in the genus Prevotella. The rrn skeleton (as determined by PFGE) and the DNA G+C content, determined to be 39.4 mol% for strain LBN 293(T), distinguished the novel isolates from the type strains of P. marshii and P. shahii. The three strains were saccharolytic and produced acetic, lactic and succinic acids as major metabolic end products. Polyphasic investigations supported the proposal of a novel species, Prevotella nanceiensis sp. nov., with LBN 293(T) (=AIP 261.03(T) =CIP 108993(T) =CCUG 54409(T)) as the type strain.
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MESH Headings
- Anaerobiosis/physiology
- Bacterial Proteins/genetics
- Bacterial Typing Techniques
- Bacteroidaceae Infections/microbiology
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA-Directed RNA Polymerases/genetics
- Electrophoresis, Gel, Pulsed-Field
- Genes, rRNA
- Humans
- Molecular Sequence Data
- Phylogeny
- Pigments, Biological/biosynthesis
- Prevotella/classification
- Prevotella/genetics
- Prevotella/isolation & purification
- Prevotella/physiology
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- C Alauzet
- Centre Hospitalier et Universitaire de Nancy, Hôpital Central, Laboratoire de Bactériologie, Nancy, France
- Université Nancy I, UMR CNRS 7565, UFR de Médecine, Laboratoire de Bactériologie, Vandoeuvre-les-Nancy, France
| | - F Mory
- Centre Hospitalier et Universitaire de Nancy, Hôpital Central, Laboratoire de Bactériologie, Nancy, France
| | - J-P Carlier
- Institut Pasteur, Centre National de Référence des Bactéries Anaérobies et du Botulisme, Paris, France
| | - H Marchandin
- Université Montpellier 1, UFR de Pharmacie, Laboratoire de Bactériologie-Virologie, EA 3755, Montpellier, France
- Centre Hospitalier et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, Montpellier, France
| | - E Jumas-Bilak
- Université Montpellier 1, UFR de Pharmacie, Laboratoire de Bactériologie-Virologie, EA 3755, Montpellier, France
| | - A Lozniewski
- Centre Hospitalier et Universitaire de Nancy, Hôpital Central, Laboratoire de Bactériologie, Nancy, France
- Université Nancy I, UMR CNRS 7565, UFR de Médecine, Laboratoire de Bactériologie, Vandoeuvre-les-Nancy, France
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Antimicrobial susceptibilities and clinical sources of Dialister species. Antimicrob Agents Chemother 2007; 51:4498-501. [PMID: 17923492 DOI: 10.1128/aac.00538-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seventy-four strains representing the four species of the genus Dialister were isolated from various clinical samples. Dialister pneumosintes and Dialister micraerophilus were the two mainly encountered species. Fifty-five isolates were tested against 14 antimicrobial agents. Decreased susceptibilities to piperacillin, metronidazole, macrolides, fluoroquinolones, and rifampin were demonstrated. The clinical impact of these decreased susceptibilities remains to be investigated but should prompt microbiologists to perform antimicrobial susceptibility testing for clinically important Dialister spp.
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Jumas-Bilak E, Carlier JP, Jean-Pierre H, Mory F, Teyssier C, Gay B, Campos J, Marchandin H. Acidaminococcus intestini sp. nov., isolated from human clinical samples. Int J Syst Evol Microbiol 2007; 57:2314-2319. [PMID: 17911303 DOI: 10.1099/ijs.0.64883-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eleven strains of a hitherto unknown, Gram-negative, anaerobic coccus were recovered from various human clinical samples of patients hospitalized in two geographically distant French hospitals. These strains displayed the morphology and growth characteristics of those related to the genus Acidaminococcus. The clinical isolates shared at least 99.9 and 99.7 % of their nucleotide positions in the 16S and 23S rRNA gene sequences, respectively. They displayed 95.6 and 88.9 % 16S and 23S rRNA gene sequence similarities, respectively, with Acidaminococcus fermentans. The 16S rRNA-based phylogeny revealed that all the clinical isolates grouped in a statistically well supported cluster separate from A. fermentans. Enzymic activity profiles as well as metabolic end product patterns, including propionic acid production, differentiated the novel bacteria from A. fermentans. Finally, phenotypic, genotypic and phylogenetic data, including large-scale chromosome structure and DNA G+C content, supported the proposal of a novel species of the genus Acidaminococcus, for which the name Acidaminococcus intestini sp. nov. is proposed. The type strain is ADV 255.99T (=AIP 283.01T=CIP 108586T=CCUG 50930T).
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MESH Headings
- Acidaminococcus/classification
- Acidaminococcus/cytology
- Acidaminococcus/isolation & purification
- Acidaminococcus/physiology
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Anaerobiosis/physiology
- Bacterial Proteins/metabolism
- Bacterial Typing Techniques
- Base Composition
- Chromosomes, Bacterial/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Enzymes/metabolism
- Female
- France
- Genes, rRNA
- Gram-Negative Bacterial Infections/microbiology
- Humans
- Male
- Middle Aged
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Estelle Jumas-Bilak
- Université Montpellier 1, Faculté de Pharmacie, Laboratoire de Bactériologie-Virologie, 15 Avenue Charles Flahault, BP 14491, 34060 Montpellier Cedex 5, France
| | - Jean-Philippe Carlier
- Institut Pasteur, Centre National de Référence des Bactéries Anaérobies et du Botulisme, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Hélène Jean-Pierre
- Centre Hospitalier et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Francine Mory
- Centre Hospitalier et Universitaire de Nancy, Hôpital Central, Laboratoire de Bactériologie, 29 avenue du Maréchal de Lattre de Tassigny, 54035 Nancy Cedex, France
| | - Corinne Teyssier
- Université Montpellier 1, Faculté de Pharmacie, Laboratoire de Bactériologie-Virologie, 15 Avenue Charles Flahault, BP 14491, 34060 Montpellier Cedex 5, France
| | - Bernard Gay
- Centre Hospitalier et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Josiane Campos
- Centre Hospitalier et 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 et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
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