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Ni S, Lv W, Ji Z, Wang K, Mei Y, Li Y. Progress of Crude Oil Gasification Technology Assisted by Microorganisms in Reservoirs. Microorganisms 2024; 12:702. [PMID: 38674646 PMCID: PMC11051786 DOI: 10.3390/microorganisms12040702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Crude oil gasification bacteria, including fermenting bacteria, hydrocarbon-oxidizing bacteria, reducing bacteria, and methanogenic bacteria, participate in multi-step reactions involving initial activation, intermediate metabolism, and the methanogenesis of crude oil hydrocarbons. These bacteria degrade crude oil into smaller molecules such as hydrogen, carbon dioxide, acetic acid, and formic acid. Ultimately, they convert it into methane, which can be utilized or stored as a strategic resource. However, the current challenges in crude oil gasification include long production cycles and low efficiency. This paper provides a summary of the microbial flora involved in crude oil gasification, the gasification metabolism pathways within reservoirs, and other relevant information. It specifically focuses on analyzing the factors that affect the efficiency of crude oil gasification metabolism and proposes suggestions for improving this efficiency. These studies deepen our understanding of the potential of reservoir ecosystems and provide valuable insights for future reservoir development and management.
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Affiliation(s)
- Shumin Ni
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Weifeng Lv
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
- State Key Laboratory of Enhanced Oil Recovery, Research Institute of Petroleum Exploration and Development, CNPC, Beijing 100083, China
| | - Zemin Ji
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Kai Wang
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Yuhao Mei
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Yushu Li
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
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2
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Prakash O, Dodsworth JA, Dong X, Ferry JG, L'Haridon S, Imachi H, Kamagata Y, Rhee SK, Sagar I, Shcherbakova V, Wagner D, Whitman WB. Proposed minimal standards for description of methanogenic archaea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37097839 DOI: 10.1099/ijsem.0.005500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.
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Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
- Symbiosis Centre for Climate Change and Sustainability, Symbiosis International (Deemed University), Lavale, Pune-412115, Maharashtra, India
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephane L'Haridon
- CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, University of Brest, F-29280, Plouzané, France
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoichi Kamagata
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8560, Japan
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Republic of Korea
| | - Isita Sagar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 3, Pushchino, Moscow, 142290, Russian Federation
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg A71-359, 14473 Potsdam, Germany
- Institut of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Antil S, Abraham JS, Sripoorna S, Maurya S, Dagar J, Makhija S, Bhagat P, Gupta R, Sood U, Lal R, Toteja R. DNA barcoding, an effective tool for species identification: a review. Mol Biol Rep 2023; 50:761-775. [PMID: 36308581 DOI: 10.1007/s11033-022-08015-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/07/2022] [Indexed: 02/01/2023]
Abstract
DNA barcoding is a powerful taxonomic tool to identify and discover species. DNA barcoding utilizes one or more standardized short DNA regions for taxon identification. With the emergence of new sequencing techniques, such as Next-generation sequencing (NGS), ONT MinION nanopore sequencing, and Pac Bio sequencing, DNA barcoding has become more accurate, fast, and reliable. Rapid species identification by DNA barcodes has been used in a variety of fields, including forensic science, control of the food supply chain, and disease understanding. The Consortium for Barcode of Life (CBOL) presents various working groups to identify the universal barcode gene, such as COI in metazoans; rbcL, matK, and ITS in plants; ITS in fungi; 16S rRNA gene in bacteria and archaea, and creating a reference DNA barcode library. In this article, an attempt has been made to analyze the various proposed DNA barcode for different organisms, strengths & limitations, recent advancements in DNA barcoding, and methods to speed up the DNA barcode reference library construction. This study concludes that constructing a reference library with high species coverage would be a major step toward identifying species by DNA barcodes. This can be achieved in a short period of time by using advanced sequencing and data analysis methods.
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Affiliation(s)
- Sandeep Antil
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | | | - S Sripoorna
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Swati Maurya
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Jyoti Dagar
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Pooja Bhagat
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, New Delhi, Delhi, 110 021, India
| | - Utkarsh Sood
- The Energy and Resources Institute, IHC Complex, New Delhi, 110003, India
| | - Rup Lal
- The Energy and Resources Institute, IHC Complex, New Delhi, 110003, India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India.
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Guindo CO, Amir L, Couderc C, Drancourt M, Grine G. Rapid identification of clinically interesting methanogens using an improved MALDI-TOF-MS assay. Access Microbiol 2022; 4:acmi000372. [PMID: 36003219 PMCID: PMC9394734 DOI: 10.1099/acmi.0.000372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
Methanogens, the archaea uniquely detoxifying fermentative hydrogen into methane in the digestive tract, are increasingly being detected in pathology situations, rendering their rapid identification mandatory. We improved the experimental protocol to identify broth-cultured methanogens by matrix-assisted laser desorption time-of-flight MS (MALDI-TOF-MS). A database incorporating 34 reference spectra derived from 16 methanogen reference strains representative of eight species supported further identification of 21 Methanobrevibacter smithii and 14 Methanobrevibacter oralis isolates broth-cultured from human stool and oral fluid, respectively, with scores >2. In addition, MALDI-TOF-MS differentiated five Methanobrevibacter smithii genotypes incorporated in the study. The data reported here found MALDI-TOF-MS as a first-line identification method for methanogens recovered from microbiota and clinical samples.
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Affiliation(s)
- Cheick Oumar Guindo
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Lynda Amir
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Carine Couderc
- Laboratoire de Microbiologie, Assistance Publique à Marseille, IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- Laboratoire de Microbiologie, Assistance Publique à Marseille, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ghiles Grine
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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Zakharyuk A, Valyshev A, Plotnikov A, Kopitsyn D, Suzina N, Shcherbakova V. Trichococcus shcherbakoviae subsp. psychrophilus subsp. nov., a psychrotolerant facultative anaerobe isolated from a cold spring. Int J Syst Evol Microbiol 2021; 71. [PMID: 34694985 DOI: 10.1099/ijsem.0.005068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A psychrotolerant facultative anaerobe, strain SKBGT, was isolated from the bottom sediments of the cold mineral spring Buxichen (Buryatia, Russia). Gram-positive non-motile cocci with a diameter of 1.75-2.5 µm were observed singly or in long chains. Cells grew in the temperature range from ̶ 5-35 °C. Growth was observed within the pH range of 7.0-9.5, with the optimum growth at pH 7.6 and at a NaCl concentration from 0-1.0 % (optimum 0.1 % (w/v)). Strain SKBGT was a chemoorganoheterotroph that used sugars and some organic acids as substrates. The predominant fatty acids in cell walls were С16:1ω9, С18:1ω9, and С16 : 0. The 16S rRNA gene sequence of strain SKBGT shared high similarity (>99 %) with those of the type strains of the genus Trichococcus. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKBGT and Trichococcus shcherbakoviae ArtT (=DSM 107162T=VKM B-3260T) were 70.1 and 95.4 %, respectively. The genomic DNA G+C content of strain SKBGT was 47.1 mol%. Compared with the type strain of T. shcherbakoviae, the new strain was characterized by a temperature optimum for growth (10 °C) significantly lower than that of T. shcherbakoviae DSM 107162T (20-30 °C). Based on phenotypic and genomic characteristics, the isolate SKBGT was classified as T. shcherbakoviae subsp. psychrophilus subsp. nov. The type strain is SKBGT (=VKM B-3241Т=JCM 33326T).
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Affiliation(s)
- Anastasiya Zakharyuk
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Prospect Nauki 5, 142290, Pushchino, Moscow Region, Russia
| | - Alexander Valyshev
- Institute of Cellular and Intracellular Symbiosis of the Ural Branch of the Russian Academy of Sciences, Pionerskaya street, 11, 460000, Orenburg, Russia
| | - Andrey Plotnikov
- Institute of Cellular and Intracellular Symbiosis of the Ural Branch of the Russian Academy of Sciences, Pionerskaya street, 11, 460000, Orenburg, Russia
| | - Dmitry Kopitsyn
- Gubkin University, Leninsky Prospect 65-1, 119991, Moscow, Russia
| | - Nataliya Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Prospect Nauki 5, 142290, Pushchino, Moscow Region, Russia
| | - Viktoria Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Prospect Nauki 5, 142290, Pushchino, Moscow Region, Russia
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6
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Du H, Sun T, Liu Y, An S, Xie H, Wang D, Igarashi Y, Imanaka T, Luo F, Ma M. Bacteria and archaea involved in anaerobic mercury methylation and methane oxidation in anaerobic sulfate-rich reactors. CHEMOSPHERE 2021; 274:129773. [PMID: 33556662 DOI: 10.1016/j.chemosphere.2021.129773] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
The identification of dominant microbes in anaerobic mercury (Hg) methylation, methylmercury (MeHg) demethylation, and methane oxidation as sulfate-reducing bacteria, methanogens or, probably, anaerobic methanotrophic archaea (ANMEs) is of great interest. To date, however, the interrelationship of bacteria and archaea involved in these processes remains unclear. Here, we demonstrated the dynamics of microorganisms participating in these processes. Anaerobic fixed-bed reactors were operated with swine manure and sludge to produce methane stably, and then, sulfate (reactor C), sulfate and Hg(II) (reactor H), and sulfate and MeHg (reactor M) were added, and the reactors were operated for 120 d, divided equally into four periods, P1-P4. The bacterial compositions changed nonsignificantly, whereas Methanosaeta in reactors H and M decreased significantly, revealing that it was irrelevant for Hg transformation. The abundances of Syntrophomonadaceae, Methanoculleus, Candidatus Methanogranum and Candidatus Methanoplasma increased continuously with time; these species probably functioned in these processes, but further evidence is needed. Desulfocella and Desulfobacterium dominated first but eventually almost vanished, while the dominant archaeal genera Methanogenium, Methanoculleus and Methanocorpusculum were closely related to ANME-1 and ANME-2. PLS-DA results indicated that both bacteria and archaea in different periods in the three reactors were clustered separately, implying that the microbial compositions in the same periods were similar and changed markedly with time.
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Affiliation(s)
- Hongxia Du
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Tao Sun
- Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Yang Liu
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Siwei An
- Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Haiying Xie
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Dingyong Wang
- Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Yasuo Igarashi
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Tadayuki Imanaka
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Feng Luo
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing, 400715, China.
| | - Ming Ma
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing, 400715, China; Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing, 400715, China.
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Benyahia H, Ouarti B, Diarra AZ, Boucheikhchoukh M, Meguini MN, Behidji M, Benakhla A, Parola P, Almeras L. Identification of Lice Stored in Alcohol Using MALDI-TOF MS. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1126-1133. [PMID: 33346344 DOI: 10.1093/jme/tjaa266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 06/12/2023]
Abstract
Lice pose major public and veterinary health problems with economic consequences. Their identification is essential and requires the development of an innovative strategy. MALDI-TOF MS has recently been proposed as a quick, inexpensive, and accurate tool for the identification of arthropods. Alcohol is one of the most frequently used storage methods and makes it possible to store samples for long periods at room temperature. Several recent studies have reported that alcohol alters protein profiles resulting from MS analysis. After preliminary studies on frozen lice, the purpose of this research was to evaluate the influence of alcohol preservation on the accuracy of lice identification by MALDI-TOF MS. To this end, lice stored in alcohol for variable periods were submitted for MS analysis and sample preparation protocols were optimized. The reproducibility and specificity of the MS spectra obtained on both these arthropod families allowed us to implement the reference MS spectra database (DB) with protein profiles of seven lice species stored in alcohol. Blind tests revealed a correct identification of 93.9% of Pediculus humanus corporis (Linnaeus, 1758) and 98.4% of the other lice species collected in the field. This study demonstrated that MALDI-TOF MS could be successfully used for the identification of lice stored in alcohol for different lengths of time.
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Affiliation(s)
- Hanene Benyahia
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Basma Ouarti
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Adama Zan Diarra
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Mehdi Boucheikhchoukh
- Department of Veterinary Sciences, Chadli Bendjedid University, El-Tarf, 36000, Algeria
| | - Mohamed Nadir Meguini
- Institute of Veterinary and Agronomic Sciences, Mohamed Cherif Messaadia University, Souk-Ahras, Algeria
| | - Makhlouf Behidji
- Institute of Veterinary and Agronomic Sciences, Mohamed Cherif Messaadia University, Souk-Ahras, Algeria
| | - Ahmed Benakhla
- Department of Veterinary Sciences, Chadli Bendjedid University, El-Tarf, 36000, Algeria
| | - Philippe Parola
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Lionel Almeras
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
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Guindo CO, Drancourt M, Grine G. Digestive tract methanodrome: Physiological roles of human microbiota-associated methanogens. Microb Pathog 2020; 149:104425. [PMID: 32745665 DOI: 10.1016/j.micpath.2020.104425] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
Methanogens are the archaea most commonly found in humans, in particular in the digestive tract and are an integral part of the digestive microbiota. They are present in humans from the earliest moments of life and represent the only known source of methane production to date. They are notably detected in humans by microscopy, fluorescent in situ hybridization, molecular biology including PCR-sequencing, metagenomics, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and culture. Methanogens present in the human digestive tract play major roles, in particular the use of hydrogen from the fermentation products of bacteria, thus promoting digestion. They are also involved in the transformation of heavy metals and in the use of trimethylamine produced by intestinal bacteria, thus preventing major health problems, in particular cardiovascular diseases. Several pieces of evidence suggest their close physical contacts with bacteria support symbiotic metabolism. Their imbalance during dysbiosis is associated with many pathologies in humans, particularly digestive tract diseases such as Crohn's disease, ulcerative colitis, diverticulosis, inflammatory bowel disease, irritable bowel syndrome, colonic polyposis, and colorectal cancer. There is a huge deficit of knowledge and partially contradictory information concerning human methanogens, so much remains to be done to fully understand their physiological role in humans. It is necessary to develop new methods for the identification and culture of methanogens from clinical samples. This will permit to isolate new methanogens species as well as their phenotypic characterization, to explore their genome by sequencing and to study the population dynamics of methanogens by specifying in particular their exact role within the complex flora associated with the mucous microbiota of human.
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Affiliation(s)
- C O Guindo
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - M Drancourt
- IHU Méditerranée Infection, Marseille, France
| | - G Grine
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, UFR Odontologie, Marseille, France.
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Sereme Y, Mezouar S, Grine G, Mege JL, Drancourt M, Corbeau P, Vitte J. Methanogenic Archaea: Emerging Partners in the Field of Allergic Diseases. Clin Rev Allergy Immunol 2020; 57:456-466. [PMID: 31522353 DOI: 10.1007/s12016-019-08766-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Archaea, which form one of four domains of life alongside Eukarya, Bacteria, and giant viruses, have long been neglected as components of the human microbiota and potential opportunistic infectious pathogens. In this review, we focus on methanogenic Archaea, which rely on hydrogen for their metabolism and growth. On one hand, methanogenic Archaea in the gut are functional associates of the fermentative digestion of dietary fibers, favoring the production of beneficial short-chain fatty acids and likely contributing to the weaning reaction during the neonatal window of opportunity. On the other hand, methanogenic Archaea trigger the activation of innate and adaptive responses and the generation of specific T and B cells in animals and humans. In mouse models, lung hypersensitivity reactions can be induced by inhaled methanogenic Archaea mimicking human professional exposure to organic dust. Changes in methanogenic Archaea of the microbiota are detected in an array of dysimmune conditions comprising inflammatory bowel disease, obesity, malnutrition, anorexia, colorectal cancer, and diverticulosis. At the subcellular level, methanogenic Archaea are activators of the TLR8-dependent NLRP3 inflammasome, modulate the release of antimicrobial peptides and drive the production of proinflammatory, Th-1, Th-2, and Th-17 cytokines. Our objective was to introduce the most recent and major pieces of evidence supporting the involvement of Archaea in the balance between health and dysimmune diseases, with a particular focus on atopic and allergic conditions.
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Affiliation(s)
- Youssouf Sereme
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Soraya Mezouar
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Ghiles Grine
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Jean Louis Mege
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
- APHM, Hôpital Timone, Service de Bactériologie - Epidémiologie - Hygiène hospitalière, Aix-Marseille University, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Pierre Corbeau
- Institute of Human Genetics, UMR9002, CNRS-Montpellier University, Montpellier, France
- Montpellier University, Montpellier, France
- Immunology Department, University Hospital, Nîmes, France
| | - Joana Vitte
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France.
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France.
- APHM, Hôpital Timone, Service de Bactériologie - Epidémiologie - Hygiène hospitalière, Aix-Marseille University, Marseille, France.
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Diarra AZ, Laroche M, Berger F, Parola P. Use of MALDI-TOF MS for the Identification of Chad Mosquitoes and the Origin of Their Blood Meal. Am J Trop Med Hyg 2019; 100:47-53. [PMID: 30526738 DOI: 10.4269/ajtmh.18-0657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a clinical microbiology tool for the systematic identification of microorganisms. It has recently been presented as an innovative tool for the rapid and accurate identification of mosquitoes and their blood meal. To evaluate the capacity of this tool to identify mosquitoes collected in a tropical environment and preserved with silica gel, we analyzed 188 mosquitoes of different species collected in Chad, which were preserved with silica gel for 2 months. The MALDI-TOF MS analysis correctly identified 96% of the mosquitoes and 37.5% of their blood meals. Using MALDI-TOF MS and molecular biology, eight mosquito species were identified, including Anopheles gambiae s.l., Anopheles rufipes, Culex quinquefasciatus, Culex neavei, Culex pipiens, Culex perexiguus, Culex rima, and Culex watti. Blood meal identification revealed that mosquitoes fed mainly on humans, birds, and cows. Matrix-assisted desorption/ionization time-of-flight mass spectrometry appears to be a promising, fast, and reliable tool to identify mosquitoes and the origin of their blood meal for samples stored with silica gel.
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Affiliation(s)
- Adama Zan Diarra
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France.,Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Maureen Laroche
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France
| | - Franck Berger
- Aix Marseille Univ, Inserm, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, Marseille, France.,SSA, CESPA, Marseille, France
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France
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11
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Trophic strategy of diverse methanogens across a river-to-sea gradient. J Microbiol 2019; 57:470-478. [PMID: 31054138 DOI: 10.1007/s12275-019-8482-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/14/2018] [Accepted: 12/19/2018] [Indexed: 10/26/2022]
Abstract
Methanogens are an important biogenic source of methane, especially in estuarine waters across a river-to-sea gradient. However, the diversity and trophic strategy of methanogens in this gradient are not clear. In this study, the diversity and trophic strategy of methanogens in sediments across the Yellow River (YR) to the Bohai Sea (BS) gradient were investigated by high-throughput sequencing based on the 16S rRNA gene. The results showed that the diversity of methanogens in sediments varied from multitrophic communities in YR samples to specific methylotrophic communities in BS samples. The methanogenic community in YR samples was dominated by Methanosarcina, while that of BS samples was dominated by methylotrophic Methanococcoides. The distinct methanogens suggested that the methanogenic community of BS sediments did not originate from YR sediment input. High-throughput sequencing of the mcrA gene revealed that active Methanococcoides dominated in the BS enrichment cultures with trimethylamine as the substrate, and methylotrophic Methanolobus dominated in the YR enrichment cultures, as detected to a limited amount in in situ sediment samples. Methanosarcina were also detected in this gradient sample. Furthermore, the same species of Methanosarcina mazei, which was widely distributed, was isolated from the area across a river-to-sea gradient by the culture-dependent method. In summary, our results showed that a distribution of diverse methanogens across a river-to-sea gradient may shed light on adaption strategies and survival mechanisms in methanogens.
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Sogodogo E, Drancourt M, Grine G. Methanogens as emerging pathogens in anaerobic abscesses. Eur J Clin Microbiol Infect Dis 2019; 38:811-818. [DOI: 10.1007/s10096-019-03510-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/04/2019] [Indexed: 01/02/2023]
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Chabriere E, Bassène H, Drancourt M, Sokhna C. MALDI-TOF MS and point of care are disruptive diagnostic tools in Africa. New Microbes New Infect 2018; 26:S83-S88. [PMID: 30402248 PMCID: PMC6205576 DOI: 10.1016/j.nmni.2018.08.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022] Open
Abstract
We review reviewing our experience of point-of-care and mass spectrometry in Senegal as two disruptive technologies promoting the rapid diagnosis of infection, permitting better medical management of patients.
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Affiliation(s)
- E. Chabriere
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - H. Bassène
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
- VITROME, Campus International IRD-UCAD de Hann, Dakar, Senegal
| | - M. Drancourt
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - C. Sokhna
- Aix Marseille Université, IRD, APHM, VITROME, IHU-Méditerranée Infection, Marseille, France
- VITROME, Campus International IRD-UCAD de Hann, Dakar, Senegal
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Abstract
Australian mosquito species significantly impact human health through nuisance biting and the transmission of endemic and exotic pathogens. Surveillance programmes designed to provide an early warning of mosquito-borne disease risk require reliable identification of mosquitoes. This study aimed to investigate the viability of Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a rapid and inexpensive approach to the identification of Australian mosquitoes and was validated using a three-step taxonomic approach. A total of 300 mosquitoes representing 21 species were collected from south-eastern New South Wales and morphologically identified. The legs from the mosquitoes were removed and subjected to MALDI-TOF MS analysis. Fifty-eight mosquitoes were sequenced at the cytochrome c oxidase subunit I (cox1) gene region and genetic relationships were analysed. We create the first MALDI-TOF MS spectra database of Australian mosquito species including 19 species. We clearly demonstrate the accuracy of MALDI-TOF MS for identification of Australian mosquitoes. It is especially useful for assessing gaps in the effectiveness of DNA barcoding by differentiating closely related taxa. Indeed, cox1 DNA barcoding was not able to differentiate members of the Culex pipiens group, Cx. quinquefasciatus and Cx. pipiens molestus, but these specimens were correctly identified using MALDI-TOF MS.
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Fournier PE, Drancourt M, Raoult D. New Laboratory Tools for Emerging Bacterial Challenges. Clin Infect Dis 2018; 65:S39-S49. [PMID: 28859351 DOI: 10.1093/cid/cix405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Since its creation, the Méditerranée-Infection foundation has aimed at optimizing the management of infectious diseases and surveying the local and global epidemiology. This pivotal role was permitted by the development of rational sampling, point-of-care tests, and extended automation as well as new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and the development of versatile and permissive culture systems. By identifying and characterizing emerging microbial pathogens, these developments provided significant breakthroughs in infectious diseases.
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Affiliation(s)
- Pierre-Edouard Fournier
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - Michel Drancourt
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - Didier Raoult
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
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Grégory D, Chaudet H, Lagier JC, Raoult D. How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota. Expert Rev Proteomics 2018; 15:217-229. [PMID: 29336192 DOI: 10.1080/14789450.2018.1429271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.
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Affiliation(s)
- Dubourg Grégory
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Hervé Chaudet
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Jean-Christophe Lagier
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
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Diarra AZ, Almeras L, Laroche M, Berenger JM, Koné AK, Bocoum Z, Dabo A, Doumbo O, Raoult D, Parola P. Molecular and MALDI-TOF identification of ticks and tick-associated bacteria in Mali. PLoS Negl Trop Dis 2017; 11:e0005762. [PMID: 28742123 PMCID: PMC5542699 DOI: 10.1371/journal.pntd.0005762] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 08/03/2017] [Accepted: 06/30/2017] [Indexed: 12/14/2022] Open
Abstract
Ticks are considered the second vector of human and animal diseases after mosquitoes. Therefore, identification of ticks and associated pathogens is an important step in the management of these vectors. In recent years, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been reported as a promising method for the identification of arthropods including ticks. The objective of this study was to improve the conditions for the preparation of tick samples for their identification by MALDI-TOF MS from field-collected ethanol-stored Malian samples and to evaluate the capacity of this technology to distinguish infected and uninfected ticks. A total of 1,333 ticks were collected from mammals in three distinct sites from Mali. Morphological identification allowed classification of ticks into 6 species including Amblyomma variegatum, Hyalomma truncatum, Hyalomma marginatum rufipes, Rhipicephalus (Boophilus) microplus, Rhipicephalus evertsi evertsi and Rhipicephalus sanguineus sl. Among those, 471 ticks were randomly selected for molecular and proteomic analyses. Tick legs submitted to MALDI-TOF MS revealed a concordant morpho/molecular identification of 99.6%. The inclusion in our MALDI-TOF MS arthropod database of MS reference spectra from ethanol-preserved tick leg specimens was required to obtain reliable identification. When tested by molecular tools, 76.6%, 37.6%, 20.8% and 1.1% of the specimens tested were positive for Rickettsia spp., Coxiella burnetii, Anaplasmataceae and Borrelia spp., respectively. These results support the fact that MALDI-TOF is a reliable tool for the identification of ticks conserved in alcohol and enhances knowledge about the diversity of tick species and pathogens transmitted by ticks circulating in Mali.
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Affiliation(s)
- Adama Zan Diarra
- Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, AP-HM, IHU - Méditerranée Infection, Marseille, France
- Malaria Research and Training Center, Département d’Epidémiologie des Affections Parasitaires, Faculté de Médecine et d’Odontostomatologie, Faculté de Pharmacie, USTTB, Bamako, Mali
| | - Lionel Almeras
- Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, AP-HM, IHU - Méditerranée Infection, Marseille, France
- Unité de Parasitologie et Entomologie, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France
| | - Maureen Laroche
- Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, AP-HM, IHU - Méditerranée Infection, Marseille, France
| | - Jean-Michel Berenger
- Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, AP-HM, IHU - Méditerranée Infection, Marseille, France
| | - Abdoulaye K. Koné
- Malaria Research and Training Center, Département d’Epidémiologie des Affections Parasitaires, Faculté de Médecine et d’Odontostomatologie, Faculté de Pharmacie, USTTB, Bamako, Mali
| | | | - Abdoulaye Dabo
- Malaria Research and Training Center, Département d’Epidémiologie des Affections Parasitaires, Faculté de Médecine et d’Odontostomatologie, Faculté de Pharmacie, USTTB, Bamako, Mali
| | - Ogobara Doumbo
- Malaria Research and Training Center, Département d’Epidémiologie des Affections Parasitaires, Faculté de Médecine et d’Odontostomatologie, Faculté de Pharmacie, USTTB, Bamako, Mali
| | - Didier Raoult
- Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, AP-HM, IHU - Méditerranée Infection, Marseille, France
| | - Philippe Parola
- Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, AP-HM, IHU - Méditerranée Infection, Marseille, France
- * E-mail:
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Aerobic culture of methanogenic archaea without an external source of hydrogen. Eur J Clin Microbiol Infect Dis 2016; 35:985-91. [DOI: 10.1007/s10096-016-2627-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 03/13/2016] [Indexed: 11/26/2022]
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Lo CI, Fall B, Sambe-Ba B, Diawara S, Gueye MW, Mediannikov O, Sokhna C, Faye N, Diemé Y, Wade B, Raoult D, Fenollar F. MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa). PLoS One 2015; 10:e0145889. [PMID: 26716681 PMCID: PMC4696746 DOI: 10.1371/journal.pone.0145889] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 12/09/2015] [Indexed: 12/26/2022] Open
Abstract
Our team in Europe has developed the routine clinical laboratory identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). To evaluate the utility of MALDI-TOF MS in tropical Africa in collaboration with local teams, we installed an apparatus in the Hôpital Principal de Dakar (Senegal), performed routine identification of isolates, and confirmed or completed their identification in France. In the case of discordance or a lack of identification, molecular biology was performed. Overall, 153/191 (80.1%) and 174/191 (91.1%) isolates yielded an accurate and concordant identification for the species and genus, respectively, with the 2 different MALDI-TOF MSs in Dakar and Marseille. The 10 most common bacteria, representing 94.2% of all bacteria routinely identified in the laboratory in Dakar (Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus haemolyticus, Enterobacter cloacae, Enterococcus faecalis, and Staphylococcus epidermidis) were accurately identified with the MALDI-TOF MS in Dakar. The most frequent misidentification in Dakar was at the species level for Achromobacter xylosoxidans, which was inaccurately identified as Achromobacter denitrificans, and the bacteria absent from the database, such as Exiguobacterium aurientacum or Kytococcus schroeteri, could not be identified. A few difficulties were observed with MALDI-TOF MS for Bacillus sp. or oral streptococci. 16S rRNA sequencing identified a novel bacterium, “Necropsobacter massiliensis.” The robust identification of microorganisms by MALDI-TOF MS in Dakar and Marseille demonstrates that MALDI-TOF MS can be used as a first-line tool in clinical microbiology laboratories in tropical countries.
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Affiliation(s)
- Cheikh I. Lo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | | | | | | | | | - Oleg Mediannikov
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Cheikh Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Ngor Faye
- Université Cheikh Anta Diop, Dakar, Senegal
| | - Yaya Diemé
- Hôpital Principal de Dakar, Dakar, Senegal
| | | | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Florence Fenollar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
- * E-mail:
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Shih CJ, Chen SC, Weng CY, Lai MC, Yang YL. Rapid identification of haloarchaea and methanoarchaea using the matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Sci Rep 2015; 5:16326. [PMID: 26541644 PMCID: PMC4635381 DOI: 10.1038/srep16326] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/13/2015] [Indexed: 12/23/2022] Open
Abstract
The aim of this study was to classify certain environmental haloarchaea and methanoarchaea using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and to expand the archaeal mass spectral database. A total of 69 archaea were collected including type strains and samples isolated locally from different environments. For extraction of the haloarchaeal total cell peptides/proteins, a simple method of acetonitrile extraction was developed. Cluster analysis conducted with the MALDI-TOF MS data overcame the high divergence in intragenomic 16S rRNA sequences in haloarchaea and clearly distinguished Methanohalophilus mahii from M. portucalensis. Putative biomarkers that can distinguish several particular archaeal genera were also assigned. In conclusion, this study expands the mass spectral database of peptide/protein fingerprints from bacteria and fungi to the archaea domain and provides a rapid identification platform for environmental archaeal samples.
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Affiliation(s)
- Chao-Jen Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chieh-Yin Weng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan;,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.,Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan
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Flaudrops C, Armstrong N, Raoult D, Chabrière E. Determination of the animal origin of meat and gelatin by MALDI-TOF-MS. J Food Compost Anal 2015. [DOI: 10.1016/j.jfca.2015.02.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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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: 521] [Impact Index Per Article: 57.9] [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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Current and past strategies for bacterial culture in clinical microbiology. Clin Microbiol Rev 2015; 28:208-36. [PMID: 25567228 DOI: 10.1128/cmr.00110-14] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome.
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Creation of an In-House Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Corynebacterineae Database Overcomes Difficulties in Identification of Nocardia farcinica Clinical Isolates. J Clin Microbiol 2015; 53:2611-21. [PMID: 26041903 DOI: 10.1128/jcm.00268-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/28/2015] [Indexed: 12/31/2022] Open
Abstract
Nocardiosis is a rare disease that is caused by Gram-positive actinobacteria of the Nocardia genus and affects predominantly immunocompromised patients. In its disseminated form, it has a predilection for the central nervous system and is associated with high mortality rates. Therefore, prompt identification of the pathogen is critical. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a relatively novel technique used for identification of microorganisms. In this work, an upgraded MALDI-TOF Biotyper database containing Corynebacterineae representatives of strains deposited in the Polish Collection of Microorganisms was created and used for identification of the strain isolated from a nocardial brain abscess, mimicking a brain tumor, in an immunocompetent patient. Testing with the API Coryne system initially incorrectly identified Rhodococcus sp., while chemotaxonomic tests, especially mycolic acid analysis, enabled correct Nocardia identification only at the genus level. Subsequent sequence analysis of 16S rRNA and secA1 genes confirmed the identification. To improve the accuracy of the results, an in-house database was constructed using optimized parameters; with the use of the database, the strain was eventually identified as Nocardia farcinica. Clinical laboratories processing various clinical strains can upgrade a commercial database to improve and to accelerate the results obtained. This is especially important in the case of Nocardia, for which valid microbial diagnosis remains challenging; reference laboratories are often required to identify and to survey these rare actinobacteria.
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Loucif L, Bendjama E, Gacemi-Kirane D, Rolain JM. Rapid identification of Streptomyces isolates by MALDI-TOF MS. Microbiol Res 2014; 169:940-7. [DOI: 10.1016/j.micres.2014.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/25/2014] [Accepted: 04/27/2014] [Indexed: 11/17/2022]
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Fotso Fotso A, Mediannikov O, Diatta G, Almeras L, Flaudrops C, Parola P, Drancourt M. MALDI-TOF mass spectrometry detection of pathogens in vectors: the Borrelia crocidurae/Ornithodoros sonrai paradigm. PLoS Negl Trop Dis 2014; 8:e2984. [PMID: 25058611 PMCID: PMC4109908 DOI: 10.1371/journal.pntd.0002984] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/14/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In Africa, relapsing fever borreliae are neglected vector-borne pathogens that cause mild to deadly septicemia and miscarriage. Screening vectors for the presence of borreliae currently requires technically demanding, time- and resource-consuming molecular methods. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has recently emerged as a tool for the rapid identification of vectors and the identification of cultured borreliae. We investigated whether MALDI-TOF-MS could detect relapsing fever borreliae directly in ticks. METHODOLOGY/PRINCIPAL FINDINGS As a first step, a Borrelia MALDI-TOF-MS database was created to house the newly determined Mean Spectrum Projections for four Lyme disease group and ten relapsing fever group reference borreliae. MALDI-TOF-MS yielded a unique protein profile for each of the 14 tested Borrelia species, with 100% reproducibility over 12 repeats. In a second proof-of-concept step, the Borrelia database and a custom software program that subtracts the uninfected O. sonrai profile were used to detect Borrelia crocidurae in 20 Ornithodoros sonrai ticks, including eight ticks that tested positive for B. crocidurae by PCR-sequencing. A B. crocidurae-specific pattern consisting of 3405, 5071, 5898, 7041, 8580 and 9757-m/z peaks was found in all B. crocidurae-infected ticks and not found in any of the un-infected ticks. In a final blind validation step, MALDI-TOF-MS exhibited 88.9% sensitivity and 93.75% specificity for the detection of B. crocidurae in 50 O. sonrai ticks, including 18 that tested positive for B. crocidurae by PCR-sequencing. MALDI-TOF-MS took 45 minutes to be completed. CONCLUSIONS/SIGNIFICANCE After the development of an appropriate database, MALDI-TOF-MS can be used to identify tick species and the presence of relapsing fever borreliae in a single assay. This work paves the way for the use of MALDI-TOF-MS for the dual identification of vectors and vectorized pathogens.
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Affiliation(s)
- Aurélien Fotso Fotso
- URMITE, UMR 6236, CNRS 7278, IRD 198, INSERM 1095, Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Oleg Mediannikov
- URMITE, UMR 6236, CNRS 7278, IRD 198, INSERM 1095, Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France; URMITE, UMR, IRD 198, Campus IRD Ham Manisty, Dakar, Senegal
| | - Georges Diatta
- URMITE, UMR, IRD 198, Campus IRD Ham Manisty, Dakar, Senegal
| | - Lionel Almeras
- URMITE, UMR 6236, CNRS 7278, IRD 198, INSERM 1095, Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Christophe Flaudrops
- Pôle de Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, CHU Timone, Marseille, France
| | - Philippe Parola
- URMITE, UMR 6236, CNRS 7278, IRD 198, INSERM 1095, Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- URMITE, UMR 6236, CNRS 7278, IRD 198, INSERM 1095, Méditerranée Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
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Ikram HI, Catherine R, Caroline M, Didier R, Hocine H, Christelle D. Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov. Stand Genomic Sci 2014; 9:956-9. [PMID: 25197441 PMCID: PMC4149028 DOI: 10.4056/sigs.4618288] [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: 11/20/2022] Open
Abstract
Halopiger goleamassiliensis strain IIH3(T) sp. nov. is a novel, extremely halophilic archaeon within the genus Halopiger. This strain was isolated from an evaporitic sediment in El Golea Lake, Ghardaïa region (Algeria). The type strain is strain IIH3(T). H. goleamassiliensis is moderately thermophilic, neutrophilic, non-motile and coccus-shaped. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,906,923 bp long genome contains 3,854 protein-encoding genes and 49 RNA genes (1 gene is 16S rRNA, 1 gene is 23S rRNA, 3 genes are 5S rRNA, and 44 are tRNA genes).
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Affiliation(s)
- Hassani Imene Ikram
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
| | | | | | | | - Hacène Hocine
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
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Samb-Ba B, Mazenot C, Gassama-Sow A, Dubourg G, Richet H, Hugon P, Lagier JC, Raoult D, Fenollar F. MALDI-TOF identification of the human Gut microbiome in people with and without diarrhea in Senegal. PLoS One 2014; 9:e87419. [PMID: 24784934 PMCID: PMC4006720 DOI: 10.1371/journal.pone.0087419] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/24/2013] [Indexed: 12/21/2022] Open
Abstract
Background In Africa, there are several problems with the specific identification of bacteria. Recently, MALDI-TOF mass spectrometry has become a powerful tool for the routine microbial identification in many clinical laboratories. Methodology/Principal Findings This study was conducted using feces from 347 individuals (162 with diarrhea and 185 without diarrhea) sampled in health centers in Dakar, Senegal. Feces were transported from Dakar to Marseille, France, where they were cultured using different culture conditions. The isolated colonies were identified using MALDI-TOF. If a colony was unidentified, 16S rRNA sequencing was performed. Overall, 2,753 isolates were tested, allowing for the identification of 189 bacteria from 5 phyla, including 2 previously unknown species, 11 species not previously reported in the human gut, 10 species not previously reported in humans, and 3 fungi. 2,718 bacterial isolates (98.8%) out of 2,750 yielded an accurate identification using mass spectrometry, as did the 3 Candida albicans isolates. Thirty-two bacterial isolates not identified by MALDI-TOF (1.2%) were identified by sequencing, allowing for the identification of 2 new species. The number of bacterial species per fecal sample was significantly higher among patients without diarrhea (8.6±3) than in those with diarrhea (7.3±3.4; P = 0.0003). A modification of the gut microbiota was observed between the two groups. In individuals with diarrhea, major commensal bacterial species such as E. coli were significantly decreased (85% versus 64%), as were several Enterococcus spp. (E. faecium and E. casseliflavus) and anaerobes, such as Bacteroides spp. (B. uniformis and B. vulgatus) and Clostridium spp. (C. bifermentans, C. orbiscindens, C. perfringens, and C. symbosium). Conversely, several Bacillus spp. (B. licheniformis, B. mojavensis, and B. pumilus) were significantly more frequent among patients with diarrhea. Conclusions/Significance MALDI-TOF is a potentially powerful tool for routine bacterial identification in Africa, allowing for a quick identification of bacterial species.
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Affiliation(s)
- Bissoume Samb-Ba
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
- Unité de Bactériologie Expérimentale, Institut Pasteur de Dakar, Dakar, Senegal
| | - Catherine Mazenot
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Amy Gassama-Sow
- Unité de Bactériologie Expérimentale, Institut Pasteur de Dakar, Dakar, Senegal
| | - Grégory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Hervé Richet
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Perrine Hugon
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Florence Fenollar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
- * E-mail:
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Manikandan M, Hua PY, Wu HF. Rapid endophytic bacterial detection by enzyme incorporated MALDI MS. RSC Adv 2014. [DOI: 10.1039/c4ra05604c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this paper, we have attempted the use of MALDI-MS for the detection of bacteria from complex real world samples such as the root nodules of plants.
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Affiliation(s)
- Muthu Manikandan
- Department of Chemistry
- National Sun Yat-Sen University
- Kaohsiung, Taiwan
- Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
| | - Pei-Yang Hua
- Department of Chemistry
- National Sun Yat-Sen University
- Kaohsiung, Taiwan
| | - Hui-Fen Wu
- Department of Chemistry
- National Sun Yat-Sen University
- Kaohsiung, Taiwan
- Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
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Hassani II, Robert C, Michelle C, Raoult D, Hacène H, Desnues C. Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov. Stand Genomic Sci 2013; 9:160-74. [PMID: 24501653 PMCID: PMC3910545 DOI: 10.4056/sigs.4578289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Halopiger djelfamassiliensis strain IIH2T sp. nov. is the type strain of Halopiger djelfamassiliensis sp. nov., a new species within the genus Halopiger. This strain, whose genome is described here, was isolated from evaporitic sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region (Algeria). H. Djelfamassiliensis is a Gram-negative, polymorphic-shaped and strictly aerobic archaeon. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,771,216 bp long genome-contains 3,761 protein-coding and 51 RNA genes, including 4 rRNA genes.
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Affiliation(s)
- Ikram Imene Hassani
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
| | | | - Caroline Michelle
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
| | - Didier Raoult
- Aix-Marseille Université, Faculté de médecine, France
| | - Hocine Hacène
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
| | - Christelle Desnues
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
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Matrix-assisted laser desorption ionization--time of flight mass spectrometry: an emerging tool for the rapid identification of mosquito vectors. PLoS One 2013; 8:e72380. [PMID: 23977292 PMCID: PMC3744494 DOI: 10.1371/journal.pone.0072380] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 07/08/2013] [Indexed: 11/19/2022] Open
Abstract
Background The identification of mosquito vectors is typically based on morphological characteristics using morphological keys of determination, which requires entomological expertise and training. The use of protein profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), which is increasingly being used for the routine identification of bacteria, has recently emerged for arthropod identification. Methods To investigate the usefulness of MALDI-TOF-MS as a mosquito identification tool, we tested protein extracts made from mosquito legs to create a database of reference spectra. The database included a total of 129 laboratory-reared and field-caught mosquito specimens consisting of 20 species, including 4 Aedes spp., 9 Anopheles spp., 4 Culex spp., Lutzia tigripes, Orthopodomyia reunionensis and Mansonia uniformis. For the validation study, blind tests were performed with 76 specimens consisting of 1 to 4 individuals per species. A cluster analysis was carried out using the MALDI-Biotyper and some spectra from all mosquito species tested. Results Biomarker mass sets containing 22 and 43 masses have been detected from 100 specimens of the Anopheles, Aedes and Culex species. By carrying out 3 blind tests, we achieved the identification of mosquito vectors at the species level, including the differentiation of An. gambiae complex, which is possible using MALDI-TOF-MS with 1.8 as the cut-off identification score. A cluster analysis performed with all available mosquito species showed that MALDI-Biotyper can distinguish between specimens at the subspecies level, as demonstrated for An gambiae M and S, but this method cannot yet be considered a reliable tool for the phylogenetic study of mosquito species. Conclusions We confirmed that even without any specific expertise, MALDI-TOF-MS profiling of mosquito leg protein extracts can be used for the rapid identification of mosquito vectors. Therefore, MALDI-TOF-MS is an alternative, efficient and inexpensive tool that can accurately identify mosquitoes collected in the field during entomological surveys.
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Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2013; 51:2182-94. [PMID: 23637301 DOI: 10.1128/jcm.00492-13] [Citation(s) in RCA: 325] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
During the past 5 years, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a powerful tool for routine identification in many clinical laboratories. We analyzed our 11-year experience in routine identification of clinical isolates (40 months using MALDI-TOF MS and 91 months using conventional phenotypic identification [CPI]). Among the 286,842 clonal isolates, 284,899 isolates of 459 species were identified. The remaining 1,951 isolates were misidentified and required confirmation using a second phenotypic identification for 670 isolates and using a molecular technique for 1,273 isolates of 339 species. MALDI-TOF MS annually identified 112 species, i.e., 36 species/10,000 isolates, compared to 44 species, i.e., 19 species/10,000 isolates, for CPI. Only 50 isolates required second phenotypic identifications during the MALDI-TOF MS period (i.e., 4.5 reidentifications/10,000 isolates) compared with 620 isolates during the CPI period (i.e., 35.2/10,000 isolates). We identified 128 bacterial species rarely reported as human pathogens, including 48 using phenotypic techniques (22 using CPI and 37 using MALDI-TOF MS). Another 75 rare species were identified using molecular methods. MALDI-TOF MS reduced the time required for identification by 55-fold and 169-fold and the cost by 5-fold and 96-fold compared with CPI and gene sequencing, respectively. MALDI-TOF MS was a powerful tool not only for routine bacterial identification but also for identification of rare bacterial species implicated in human infectious diseases. The ability to rapidly identify bacterial species rarely described as pathogens in specific clinical specimens will help us to study the clinical burden resulting from the emergence of these species as human pathogens, and MALDI-TOF MS may be considered an alternative to molecular methods in clinical laboratories.
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Biswas S, Rolain JM. Use of MALDI-TOF mass spectrometry for identification of bacteria that are difficult to culture. J Microbiol Methods 2013; 92:14-24. [DOI: 10.1016/j.mimet.2012.10.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 10/25/2012] [Accepted: 10/29/2012] [Indexed: 01/22/2023]
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Zhai XH, Yu JK, Yang FQ, Zheng S. Identification of a new protein biomarker for colorectal cancer diagnosis. Mol Med Rep 2012; 6:444-8. [PMID: 22614045 DOI: 10.3892/mmr.2012.923] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 05/15/2012] [Indexed: 11/06/2022] Open
Abstract
As one of the most common cancers, colorectal cancer (CRC) is a major public health issue worldwide. Thus, the identification of novel biomarkers to aid in the early diagnosis of CRC is crucial. The aim of the present study was to identify a novel protein biomarker for CRC, and to identify its structure. In this study, a total of 99 serum samples from 73 CRC patients and 26 healthy controls were collected and analyzed by SELDI-TOF-MS. The biomarkers were separated using HPLC and detected with MALDI-TOF-MS. The qualified peaks were ranked by p-value of non-parametric tests and the top 10 peaks displaying significant differences were selected. Among the 10 protein biomarkers, the concentration of a 3.9‑kDa protein in the serum of the CRC patients was much lower than that in the healthy controls. Therefore, the 3.9‑kDa protein was selected as a biomarker for CRC and its separation and purification were performed. The structure of the 3.9-kDa protein biomarker was determined by LC-MS/MS, and was confirmed to be a fragment of serine/theonine kinase 4 (MST1/STK4). The 3.9‑kDa protein biomarker had high sensitivity and specificity for CRC, and its potential clinical application warrants further investigation.
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Affiliation(s)
- Xiao-Hui Zhai
- Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
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