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Chang YJ, Pukall R, Saunders E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Goodwin L, Pitluck S, Mikhailova N, Liolios K, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brettin T, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Acidaminococcus fermentans type strain (VR4). Stand Genomic Sci 2010; 3:1-14. [PMID: 21304687 PMCID: PMC3035267 DOI: 10.4056/sigs.1002553] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Acidaminococcus fermentans (Rogosa 1969) is the type species of the genus Acidaminococcus, and is of phylogenetic interest because of its isolated placement in a genomically little characterized region of the Firmicutes. A. fermentans is known for its habitation of the gastrointestinal tract and its ability to oxidize trans-aconitate. Its anaerobic fermentation of glutamate has been intensively studied and will now be complemented by the genomic basis. The strain described in this report is a nonsporulating, nonmotile, Gram-negative coccus, originally isolated from a pig alimentary tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Acidaminococcaceae, and the 2,329,769 bp long genome with its 2,101 protein-coding and 81 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Jumas-Bilak E, Carlier JP, Jean-Pierre H, Mory F, Teyssier C, Gay B, Campos J, Marchandin H. Acidaminococcus intestini sp. nov., isolated from human clinical samples. Int J Syst Evol Microbiol 2007; 57:2314-2319. [PMID: 17911303 DOI: 10.1099/ijs.0.64883-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eleven strains of a hitherto unknown, Gram-negative, anaerobic coccus were recovered from various human clinical samples of patients hospitalized in two geographically distant French hospitals. These strains displayed the morphology and growth characteristics of those related to the genus Acidaminococcus. The clinical isolates shared at least 99.9 and 99.7 % of their nucleotide positions in the 16S and 23S rRNA gene sequences, respectively. They displayed 95.6 and 88.9 % 16S and 23S rRNA gene sequence similarities, respectively, with Acidaminococcus fermentans. The 16S rRNA-based phylogeny revealed that all the clinical isolates grouped in a statistically well supported cluster separate from A. fermentans. Enzymic activity profiles as well as metabolic end product patterns, including propionic acid production, differentiated the novel bacteria from A. fermentans. Finally, phenotypic, genotypic and phylogenetic data, including large-scale chromosome structure and DNA G+C content, supported the proposal of a novel species of the genus Acidaminococcus, for which the name Acidaminococcus intestini sp. nov. is proposed. The type strain is ADV 255.99T (=AIP 283.01T=CIP 108586T=CCUG 50930T).
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MESH Headings
- Acidaminococcus/classification
- Acidaminococcus/cytology
- Acidaminococcus/isolation & purification
- Acidaminococcus/physiology
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Anaerobiosis/physiology
- Bacterial Proteins/metabolism
- Bacterial Typing Techniques
- Base Composition
- Chromosomes, Bacterial/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Enzymes/metabolism
- Female
- France
- Genes, rRNA
- Gram-Negative Bacterial Infections/microbiology
- Humans
- Male
- Middle Aged
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Estelle Jumas-Bilak
- Université Montpellier 1, Faculté de Pharmacie, Laboratoire de Bactériologie-Virologie, 15 Avenue Charles Flahault, BP 14491, 34060 Montpellier Cedex 5, France
| | - Jean-Philippe Carlier
- Institut Pasteur, Centre National de Référence des Bactéries Anaérobies et du Botulisme, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Hélène Jean-Pierre
- Centre Hospitalier et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Francine Mory
- Centre Hospitalier et Universitaire de Nancy, Hôpital Central, Laboratoire de Bactériologie, 29 avenue du Maréchal de Lattre de Tassigny, 54035 Nancy Cedex, France
| | - Corinne Teyssier
- Université Montpellier 1, Faculté de Pharmacie, Laboratoire de Bactériologie-Virologie, 15 Avenue Charles Flahault, BP 14491, 34060 Montpellier Cedex 5, France
| | - Bernard Gay
- Centre Hospitalier et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Josiane Campos
- Centre Hospitalier et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Hélène Marchandin
- Centre Hospitalier et Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
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Helander IM, Haikara A, Sadovskaya I, Vinogradov E, Salkinoja-Salonen MS. Lipopolysaccharides of anaerobic beer spoilage bacteria of the genusPectinatus– lipopolysaccharides of a Gram-positive genus. FEMS Microbiol Rev 2004; 28:543-52. [PMID: 15539073 DOI: 10.1016/j.femsre.2004.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2004] [Revised: 04/07/2004] [Accepted: 05/11/2004] [Indexed: 11/18/2022] Open
Abstract
Bacteria of the genus Pectinatus emerged during the seventies as contaminants and spoilage organisms in packaged beer. This genus comprises two species, Pectinatus cerevisiiphilus and Pectinatus frisingensis; both are strict anaerobes. On the basis of genomic properties the genus is placed among low GC Gram-positive bacteria (phylum Firmicutes, class Clostridia, order Clostridiales, family Acidaminococcaceae). Despite this assignment, Pectinatus bacteria possess an outer membrane and lipopolysaccharide (LPS) typical of Gram-negative bacteria. The present review compiles the structural and compositional studies performed on Pectinatus LPS. These lipopolysaccharides exhibit extensive heterogeneity, i.e. several macromolecularly and structurally distinct LPS molecules are produced by each strain. Whereas heterogeneity is a common property in lipopolysaccharides, Pectinatus LPS have been shown to contain exceptional carbohydrate structures, consisting of a fairly conserved core region that carries a large non-repetitive saccharide that probably replaces the O-specific chain. Such structures represent a novel architectural principle of the LPS molecule.
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Affiliation(s)
- Ilkka M Helander
- Division of Microbiology, Department of Applied Chemistry and Microbiology, University of Helsinki, Finland.
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Tourova TP, Boulygina ES, Zhilina TN, Hanson RS, Zavarzin GA. Phylogenetic Study of Haloanaerobic Bacteria by 16S Ribosomal RNA Sequences Analysis. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80389-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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The Importance of Using Outgroup Reference Organisms in Phylogenetic Studies: the Atopobium Case. Syst Appl Microbiol 1994. [DOI: 10.1016/s0723-2020(11)80029-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Phascolarctobacterium faecium gen. nov, spec. nov., a Novel Taxon of the Sporomusa Group of Bacteria. Syst Appl Microbiol 1993. [DOI: 10.1016/s0723-2020(11)80269-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Rainey FA, Ward NL, Morgan HW, Toalster R, Stackebrandt E. Phylogenetic analysis of anaerobic thermophilic bacteria: aid for their reclassification. J Bacteriol 1993; 175:4772-9. [PMID: 7687600 PMCID: PMC204929 DOI: 10.1128/jb.175.15.4772-4779.1993] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Small subunit rDNA sequences were determined for 20 species of the genera Acetogenium, Clostridium, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobium, and Thermobacteroides, 3 non-validly described species, and 5 isolates of anaerobic thermophilic bacteria, providing a basis for a phylogenetic analysis of these organisms. Several species contain a version of the molecule significantly longer than that of Escherichia coli because of the presence of inserts. On the basis of normal evolutionary distances, the phylogenetic tree indicates that all bacteria investigated in this study with a maximum growth temperature above 65 degrees C form a supercluster within the subphylum of gram-positive bacteria that also contains Clostridium thermosaccharolyticum and Clostridium thermoaceticum, which have been previously sequenced. This supercluster appears to be equivalent in its phylogenetic depth to the supercluster of mesophilic clostridia and their nonspore-forming relatives. Several phylogenetically and phenotypically coherent clusters that are defined by sets of signature nucleotides emerge within the supercluster of thermophiles. Clostridium thermobutyricum and Clostridium thermopalmarium are members of Clostridium group I. A phylogenetic tree derived from transversion distances demonstrated the artificial clustering of some organisms with high rDNA G+C moles percent, i.e., Clostridium fervidus and the thermophilic, cellulolytic members of the genus Clostridium. The results of this study can be used as an aid for future taxonomic restructuring of anaerobic sporogenous and asporogenous thermophillic, gram-positive bacteria.
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Affiliation(s)
- F A Rainey
- Department of Microbiology, University of Queensland, St. Lucia, Australia
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