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Forman-Ankjaer B, Hvid-Jensen F, Kobel CM, Greve T. Short communication: first case of bacteraemia caused by Dielma fastidiosa in a patient hospitalized with diverticulitis. APMIS 2024; 132:130-133. [PMID: 38095319 DOI: 10.1111/apm.13367] [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: 10/11/2023] [Accepted: 11/24/2023] [Indexed: 01/09/2024]
Abstract
Dielma fastidiosa is a gram-negative, anaerobic rod belonging to the family Erysipelotrichaceae. D. fastidiosa has previously been isolated in human stool samples as part of the commensal flora; however, prior to this case, it has never been identified as a human pathogen. We present the first case of bacteraemia with D. fastidiosa. Bacterial growth in the blood culture bottle was detected by the automated blood culture system BacT/ALERT 3D. Culturing was performed, and bacterial colonies were identified as D. fastidiosa using MALDI-TOF MS. A subsequent whole-genome sequencing using Illumina NovaSeq was performed, and a phylogenetic tree depicting all available sequences of D. fastidiosa was generated. The reference MALDI-TOF spectrum and species identification was compared with the previously published spectrum. Whole-genome sequencing confirmed the tentative MALDI-TOF species identification. Notably, the maximum-likelihood-based phylogenetic analysis placed the D. fastidiosa isolate from this clinical case within the known variation of the eight publicly available sequences of this species. We identified D. fastidiosa by whole-genome sequencing followed by maximum-likelihood analysis as a possible pathogen in this case of bacteraemia in a patient hospitalized with diverticulitis.
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Affiliation(s)
| | | | - Carl Mathias Kobel
- Microbial Ecology and Meta-Omics group, Norwegian University of Life Sciences, Ås, Norway
| | - Thomas Greve
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
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2
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Yang M, Guo X, Chen T, Li P, Xiao T, Dai Z, Hu Y. Effect of dietary replacement of fish meal by poultry by-product meal on the growth performance, immunity, and intestinal health of juvenile red swamp crayfish, procambarus clarkia. FISH & SHELLFISH IMMUNOLOGY 2022; 131:381-390. [PMID: 36257552 DOI: 10.1016/j.fsi.2022.10.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 10/05/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
The present study was conducted to investigate the dietary replacement of fish meal with poultry by-product meal (PBM) on the growth performance, immunity, antioxidant properties, and intestinal health of red swamp crayfish (Procambarus clarkia). A diet containing 20% fish meal (FM) and complex plant ingredients as the main protein resources was set as the FM group (crude protein 32%, crude lipid 6%). Four diets replacing 25%, 50%, 75%, and 100% fish meal of the FM diet with PBM were set as the PBM25, PBM50, PBM75, and PBM100 groups, respectively. Compared to the FM group, the PBM100 diet significantly decreased growth performance and feed utilization of crayfish, while markedly increasing the activity of serum aspartate aminotransferase. The immune response was depressed in crayfish fed the PBM100 diet as the activities of serum lysozyme and phenoloxidase, gene expression of anti-lipopolysaccharide factors (alf), cyclophilin A (cypa), crustin, and hemocyanin-1 (hep-1) in hepatopancreas were remarkably decreased. The activities of antioxidases and expression of antioxidant-relevant genes in the hepatopancreas were not influenced by PBM inclusion. Crayfish fed different diets exhibited no obvious symptoms of enteritis, but the PBM100 diet destructed intestinal morphology by significantly decreasing the average length of longitudinal ridges. The α-diversity and overall community structure were not significantly influenced but variations were found in the relative abundance of some genera by PBM inclusion. In summary, CAP could successfully replace 75% dietary FM in a basal diet containing 20% fish meal, while higher CAP level compromised growth performance, immunity, and intestinal histology of crayfish.
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Affiliation(s)
- Mengxi Yang
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Xiaorui Guo
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Tuo Chen
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Peng Li
- North American Renderers Association, Alexandria, VA, 22314, USA
| | - Tiaoyi Xiao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Zhenyan Dai
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Yi Hu
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, College of Animal Science and Technology, Hunan Agricultural University, 1 Nongda Road, Changsha, 410128, Hunan, China.
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Wu Q, Zou D, Zheng X, Liu F, Li L, Xiao Z. Effects of antibiotics on anaerobic digestion of sewage sludge: Performance of anaerobic digestion and structure of the microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157384. [PMID: 35843318 DOI: 10.1016/j.scitotenv.2022.157384] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 05/16/2023]
Abstract
As a common biological engineering technology, anaerobic digestion can stabilize sewage sludge and convert the carbon compounds into renewable energy (i.e., methane). However, anaerobic digestion of sewage sludge is severely affected by antibiotics. This review summarizes the effects of different antibiotics on anaerobic digestion of sewage sludge, including production of methane and volatile fatty acids (VFAs), and discusses the impact of antibiotics on biotransformation processes (solubilization, hydrolysis, acidification, acetogenesis and methanogenesis). Moreover, the effects of different antibiotics on microbial community structure (bacteria and archaea) were determined. Most of the research results showed that antibiotics at environmentally relevant concentrations can reduce biogas production mainly by inhibiting methanogenic processes, that is, methanogenic archaea activity, while a few antibiotics can improve biogas production. Moreover, the combination of multiple environmental concentrations of antibiotics inhibited the efficiency of methane production from sludge anaerobic digestion. In addition, some lab-scale pretreatment methods (e.g., ozone, ultrasonic combined ozone, zero-valent iron, Fe3+ and magnetite) can promote the performance of anaerobic digestion of sewage sludge inhibited by antibiotics.
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Affiliation(s)
- Qingdan Wu
- College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan 410128, China; Key Laboratory for Rural Ecosystem Health in Dongting Lake Area of Hunan Province, Changsha, Hunan 410128, China
| | - Dongsheng Zou
- College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan 410128, China; Key Laboratory for Rural Ecosystem Health in Dongting Lake Area of Hunan Province, Changsha, Hunan 410128, China
| | - Xiaochen Zheng
- College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan 410128, China; Key Laboratory for Rural Ecosystem Health in Dongting Lake Area of Hunan Province, Changsha, Hunan 410128, China
| | - Fen Liu
- College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan 410128, China; Key Laboratory for Rural Ecosystem Health in Dongting Lake Area of Hunan Province, Changsha, Hunan 410128, China; College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Longcheng Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhihua Xiao
- College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan 410128, China; Key Laboratory for Rural Ecosystem Health in Dongting Lake Area of Hunan Province, Changsha, Hunan 410128, China.
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4
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Copranaerobaculum intestinale gen. nov., sp. nov., a novel anaerobic bacterium isolated from human faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005373] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel obligate anaerobic organism, designated DONG20-135T, was isolated from human faeces collected in Beijing, PR China. Cells were Gram-stain-negative, rod-shaped, non-motile and non-spore-forming. Growth occurred at 25‒45 °C (optimum, 30‒35 °C), a pH range of 6–9 (optimum, pH 8) and in the presence of 0‒3.5 % (w/v) NaCl (optimum, 0.5‒1.5 %). The major fatty acids were C16 : 0, C18 : 1
ω9c and C10 : 0, the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, four glycolipids, six aminolipids, three aminophospholipids and four unidentified lipids. No respiratory quinones were detected. The cell-wall peptidoglycan of the strain was A1γ type, containing meso-diaminopimelic acid. The 16S rRNA gene sequences shared a lower identity (<92.7 % similarity) with the described species. The phylogenetic tree based on 16S rRNA gene sequences and the protein-concatamer tree showed that strain DONG20-135T formed a distinct lineage within the family
Erysipelotrichaceae
. The genomic DNA G + C content was 42.2 mol%. Based on the results of phenotypic, chemotaxonomic and genomic analyses, strain DONG20-135T represents a novel genus of the family
Erysipelotrichaceae
, for which the name Copranaerobaculum intestinale gen. nov., sp. nov. is proposed (=KCTC 15868T=CGMCC 1.17357T).
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5
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Sánchez AL, Lafond M. Colorful orthology clustering in bounded-degree similarity graphs. J Bioinform Comput Biol 2021; 19:2140010. [PMID: 34775924 DOI: 10.1142/s0219720021400102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Clustering genes in similarity graphs is a popular approach for orthology prediction. Most algorithms group genes without considering their species, which results in clusters that contain several paralogous genes. Moreover, clustering is known to be problematic when in-paralogs arise from ancient duplications. Recently, we proposed a two-step process that avoids these problems. First, we infer clusters of only orthologs (i.e. with only genes from distinct species), and second, we infer the missing inter-cluster orthologs. In this paper, we focus on the first step, which leads to a problem we call Colorful Clustering. In general, this is as hard as classical clustering. However, in similarity graphs, the number of species is usually small, as well as the neighborhood size of genes in other species. We therefore study the problem of clustering in which the number of colors is bounded by [Formula: see text], and each gene has at most [Formula: see text] neighbors in another species. We show that the well-known cluster editing formulation remains NP-hard even when [Formula: see text] and [Formula: see text]. We then propose a fixed-parameter algorithm in [Formula: see text] to find the single best cluster in the graph. We implemented this algorithm and included it in the aforementioned two-step approach. Experiments on simulated data show that this approach performs favorably to applying only an unconstrained clustering step.
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Affiliation(s)
- Alitzel López Sánchez
- Computer Science Department, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Manuel Lafond
- Computer Science Department, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec J1K 2R1, Canada
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6
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Long F, Wang L, Cai W, Lesnik K, Liu H. Predicting the performance of anaerobic digestion using machine learning algorithms and genomic data. WATER RESEARCH 2021; 199:117182. [PMID: 33975088 DOI: 10.1016/j.watres.2021.117182] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Modeling of anaerobic digestion (AD) is crucial to better understand the process dynamics and to improve the digester performance. This is an essential yet difficult task due to the complex and unknown interactions within the system. The application of well-developed data mining technologies, such as machine learning (ML) and microbial gene sequencing techniques are promising in overcoming these challenges. In this study, we investigated the feasibility of 6 ML algorithms using genomic data and their corresponding operational parameters from 8 research groups to predict methane yield. For classification models, random forest (RF) achieved accuracies of 0.77 using operational parameters alone and 0.78 using genomic data at the bacterial phylum level alone. The combination of operational parameters and genomic data improved the prediction accuracy to 0.82 (p<0.05). For regression models, a low root mean square error of 0.04 (relative root mean square error =8.6%) was acquired by neural network using genomic data at the bacterial phylum level alone. Feature importance analysis by RF suggested that Chloroflexi, Actinobacteria, Proteobacteria, Fibrobacteres, and Spirochaeta were the top 5 most important phyla although their relative abundances were ranging only from 0.1% to 3.1%. The important features identified could provide guidance for early warning and proactive management of microbial communities. This study demonstrated the promising application of ML techniques for predicting and controlling AD performance.
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Affiliation(s)
- Fei Long
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA
| | - Luguang Wang
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA
| | - Wenfang Cai
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | | | - Hong Liu
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA.
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7
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Jiang X, Qin Z, Feng L, Chen Y, Chen J, Zhang X, Zhang Z, Guo Y, Sun J. Volatile fatty acids production from waste activated sludge during anaerobic fermentation: The effect of superfine sand. BIORESOURCE TECHNOLOGY 2021; 319:124249. [PMID: 33254471 DOI: 10.1016/j.biortech.2020.124249] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/03/2020] [Accepted: 10/08/2020] [Indexed: 06/12/2023]
Abstract
Superfine sand in waste activated sludge (WAS) increased the uncertainty of anaerobic fermentation. Experiments showed that VFAs production from WAS was positively affected by superfine sand, with an increase from 2513 mg COD/L in the control (without superfine sand) to 3002 mg COD/L with superfine sand. A mechanism study demonstrated that the main factor responsible for the improved VFAs accumulation in response to superfine sand was acetic acid, which increased by nearly 30%. Further investigation exhibited that the process of solubilization and acidification were facilitated by superfine sand and the abundance of anaerobic functional microorganisms was greatly increased. Moreover, the activities of acetate kinase (AK) as well as the quantity of AK encoding gene were greatly promoted by superfine sand. The heat release during WAS anaerobic fermentation with superfine sand was higher than that without superfine sand (25.8 × 10-3 versus 24.7 × 10-3 W·min at about 70 min).
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Affiliation(s)
- Xiupeng Jiang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Changzhou University Huaide College, 136 Xingang Road, Jingjiang, Jiangsu Province 214500, China
| | - Zhiyi Qin
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Leiyu Feng
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Gansu Lanfei Environmental Protection Technology Co., Ltd, 18 Yannan Road, Lanzhou, Gansu Province 730010, China.
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Jianguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xianzhong Zhang
- Shanghai Urban Construction Design & Research Institute (Group) Co., Ltd., 3447 Dongfang Road, Shanghai 200125, China
| | - Zhenguang Zhang
- Shanghai Road and Bridge Group Co.,Ltd., 36 Guoke Road, Shanghai 200433, China
| | - Yingqing Guo
- Changzhou University Huaide College, 136 Xingang Road, Jingjiang, Jiangsu Province 214500, China
| | - Jing Sun
- Gansu Lanfei Environmental Protection Technology Co., Ltd, 18 Yannan Road, Lanzhou, Gansu Province 730010, China
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8
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Anani H, Abou Abdallah R, Chelkha N, Fontanini A, Ricaboni D, Mailhe M, Raoult D, Fournier PE. Draft genome and description of Merdibacter massiliensis gen.nov., sp. nov., a new bacterium genus isolated from the human ileum. Sci Rep 2019; 9:7931. [PMID: 31138831 PMCID: PMC6538751 DOI: 10.1038/s41598-019-44343-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/09/2019] [Indexed: 12/22/2022] Open
Abstract
We used phenotypic, genomic and phylogenetic information following the taxono-genomics approach to demonstrate that strain Marseille–P3254, isolated from an ileal sample of a 76-year old woman who underwent upper and lower digestive tract endoscopy for esophagitis and colonic polyp, is representative of a novel bacterial genus within the family Erysipelotrichaceae in the phylum Firmicutes. It is an anaerobic Gram-negative bacterium without catalase and oxidase activities. The genome of strain Marseille–P3254 is 2,468,496-bp long with a 40.1% G + C content. This new bacterium is most closely related to Eubacterium dolichum, with which it shares 90.7% 16S rRNA sequence similarity. In addition, genomic comparison using the digital DNA–DNA hybridization and OrthoANI analyses between the novel organism and the E. dolichum type strain revealed identities of 25.2 and 68.91%, respectively. The major fatty acids were C16: 0, C18: 1n9 and C18: 0. Based on these data, we propose the creation of the new genus Merdibacter gen. nov., with strain Marseille-P3254T (=CSUR P3254 = DSM 103534) being the type strain of the new species Merdibacter 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 Méditerranéennes (VITROME), 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 Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nisrine Chelkha
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Anthony Fontanini
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Davide Ricaboni
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Morgane Mailhe
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, 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 Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
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9
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Bonnet M, Mailhe M, Ricaboni D, Labas N, Richez M, Vitton V, Benezech A, Fournier PE, Million M, Raoult D, Khelaifia S. Genome sequence and description of Traorella massiliensis gen. nov., sp. nov., a new bacterial genus isolated from human left colon. New Microbes New Infect 2019; 29:100520. [PMID: 30949346 PMCID: PMC6428956 DOI: 10.1016/j.nmni.2019.100520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/07/2019] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
A strictly anaerobic, motile, non-spore-forming, Gram-negative, rod-shaped bacterium designated Marseille-P3110T was isolated from the left colon cleansing of a 76-year-old Frenchwoman. Its 16S ribosomal RNA (rRNA) gene showed a 93.2% similarity level with the 16S rRNA of Dielma fastidiosa strain JC13, the closest species with a validly published name. The genome of Marseille-P3110T is 2 607 061 bp long with 35.99% G+C content. Of the 2642 predicted genes, 2582 were protein-coding genes and 60 were RNAs, including five 16S rRNA genes.
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Affiliation(s)
- M. Bonnet
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - M. Mailhe
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - D. Ricaboni
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Département des sciences cliniques et biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - N. Labas
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - M. Richez
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - V. Vitton
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - A. Benezech
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - P.-E. Fournier
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
- Département des sciences cliniques et biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - M. Million
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - S. Khelaifia
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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10
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Xie J, Duan X, Feng L, Yan Y, Wang F, Dong H, Jia R, Zhou Q. Influence of sulfadiazine on anaerobic fermentation of waste activated sludge for volatile fatty acids production: Focusing on microbial responses. CHEMOSPHERE 2019; 219:305-312. [PMID: 30543966 DOI: 10.1016/j.chemosphere.2018.12.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/10/2018] [Accepted: 12/02/2018] [Indexed: 06/09/2023]
Abstract
Extensive studies on anaerobic fermentation of waste activated sludge (WAS) for volatile fatty acids (VFAs) production focused on the effects of operating parameters and pretreatment methods, and little information is available for those of organic pollutants which were absorbed on sludge. The influence of sulfadiazine (SDZ), a typical antibiotic pollutant in WAS, on VFAs production during anaerobic fermentation was investigated in this study. The accumulation of VFAs was remarkably affected in the presence of SDZ. When the content of SDZ was 50 mg per kilogram dry sludge the concentration of VFAs from sludge was 2032.8 mg COD/L, much higher than that of control (1540.2 mg COD/L). Mechanism investigation revealed that the content of extracellular polymeric substances (EPS) from sludge was increased due to the presence of SDZ, which provided more substrates, i.e., protein and carbohydrate, and created a favorable environment for anaerobes. The hydrolysis and acidification of WAS were stimulated by SDZ, and the functional microorganisms were advantageous to VFAs production. The activities of protease, α-glucosidase and acetate kinase were promoted when SDZ occurred, which were beneficial for hydrolysis and acidification. The effect of SDZ on pure strains further confirmed that the formation of VFAs during anaerobic fermentation was stimulated by SDZ.
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Affiliation(s)
- Jing Xie
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Xu Duan
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Leiyu Feng
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
| | - Yuanyuan Yan
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Feng Wang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Haiqing Dong
- Shanghai East Hospital, The Institute for Biomedical Engineering & Nano Science (iNANO), School of Medicine, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Renyong Jia
- Shanghai Urban Construction Design & Research Institute (Group) Co., Ltd., 3447 Dongfang Road, Shanghai, 200125, China
| | - Qi Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
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11
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Munson E, Carroll KC. An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017. J Clin Microbiol 2019; 57:e01181-18. [PMID: 30257907 PMCID: PMC6355528 DOI: 10.1128/jcm.01181-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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12
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Lagier JC, Bilen M, Cadoret F, Drancourt M, Fournier PE, La Scola B, Raoult D. Naming microorganisms: the contribution of the IHU Méditerranée Infection, Marseille, France. New Microbes New Infect 2018; 26:S89-S95. [PMID: 30402249 PMCID: PMC6205575 DOI: 10.1016/j.nmni.2018.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/13/2018] [Accepted: 08/03/2018] [Indexed: 12/22/2022] Open
Abstract
The number of isolated new microorganisms has dramatically increased after the readaption of culture using the culturomics approach. Each of these microorganisms is deposited in an international strain collection institute, with its name being attributed and published by the scientist who isolated it. The attributed name is of Latin or Latinized origin and chosen on the basis of the geographical location of the sample collection, the institute or geographical region where the project was being performed, the name of a concerned scientist, and characteristics of the sample or the microorganism. Our institution has played an important role in the isolation of new microorganisms, with the first effort reporting 468 new bacterial species (3% of the bacterial species isolated at least once worldwide) and 327 species isolated for the first time from human beings, which in turn resulted in an increase of 30% of the total number of microorganisms isolated. Additionally, more than 100 giant viruses, including seven new species, have been isolated at our institute. In the present work, after recalling the rules of nomenclature, we detail the naming of the new microorganisms chosen at our laboratory. The most common species name was massiliensis, attributed 161 times. We consider it imperative for the cultivators, who have frequently made considerable efforts in the field of microbial culture, to be the ones who name the newly isolated microorganisms, taking into consideration the Latinized nomenclature standards.
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Affiliation(s)
| | - M. Bilen
- Aix-Marseille Univ, IRD, MEPHI, France
| | | | | | - P.-E. Fournier
- Aix-Marseille Univ, IRD, VITROME, APHM, IHU Méditerranée Infection, Marseille, France
| | | | - D. Raoult
- Aix-Marseille Univ, IRD, MEPHI, France
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13
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Lun H, Yang W, Zhao S, Jiang M, Xu M, Liu F, Wang Y. Altered gut microbiota and microbial biomarkers associated with chronic kidney disease. Microbiologyopen 2018; 8:e00678. [PMID: 30088332 PMCID: PMC6460263 DOI: 10.1002/mbo3.678] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/25/2018] [Accepted: 05/22/2018] [Indexed: 01/06/2023] Open
Abstract
The present study aimed to determine the differences in gut microbiota between patients with chronic kidney disease (CKD) and healthy controls (HC) and search for better microbial biomarkers associated with CKD. The 16S rRNA gene sequencing approach was used to investigate the differences in gut microbiota between the CKD and HC groups. The study found that 12 phylotypes were overrepresented in the CKD group and 19 in the HC group at the genus level. Furthermore, genera Lachnospira and Ruminococcus_gnavus performed the best in differentiating between HC and CKD populations. In addition, this novel study found that the genera Holdemanella, Megamonas, Prevotella 2, Dielma, and Scardovia were associated with the progression of CKD and hemodialysis. In conclusion, the composition of gut microbiota was different in CKD populations compared with healthy populations, and Lachnospira and R._gnavus were better microbial biomarkers. In addition, five phylotypes, including Holdemanella, Megamonas, Prevotella2, Dielma, and Scardovia, served as an indicator of the progression of CKD and hemodialysis. However, large‐scale prospective studies should be performed to identify the reliability of the set of these phylotypes as biomarkers.
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Affiliation(s)
- Hengzhong Lun
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China.,The Department of Clinical Laboratory, Taian City Central Hospital, Taian, Shandong, China
| | - Weihua Yang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Shuping Zhao
- The Department of Clinical Laboratory, Taian City Central Hospital, Taian, Shandong, China
| | - Meijie Jiang
- The Department of Clinical Laboratory, Taian City Central Hospital, Taian, Shandong, China
| | - Mingjie Xu
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Fenfen Liu
- The Department of Nephrology, Taian City Central Hospital, Taian, Shandong, China
| | - Yunshan Wang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong, China
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14
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Eid HM, Wright ML, Anil Kumar NV, Qawasmeh A, Hassan STS, Mocan A, Nabavi SM, Rastrelli L, Atanasov AG, Haddad PS. Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients. Front Pharmacol 2017; 8:387. [PMID: 28713266 PMCID: PMC5493053 DOI: 10.3389/fphar.2017.00387] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/02/2017] [Indexed: 01/11/2023] Open
Abstract
Metabolic syndrome is a cluster of three or more metabolic disorders including insulin resistance, obesity, and hyperlipidemia. Obesity has become the epidemic of the twenty-first century with more than 1.6 billion overweight adults. Due to the strong connection between obesity and type 2 diabetes, obesity has received wide attention with subsequent coining of the term "diabesity." Recent studies have identified unique contributions of the immensely diverse gut microbiota in the pathogenesis of obesity and diabetes. Several mechanisms have been proposed including altered glucose and fatty acid metabolism, hepatic fatty acid storage, and modulation of glucagon-like peptide (GLP)-1. Importantly, the relationship between unhealthy diet and a modified gut microbiota composition observed in diabetic or obese subjects has been recognized. Similarly, the role of diet rich in polyphenols and plant polysaccharides in modulating gut bacteria and its impact on diabetes and obesity have been the subject of investigation by several research groups. Gut microbiota are also responsible for the extensive metabolism of polyphenols thus modulating their biological activities. The aim of this review is to shed light on the composition of gut microbes, their health importance and how they can contribute to diseases as well as their modulation by polyphenols and polysaccharides to control obesity and diabetes. In addition, the role of microbiota in improving the oral bioavailability of polyphenols and hence in shaping their antidiabetic and antiobesity activities will be discussed.
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Affiliation(s)
- Hoda M. Eid
- Natural Health Products and Metabolic Diseases Laboratory, Department of Pharmacology and Physiology, Université de MontréalMontréal, QC, Canada
- Canadian Institutes of Health Research Team in Aboriginal Antidiabetic MedicinesMontréal, QC, Canada
- Department of Pharmacognosy, University of Beni-SuefBeni-Suef, Egypt
| | - Michelle L. Wright
- Nell Hodgson Woodruff School of Nursing, Emory UniversityAtlanta, GA, United States
| | - N. V. Anil Kumar
- Department of Chemistry, Manipal Institute of Technology, Manipal UniversityManipal, India
| | | | - Sherif T. S. Hassan
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences BrnoBrno, Czechia
| | - Andrei Mocan
- Department of Pharmaceutical Botany, Iuliu Hatieganu University of Medicine and PharmacyCluj-Napoca, Romania
- ICHAT and Institute for Life Sciences, University of Agricultural Sciences and Veterinary MedicineCluj-Napoca, Romania
| | - Seyed M. Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical SciencesTehran, Iran
| | - Luca Rastrelli
- Dipartimento di Farmacia, University of SalernoFisciano, Italy
| | - Atanas G. Atanasov
- Institute of Genetics and Animal Breeding, Polish Academy of SciencesJastrzebiec, Poland
- Department of Pharmacognosy, University of ViennaVienna, Austria
- Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of ViennaVienna, Austria
| | - Pierre S. Haddad
- Natural Health Products and Metabolic Diseases Laboratory, Department of Pharmacology and Physiology, Université de MontréalMontréal, QC, Canada
- Canadian Institutes of Health Research Team in Aboriginal Antidiabetic MedicinesMontréal, QC, Canada
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15
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Mailhe M, Ricaboni D, Vitton V, Lagier JC, Fournier PE, Raoult D. 'Traorella massiliensis' gen. nov., sp. nov., a new bacterial species isolated from the left colon of a 76-year-old woman. New Microbes New Infect 2017; 17:13-14. [PMID: 28275430 PMCID: PMC5328705 DOI: 10.1016/j.nmni.2016.12.009] [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: 11/20/2016] [Revised: 12/07/2016] [Accepted: 12/07/2016] [Indexed: 10/26/2022] Open
Abstract
We present here the summary of main characteristics of 'Traorella massiliensis' strain Marseille-P3110T, which was isolated from a left colon liquid sample of a 76-year-old woman.
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Affiliation(s)
- M. Mailhe
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - D. Ricaboni
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
- Département des sciences cliniques et biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Via GB Grassi, 74, 20157 Milan, Italy
| | - V. Vitton
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
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16
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Ricaboni D, Mailhe M, Cadoret F, Vitton V, Fournier PE, Raoult D, Lagier JC. 'Merdibacter massiliensis' gen. nov., sp. nov., isolated from human ileum. New Microbes New Infect 2017; 15:89-91. [PMID: 28050253 PMCID: PMC5192474 DOI: 10.1016/j.nmni.2016.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 11/15/2016] [Accepted: 11/18/2016] [Indexed: 12/22/2022] Open
Abstract
We report here the main characteristics of 'Merdibacter massiliensis' strain Marseille-P3254T (= CSUR P3254 = DSM 103475), which was isolated from human ileum.
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Affiliation(s)
- D. Ricaboni
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
- Service de Gastroenterologie, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - M. Mailhe
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - F. Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - V. Vitton
- Department of Biomedical and Clinical Sciences, 3rd Division of Clinical Infectious Disease, University of Milan, Luigi Sacco Hospital, Milan, Italy
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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17
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2016; 66:2463-2466. [DOI: 10.1099/ijsem.0.001149] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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18
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Tegtmeier D, Riese C, Geissinger O, Radek R, Brune A. Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., two fermenting bacteria isolated from insect guts, and emended description of the family Erysipelotrichaceae. Syst Appl Microbiol 2016; 39:319-29. [PMID: 27270136 DOI: 10.1016/j.syapm.2016.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/13/2016] [Accepted: 05/17/2016] [Indexed: 11/30/2022]
Abstract
Two novel, obligately anaerobic Firmicutes from the family Erysipelotrichaceae were isolated from the intestinal tracts of a cockroach (strain ErySL, Shelfordella lateralis) and a scarab beetle larva (strain Pei061, Pachnoda ephippiata). Phylogenetic analysis indicated that the strains belong to a monophyletic group of hitherto uncultured bacteria from insect guts that are only distantly related to any described species (<90% 16S rRNA gene sequence similarity). Ultrastructural analysis revealed a Gram-positive cell envelope and, in the case of strain ErySL, a wide electron-lucent space between the cytoplasmic membrane and cell wall. In older cultures, cells formed pleomorphic rods with a thicker peptidoglycan layer. Both strains were obligately anaerobic and fermented glucose to formate, ethanol, and acetate as major products, but strain Pei061 tolerated up to 1% oxygen in the headspace. The same type of metabolism was observed with Erysipelothrix inopinata, except that the latter grew, albeit poorly, even under air. However, previous claims of a microaerophilic or facultatively anaerobic metabolism in the genus Erysipelothrix could not be substantiated. Based on phenotypic and phylogenetic evidence, we propose to classify the isolates as members of a new genus, Breznakia blatticola gen. nov. sp. nov. and Breznakia pachnodae sp. nov., with strain ErySL(T) (=DSM 28867(T)=JCM 30190(T)) and strain Pei061(T) (=DSM 16784(T)=JCM 30191(T)) as type strains, and provide an emended description of the family Erysipelotrichaceae.
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Affiliation(s)
- Dorothee Tegtmeier
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Cornelius Riese
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Oliver Geissinger
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Renate Radek
- Institute of Biology/Zoology, Free University of Berlin, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany.
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19
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Angelakis E, Lagier JC. Samples and techniques highlighting the links between obesity and microbiota. Microb Pathog 2016; 106:119-126. [PMID: 26828871 DOI: 10.1016/j.micpath.2016.01.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/23/2016] [Accepted: 01/28/2016] [Indexed: 12/17/2022]
Abstract
The composition of gut microbiota and its relationship to human health, particularly its links with obesity remain an ongoing challenge for scientists. The current gold standard for exploring human gut microbiota consists of using stool samples and only applying next generations sequencing techniques, which sometimes generate contradictory results. Here, we comprehensively describe nutrient absorption, fat digestion, carbohydrate and protein absorption, demonstrating that absorption of these diverse nutrients occurs mainly in the stomach and small intestine. Indeed, bariatric surgery, including Roux-en-Y, removes part of the upper intestine, resulting in weight loss, while colonic surgery is associated with a stable weight. However, most studies only use stool samples rather than small intestine samples because of the easy with which this can be accessed. Metagenomics studies are associated with several biases such as extraction and primer biases and depth bias, including the more modern platforms. High-throughput culture-dependent techniques, such as culturomics, which uses rapid identification methods such as MALDI-TOF, remain time-consuming, but have demonstrated their complementarity with molecular techniques. In conclusion, we believe that a comprehensive analysis of the relationships between obesity and gut microbiota requires large-scale studies coupling metagenomics and culture-dependent research, in order to analyse both small intestine and stool samples.
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Affiliation(s)
- Emmanouil Angelakis
- Aix-Marseille Université URMITE, UM63, IHU Méditerranée Infection, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université URMITE, UM63, IHU Méditerranée Infection, CNRS 7278, IRD 198, INSERM 1095, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France.
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20
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Ziganshina EE, Belostotskiy DE, Ilinskaya ON, Boulygina EA, Grigoryeva TV, Ziganshin AM. Effect of the Organic Loading Rate Increase and the Presence of Zeolite on Microbial Community Composition and Process Stability During Anaerobic Digestion of Chicken Wastes. MICROBIAL ECOLOGY 2015; 70:948-60. [PMID: 26045158 DOI: 10.1007/s00248-015-0635-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/22/2015] [Indexed: 05/24/2023]
Abstract
This study investigates the effect of the organic loading rate (OLR) increase from 1.0 to 3.5 g VS L(-1) day(-1) at constant hydraulic retention time (HRT) of 35 days on anaerobic reactors' performance and microbial diversity during mesophilic anaerobic digestion of ammonium-rich chicken wastes in the absence/presence of zeolite. The effects of anaerobic process parameters on microbial community structure and dynamics were evaluated using a 16S ribosomal RNA gene-based pyrosequencing approach. Maximum 12 % of the total ammonia nitrogen (TAN) was efficiently removed by zeolite in the fixed zeolite reactor (day 87). In addition, volatile fatty acids (VFA) in the fixed zeolite reactor accumulated in lower concentrations at high OLR of 3.2-3.5 g VS L(-1) day(-1). Microbial communities in the fixed zeolite reactor and reactor without zeolite were dominated by various members of Bacteroidales and Methanobacterium sp. at moderate TAN and VFA levels. The increase of the OLR accompanied by TAN and VFA accumulation and increase in pH led to the predominance of representatives of the family Erysipelotrichaceae and genera Clostridium and Methanosarcina. Methanosarcina sp. reached relative abundances of 94 and 57 % in the fixed zeolite reactor and reactor without zeolite at the end of the experimental period, respectively. In addition, the diminution of Synergistaceae and Crenarchaeota and increase in the abundance of Acholeplasmataceae in parallel with the increase of TAN, VFA, and pH values were observed.
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Affiliation(s)
- Elvira E Ziganshina
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan, 420008, The Republic of Tatarstan, Russia
| | - Dmitry E Belostotskiy
- Department of Technologies, A. E. Arbuzov Institute of Organic and Physical Chemistry, Russian Academy of Sciences, Kazan, 420088, The Republic of Tatarstan, Russia
| | - Olga N Ilinskaya
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan, 420008, The Republic of Tatarstan, Russia
| | - Eugenia A Boulygina
- Laboratory of Omics Technologies, Kazan (Volga Region) Federal University, Kazan, 420008, The Republic of Tatarstan, Russia
| | - Tatiana V Grigoryeva
- Laboratory of Omics Technologies, Kazan (Volga Region) Federal University, Kazan, 420008, The Republic of Tatarstan, Russia
| | - Ayrat M Ziganshin
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan, 420008, The Republic of Tatarstan, Russia.
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21
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Dubourg G, Cimmino T, Senkar SA, Lagier JC, Robert C, Flaudrops C, Brouqui P, Raoult D, Fournier PE, Rolain JM. Noncontiguous finished genome sequence and description of Paenibacillus antibioticophila sp. nov. GD11(T), the type strain of Paenibacillus antibioticophila. New Microbes New Infect 2015; 8:137-47. [PMID: 27257493 PMCID: PMC4877408 DOI: 10.1016/j.nmni.2015.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/07/2015] [Accepted: 10/07/2015] [Indexed: 11/22/2022] Open
Abstract
Paenibacillus antibioticophila strain GD11T sp. nov. is the type strain of a new species within the genus Paenibacillus. This strain, whose genome is described here, was isolated from human faeces of a 63-year-old woman with multidrug-resistant tuberculosis who was receiving numerous antibiotics at the time of stool collection. P. antibioticophila is a Gram-positive aerobic bacterium. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 5 562 631 bp long genome contains 5084 protein-coding and 71 RNA genes.
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Affiliation(s)
- G Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
| | - T Cimmino
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - S A Senkar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - J-C Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
| | - C Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - C Flaudrops
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - P Brouqui
- Service des Maladies Infectieuses et Tropicales. Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
| | - J-M Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
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Belostotskiy DE, Ziganshina EE, Siniagina M, Boulygina EA, Miluykov VA, Ziganshin AM. Impact of the substrate loading regime and phosphoric acid supplementation on performance of biogas reactors and microbial community dynamics during anaerobic digestion of chicken wastes. BIORESOURCE TECHNOLOGY 2015; 193:42-52. [PMID: 26117234 DOI: 10.1016/j.biortech.2015.06.066] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/09/2015] [Accepted: 06/13/2015] [Indexed: 05/27/2023]
Abstract
This study evaluates the effects of increasing organic loading rate (OLR) and decreasing hydraulic retention time (HRT) as well as phosphoric acid addition on mesophilic reactors' performance and biogas production from chicken wastes. Furthermore, microbial community composition in reactors was characterized by a 16S rRNA gene-based pyrosequencing analysis. Each step of increasing OLR impacted on the activity of microorganisms what caused a temporary decrease in biogas production. The addition of phosphoric acid resulted in the increased biogas production with values between 361 and 447 mL g(VS)(-1) from day 61 to day 74 compared to control reactor (309-350 mL g(VS)(-1)). With reactors' operation, Bacteroidetes phylotypes were noticeably replaced with Firmicutes representatives, and significant increase of Clostridium sp. was identified. Within Euryarchaeota, Methanosarcina sp. dominated in all analyzed samples, in which high ammonium levels were detected (3.4-4.9 NH4(+)-N g L(-1)). These results can help in better understanding the anaerobic digestion process of simultaneously ammonium/phosphate-rich substrates.
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Affiliation(s)
- Dmitry E Belostotskiy
- Department of Technologies, A.E. Arbuzov Institute of Organic and Physical Chemistry, RAN, Kazan 420088, The Republic of Tatarstan, Russia
| | - Elvira E Ziganshina
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan 420008, The Republic of Tatarstan, Russia
| | - Maria Siniagina
- Laboratory of Omics Technologies, Kazan (Volga Region) Federal University, Kazan 420008, The Republic of Tatarstan, Russia
| | - Eugenia A Boulygina
- Laboratory of Omics Technologies, Kazan (Volga Region) Federal University, Kazan 420008, The Republic of Tatarstan, Russia
| | - Vasili A Miluykov
- Department of Technologies, A.E. Arbuzov Institute of Organic and Physical Chemistry, RAN, Kazan 420088, The Republic of Tatarstan, Russia
| | - Ayrat M Ziganshin
- Department of Microbiology, Kazan (Volga Region) Federal University, Kazan 420008, The Republic of Tatarstan, Russia.
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Faecalibaculum rodentium gen. nov., sp. nov., isolated from the faeces of a laboratory mouse. Antonie van Leeuwenhoek 2015; 108:1309-1318. [PMID: 26349481 DOI: 10.1007/s10482-015-0583-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 09/02/2015] [Indexed: 01/31/2023]
Abstract
A novel strictly anaerobic strain, ALO17(T), was isolated from mouse faeces and found to produce lactic acid as a major metabolic end product. The isolate was observed to be Gram-stain positive, non-motile, non-spore forming small rods, oxidase and catalase negative, and to form cream-coloured colonies on DSM 104 agar plates. The NaCl range for growth was determined to be 0-2 % (w/v). The isolate was found to grow optimally at 37 °C, with 0.5 % (w/v) NaCl and at pH 7. The cell wall hydrolysates were found to contain ribose as a major sugar. The genomic DNA G+C content was determined to be 52.3 mol%. A phylogenetic analysis of the 16S rRNA gene sequence revealed that Holdemanella biformis DSM 3989(T), Faecalicoccus pleomorphus ATCC 29734(T), Faecalitalea cylindroides ATCC 27803(T), and Allobaculum stercoricanis DSM 13633(T) are closely related to the isolate (87.4, 87.3, 86.9 and 86.9 % sequence similarity), respectively. The major cellular fatty acids (>10 %) of the isolate were identified as C18:1 cis 9 FAME (36.9 %), C16:0 FAME (33.7 %) and C18:0 FAME (13.2 %). In contrast to the tested reference strains, C20:0 FAME (4.0 %) was detected only in strain ALO17(T) whilst C16:0 DMA was absent. The isolate also differed in its substrate oxidation profiles from the reference strains by being positive for D-melibiose and stachyose but negative for N-acetyl-D-galactosamine and 3-methyl-D-glucose. On the basis of polyphasic taxonomic evidence from this study, the isolate is concluded to belong to a novel genus within the family Erysipelothricaceae. We propose the name Faecalibaculum rodentium gen. nov., sp. nov. to accommodate strain ALO17(T) (=KCTC 15484(T) = JCM 30274(T)) as the type strain.
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24
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Bittar F, Bibi F, Ramasamy D, Lagier JC, Azhar EI, Jiman-Fatani AA, Al-Ghamdi AK, Nguyen TT, Yasir M, Fournier PE, Raoult D. Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov. Stand Genomic Sci 2015; 10:47. [PMID: 26380635 PMCID: PMC4572673 DOI: 10.1186/s40793-015-0024-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/21/2015] [Indexed: 11/13/2022] Open
Abstract
Strain JCE(T) was isolated from the fecal sample of a 24-year-old obese man living in Jeddah, Saudi Arabia. It is an aerobic, Gram-positive, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.5 % with Bacillus niacini, the phylogenetically closest species with standing nomenclature. Moreover, the strain JCE(T) presents many phenotypic differences, when it is compared to other Bacillus species, and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,762,944 bp long genome (1 chromosome but no plasmid) contains 4,654 protein-coding and 98 RNAs genes, including 92 tRNA genes. The strain JCE(T) differs from most of the other closely Bacillus species by more than 1 % in G + C content. In addition, digital DNA-DNA hybridization values for the genome of the strain JCE(T) against the closest Bacillus genomes range between 19.5 to 28.1, that confirming again its new species status. On the basis of these polyphasic data made of phenotypic and genomic analyses, we propose the creation of Bacillus jeddahensis sp. nov. that contains the strain JCE(T).
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Affiliation(s)
- Fadi Bittar
- />URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Fehmida Bibi
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Esam I. Azhar
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- />Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif A. Jiman-Fatani
- />Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed K. Al-Ghamdi
- />Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ti Thien Nguyen
- />URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Muhammad Yasir
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Didier Raoult
- />URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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25
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The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 2015; 28:237-64. [PMID: 25567229 DOI: 10.1128/cmr.00014-14] [Citation(s) in RCA: 507] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.
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26
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Sankar SA, Lagier JC, Pontarotti P, Raoult D, Fournier PE. The human gut microbiome, a taxonomic conundrum. Syst Appl Microbiol 2015; 38:276-86. [DOI: 10.1016/j.syapm.2015.03.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/16/2023]
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27
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Angelakis E, Bibi F, Ramasamy D, Azhar EI, Jiman-Fatani AA, Aboushoushah SM, Lagier JC, Robert C, Caputo A, Yasir M, Fournier PE, Raoult D. Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov. Stand Genomic Sci 2014; 9:8. [PMID: 25780501 PMCID: PMC4334108 DOI: 10.1186/1944-3277-9-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 12/03/2022] Open
Abstract
Clostridium saudii strain JCC(T) sp. nov. is the type strain of C. saudii sp. nov., a new species within the genus Clostridia. This strain, whose genome is described here, was isolated from a fecal sample collected from an obese 24-year-old (body mass index 52 kg/m2) man living in Jeddah, Saudi Arabia. C. saudii is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,653,762 bp long genome contains 3,452 protein-coding and 53 RNA genes, including 4 rRNA genes.
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Affiliation(s)
- Emmanouil Angelakis
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Dhamodharan Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif A Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sally M Aboushoushah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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28
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Angelakis E, Raoult D. Methods for the discovery of emerging pathogens. Microb Pathog 2014; 77:114-8. [PMID: 25014736 PMCID: PMC7127287 DOI: 10.1016/j.micpath.2014.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 06/23/2014] [Indexed: 01/18/2023]
Abstract
Recently, there has been a steady increase in the number of recognized pathogenic microorganisms, specifically bacteria. The development of genetic technologies, MALDI-TOF mass spectrometry and new culturing techniques has significantly widened the repertoire of known microorganisms and therefore pathogenic microorganisms. The repertoire of infectious agents has been studied in various environments including water, soil, pets, livestock, wildlife and arthropods. Using different methods, many known pathogens can be identified in these samples; therefore, the impact of emergent pathogens on humans can be examined and novel pathogens can be identified. In this special issue, we discuss the identification of emerging pathogens in the environment and animals.
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Affiliation(s)
- Emmanouil Angelakis
- URMITE CNRS-IRD 198 UMR 6236, Université de la Méditerranée, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France.
| | - Didier Raoult
- URMITE CNRS-IRD 198 UMR 6236, Université de la Méditerranée, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France
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29
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Padmanabhan R, Dubourg G, Nguyen TT, Couderc C, Rossi-Tamisier M, Caputo A, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov. Stand Genomic Sci 2014; 9:1144-58. [PMID: 25197489 PMCID: PMC4149003 DOI: 10.4056/sigs.5399696] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Collinsella massiliensis strain GD3(T) is the type strain of Collinsella massiliensis sp. nov., a new species within the genus Collinsella. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old French Caucasoid woman who had been admitted to intensive care unit for Guillain-Barré syndrome. Collinsella massiliensis is a Gram-positive, obligate anaerobic, non motile and non sporulating bacillus. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes, including 1 rRNA operon.
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Affiliation(s)
- Roshan Padmanabhan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Gregory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Jean-Christophe lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Thi-Thien Nguyen
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Carine Couderc
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Morgane Rossi-Tamisier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
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30
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Keita MB, Padhmananabhan R, Caputo A, Robert C, Delaporte E, Raoult D, Fournier PE, Bittar F. Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov. Stand Genomic Sci 2014; 9:1031-45. [PMID: 25197481 PMCID: PMC4149019 DOI: 10.4056/sigs.5189179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Strain G1(T) sp. nov. is the type strain of Paenibacillus gorillae a newly proposed species within the genus Paenibacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. P. gorillae is a facultative anaerobic, Gram-negative, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,257,967 bp long genome (one chromosome but no plasmid) contains 5,856 protein-coding and 62 RNAs genes, including 60 tRNA genes.
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Affiliation(s)
| | | | - Aurélia Caputo
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Catherine Robert
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | | | - Didier Raoult
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
- King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | | | - Fadi Bittar
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
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31
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Lagier JC, Bibi F, Ramasamy D, Azhar EI, Robert C, Yasir M, Jiman-Fatani AA, Alshali KZ, Fournier PE, Raoult D. Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov. Stand Genomic Sci 2014; 9:1003-19. [PMID: 25197479 PMCID: PMC4148971 DOI: 10.4056/sigs.5571026] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium jeddahense strain JCD(T) (= CSUR P693 = DSM 27834) is the type strain of C. jeddahense sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of an obese 24 year-old Saudian male (BMI=52 kg/m(2)). Clostridium jeddahense strain JCD(T) is an obligate Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,613,503 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 51.95% and contains 3,462 protein-coding and 53 RNA genes, including 4 rRNA genes.
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Affiliation(s)
- Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278 – IRD 198, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Dhamodharan Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278 – IRD 198, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278 – IRD 198, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Khalid Z. Alshali
- Department of Medicine, Faculty of Medicine, King Abdulaziz University, PO Box 80215, Jeddah, Postal code 21589, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278 – IRD 198, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278 – IRD 198, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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32
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Edouard S, Bibi F, Dhamodharan R, Lagier JC, Azhar EI, Robert C, Caputo A, Yasir M, Jiman-Fatani AA, Alawi M, Fournier PE, Raoult D. Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov. Stand Genomic Sci 2014; 9:987-1002. [PMID: 25197478 PMCID: PMC4149016 DOI: 10.4056/sigs.5561028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Corynebacterium jeddahense sp. nov., strain JCBT, is the type strain of Corynebacterium jeddahense sp. nov., a new species within the genus Corynebacterium. This strain, whose genome is described here, was isolated from fecal flora of a 24-year-old Saudi male suffering from morbid obesity. Corynebacterium jeddahense is a Gram-positive, facultative anaerobic, nonsporulating bacillus. Here, we describe the features of this bacterium, together with the complete genome sequencing and annotation, and compare it to other member of the genus Corynebacterium. The 2,472,125 bp-long genome (1 chromosome but not plasmid) contains 2,359 protein-coding and 53 RNA genes, including 1 rRNA operon.
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Affiliation(s)
- Sophie Edouard
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Ramasamy Dhamodharan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Esam Ibraheen Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia . ; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Asif Ahmad Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maha Alawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia ; Infection Control Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France ; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
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Edouard S, Sankar S, Dangui NPM, Lagier JC, Michelle C, Raoult D, Fournier PE. Genome sequence and description of Nesterenkonia massiliensis sp. nov. strain NP1(T.). Stand Genomic Sci 2014; 9:866-82. [PMID: 25197469 PMCID: PMC4148991 DOI: 10.4056/sigs.5631022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nesterenkonia massiliensis sp. nov., strain NP1T, is the type strain of Nesterenkonia massiliensis sp. nov., a new species within the genus Nesterenkonia. This strain, whose genome is described here, was isolated from the feces of a 32-year-old French woman suffering from AIDS and living in Marseille. Nesterenkonia massiliensis is a Gram-positive aerobic coccus. Here, we describe the features of this bacterium, together with the complete genome sequencing and annotation. The 2,726,371 bp long genome (one chromosome but no plasmid) contains 2,663 protein-coding and 51 RNA genes, including 1 rRNA operon.
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Affiliation(s)
- Sophie Edouard
- Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Senthil Sankar
- Aix-Marseille Université, Faculté de médecine, Marseille, France
| | | | | | | | - Didier Raoult
- Aix-Marseille Université, Faculté de médecine, Marseille, France . ; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Bendjama E, Loucif L, Diene SM, Michelle C, Gacemi-Kirane D, Rolain JM. Non-contiguous finished genome sequence and description of Bacillus massilioalgeriensis sp. nov. Stand Genomic Sci 2014; 9:1046-61. [PMID: 25197482 PMCID: PMC4149007 DOI: 10.4056/sigs.5459590] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strain EB01T sp. nov. is the type strain of Bacillus massilioalgeriensis, a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from sediment sample of the hypersaline lake Ezzemoul sabkha in northeastern Algeria. B. massilioalgeriensis is a facultative anaerobic Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,269,577 bp long genome contains 5,098 protein-coding and 95 RNA genes, including 12 rRNA genes.
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Affiliation(s)
- Esma Bendjama
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France . ; Département de Biochimie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie ; Département des Sciences Biologiques, Faculté des Sciences, Université El Hadj Lakhdar, Batna, Algérie
| | - Lotfi Loucif
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France . ; Département de Biochimie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie ; Département des Sciences Biologiques, Faculté des Sciences, Université El Hadj Lakhdar, Batna, Algérie
| | - Seydina M Diene
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Caroline Michelle
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Djamila Gacemi-Kirane
- Département de Biochimie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie
| | - Jean-Marc Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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Bendjama E, Loucif L, Diene SM, Michelle C, Gacemi-Kirane D, Rolain JM. Non-contiguous finished genome sequence and description of Paucisalibacillus algeriensis sp. nov. Stand Genomic Sci 2014; 9:1352-65. [PMID: 25197503 PMCID: PMC4148997 DOI: 10.4056/sigs.5611012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Paucisalibacillus algeriensis strain EB02T is the type strain of Paucisalibacillus algeriensis sp. nov., a new species within the genus Paucisalibacillus. This strain, whose genome is described here, was isolated from soil sample from the hypersaline lake Ezzemoul Sabkha in northeastern Algeria. Paucisalibacillus algeriensis is a Gram-positive and strictly aerobic bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,006,766 bp long genome (1 chromosome but no plasmid) exhibits a low G+C content of 36% and contains 3,956 protein-coding and 82 RNA genes, including 9 rRNA genes.
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Affiliation(s)
- Esma Bendjama
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France . ; Département de Biochimie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie . ; Département des Sciences Biologiques, Faculté des Sciences, Université El Hadj Lakhdar, Batna, Algérie
| | - Lotfi Loucif
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France . ; Département de Biochimie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie . ; Département des Sciences Biologiques, Faculté des Sciences, Université El Hadj Lakhdar, Batna, Algérie
| | - Seydina M Diene
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Caroline Michelle
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Djamila Gacemi-Kirane
- Département de Biochimie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie
| | - Jean-Marc Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UMR CNRS, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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Keita MB, Padhmanabhan R, Caputo A, Robert C, Delaporte E, Raoult D, Fournier PE, Bittar F. Non-contiguous finished genome sequence and description of Gorillibacterium massiliense gen. nov, sp. nov., a new member of the family Paenibacillaceae. Stand Genomic Sci 2014; 9:807-20. [PMID: 25197465 PMCID: PMC4148990 DOI: 10.4056/sigs.5199182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strain G5(T) gen. nov., sp. nov. is the type strain of Gorillibacterium massiliense, a newly proposed genus within the family Paenibacillaceae. This strain, whose genome is described here, was isolated in France from a stool sample of a wild Gorilla gorilla subsp. gorilla from Cameroon. G. massiliense is a facultatively anaerobic, Gram negative rod. Here we describe the features of this bacterium, together with the complete genome sequence and annotation. The 5,546,433 bp long genome (1 chromosome but no plasmid) contains 5,145 protein-coding and 76 RNA genes, including 69 tRNA genes.
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Affiliation(s)
| | | | - Aurélia Caputo
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Catherine Robert
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | | | - Didier Raoult
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France ; King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | | | - Fadi Bittar
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
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Padmanabhan R, Dubourg G, Lagier JC, Couderc C, Michelle C, Raoult D, Fournier PE. Genome sequence and description of Corynebacterium ihumii sp. nov. Stand Genomic Sci 2014; 9:1128-43. [PMID: 25197488 PMCID: PMC4149009 DOI: 10.4056/sigs.5149006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Corynebacterium ihumii strain GD7T sp. nov. is proposed as the type strain of a new species, which belongs to the family Corynebacteriaceae of the class Actinobacteria. This strain was isolated from the fecal flora of a 62 year-old male patient, as a part of the culturomics study. Corynebacterium ihumii is a Gram positive, facultativly anaerobic, nonsporulating bacillus. Here, we describe the features of this organism, together with the high quality draft genome sequence, annotation and the comparison with other member of the genus Corynebacteria. C. ihumii genome is 2,232,265 bp long (one chromosome but no plasmid) containing 2,125 protein-coding and 53 RNA genes, including 4 rRNA genes. The whole-genome shotgun sequence of Corynebacterium ihumii strain GD7T sp. nov has been deposited in EMBL under accession number GCA_000403725.
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Affiliation(s)
- Roshan Padmanabhan
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, IHU Méditerranée-Infection, Aix-Marseille Université, Faculté de médecine, France
| | - Grégory Dubourg
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, IHU Méditerranée-Infection, Aix-Marseille Université, Faculté de médecine, France
| | - Jean-Christophe Lagier
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, IHU Méditerranée-Infection, Aix-Marseille Université, Faculté de médecine, France
| | - Carine Couderc
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, IHU Méditerranée-Infection, Aix-Marseille Université, Faculté de médecine, France
| | - Caroline Michelle
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, IHU Méditerranée-Infection, Aix-Marseille Université, Faculté de médecine, France
| | - Didier Raoult
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, IHU Méditerranée-Infection, Aix-Marseille Université, Faculté de médecine, France ; Special Unit Agents, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- URMITE, UM63, CNRS7278, IRD198, Inserm1095, IHU Méditerranée-Infection, Aix-Marseille Université, Faculté de médecine, France
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Ramasamy D, Lagier JC, Rossi-Tamisier M, Pfleiderer A, Michelle C, Couderc C, Raoult D, Fournier PE. Genome sequence and description of Bacteroides timonensis sp. nov. Stand Genomic Sci 2014; 9:1181-97. [PMID: 25197491 PMCID: PMC4148978 DOI: 10.4056/sigs.5389564] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacteroides timonensis strain AP1T (= CSUR P194 = DSM 26083) is the type strain of B. timonensis sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasoid female who suffered from severe anorexia nervosa. Bacteroides timonensis is a Gram-negative, obligate anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 7,130,768 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 43.3% and contains 5,786 protein-coding and 59 RNA genes, including 2 rRNA genes.
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Affiliation(s)
- Dhamodharan Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Morgane Rossi-Tamisier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Anne Pfleiderer
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Caroline Michelle
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Carine Couderc
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France ; King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
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Ramasamy D, Dubourg G, Robert C, Caputo A, Papazian L, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Enorma timonensis sp. nov. Stand Genomic Sci 2014; 9:970-86. [PMID: 25197477 PMCID: PMC4149031 DOI: 10.4056/sigs.4878632] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enorma timonensis strain GD5(T) sp. nov., is the type strain of E. timonensis sp. nov., a new member of the genus Enorma within the family Coriobacteriaceae. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old woman hospitalized for 3 months in an intensive care unit. E. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,365,123 bp long genome (1 chromosome but no plasmid) contains 2,060 protein-coding and 52 RNA genes, including 4 rRNA genes.
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Affiliation(s)
- Dhamodaran Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université
| | - Gregory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université
| | - Laurent Papazian
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université ; Service de Réanimation Médicale, Hôpital Nord, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université ; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université ; Correspondence: Pierre-Edouard Fournier ( )
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Pfleiderer A, Mishra AK, Lagier JC, Robert C, Caputo A, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Alistipes ihumii sp. nov. Stand Genomic Sci 2014; 9:1221-35. [PMID: 25197494 PMCID: PMC4149002 DOI: 10.4056/sigs.4698398] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alistipes ihumii strain AP11T sp. nov. is the type strain of A. ihumii sp. nov., a new species within the genus Alistipes. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasian female, suffering from a severe restrictive form of anorexia nervosa since the age of 12 years. A. ihumii is a Gram-negative anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,753,264 bp long genome (one chromosome but no plasmid) contains 2,254 protein-coding and 47 RNA genes, including 3 rRNA genes.
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Affiliation(s)
- Anne Pfleiderer
- Aix-Marseille Université, URMITE, UM63, Faculté de médecine, Marseille, France
| | - Ajay Kumar Mishra
- Aix-Marseille Université, URMITE, UM63, Faculté de médecine, Marseille, France
| | | | - Catherine Robert
- Aix-Marseille Université, URMITE, UM63, Faculté de médecine, Marseille, France
| | - Aurelia Caputo
- Aix-Marseille Université, URMITE, UM63, Faculté de médecine, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, Faculté de médecine, Marseille, France ; King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
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Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M, Sentausa E, Raoult D, Fournier PE. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 2014; 64:384-391. [DOI: 10.1099/ijs.0.057091-0] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Currently, bacterial taxonomy relies on a polyphasic approach based on the combination of phenotypic and genotypic characteristics. However, the current situation is paradoxical in that the genetic criteria that are used, including DNA–DNA hybridization, 16S rRNA gene sequence nucleotide similarity and phylogeny, and DNA G+C content, have significant limitations, but genome sequences that contain the whole genetic information of bacterial strains are not used for taxonomic purposes, despite the decreasing costs of sequencing and the increasing number of available genomes. Recently, we diversified bacterial culture conditions with the aim of isolating uncultivated bacteria. To classify the putative novel species that we cultivated, we used a polyphasic strategy that included phenotypic as well as genomic criteria (genome characteristics as well as genomic sequence similarity). Herein, we review the pros and cons of genome sequencing for taxonomy and propose that the incorporation of genome sequences in taxonomic studies has the advantage of using reliable and reproducible data. This strategy, which we name taxono-genomics, may contribute to the taxonomic classification of bacteria.
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Affiliation(s)
- Dhamodharan Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Ajay Kumar Mishra
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Roshan Padhmanabhan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Morgane Rossi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Erwin Sentausa
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
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Mishra AK, Lagier JC, Pfleiderer A, Nguyen TT, Caputo A, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov. Stand Genomic Sci 2013; 9:395-409. [PMID: 24976895 PMCID: PMC4062643 DOI: 10.4056/sigs.4628316] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Holdemania massiliensis strain AP2(T) sp. nov. is the type strain of H. massiliensis sp. nov., a new species within the genus Holdemania. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasian female suffering from severe restrictive anorexia nervosa. H. massiliensis is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,795,625 bp-long genome (one chromosome but no plasmid) contains 3,461 protein-coding and 49 RNA genes, including 3 rRNA genes.
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Affiliation(s)
- Ajay Kumar Mishra
- URMITE, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France*
| | - Jean-Christophe Lagier
- URMITE, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France*
| | - Anne Pfleiderer
- URMITE, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France*
| | - Thi Thien Nguyen
- URMITE, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France*
| | - Aurelia Caputo
- URMITE, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France*
| | - Didier Raoult
- URMITE, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France*
- King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- URMITE, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Faculté de Médecine, Marseille, France*
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Padmanabhan R, Lagier JC, Dangui NPM, Michelle C, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov. Stand Genomic Sci 2013; 8:525-38. [PMID: 24501636 PMCID: PMC3910696 DOI: 10.4056/sigs.4077819] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Megasphaera massiliensis strain NP3(T) sp. nov. is the type strain of Megasphaera massiliensis sp. nov., a new species within the genus Megasphaera. This strain, whose genome is described here, was isolated from the fecal flora of an HIV-infected patient. M. massiliensis is a Gram-negative, obligate anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,661,757 bp long genome (1 chromosome but no plasmid) contains 2,577 protein-coding and 61 RNA genes, including 5 rRNA genes.
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Affiliation(s)
- Roshan Padmanabhan
- Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France
| | | | | | - Caroline Michelle
- Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France
| | - Carine Couderc
- Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France
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Mishra AK, Pfleiderer A, Lagier JC, Robert C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov. Stand Genomic Sci 2013; 8:465-79. [PMID: 24501631 PMCID: PMC3910694 DOI: 10.4056/sigs.4087826] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus massilioanorexius strain AP8(T) sp. nov. is the type strain of B. massilioanorexius sp. nov., a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old Caucasian French female suffering from a severe form of anorexia nervosa since the age of 12 years. B. massilioanorexius is a Gram-positive aerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,616,135 bp long genome (one chromosome but no plasmid) contains 4,432 protein-coding and 87 RNA genes, including 8 rRNA genes.
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Affiliation(s)
| | - Anne Pfleiderer
- Aix-Marseille Université, URMITE, Faculté de médecine, France
| | | | | | - Didier Raoult
- Aix-Marseille Université, URMITE, Faculté de médecine, France
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Hugon P, Ramasamy D, Robert C, Couderc C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Kallipyga massiliensis gen. nov., sp. nov., a new member of the family Clostridiales Incertae Sedis XI. Stand Genomic Sci 2013; 8:500-15. [PMID: 24501634 PMCID: PMC3910704 DOI: 10.4056/sigs.4047997] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Kallipyga massiliensis strain ph2(T) is the type strain of Kallipyga massiliensis gen. nov., sp. nov., the type species of the new genus Kallipyga within the family Clostridiales Incertae Sedis XI. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. K. massiliensis is an obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,770,679 bp long genome (1 chromosome but no plasmid) contains 1,575 protein-coding and 50 RNA genes, including 4 rRNA genes.
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Affiliation(s)
- Perrine Hugon
- Aix-Marseille Université, Faculté de médecine, Marseille, France
| | | | - Catherine Robert
- Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Carine Couderc
- Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Faculté de médecine, Marseille, France
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