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Green GBH, Williams MB, Brandom JL, Chehade SB, Fay CX, Morrow CD, Lawrence AL, Bej AK, Watts SA. A Bacterial-Sourced Protein Diet Induces Beneficial Shifts in the Gut Microbiome of the Zebrafish, Danio rerio. Curr Dev Nutr 2024; 8:102077. [PMID: 38357379 PMCID: PMC10865222 DOI: 10.1016/j.cdnut.2024.102077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024] Open
Abstract
Background Bacterial-sourced single-cell proteins (SCPs) offer an alternative protein source for diet formulation for Zebrafish (Danio rerio) and other aquaculture models. In addition, the use of a single-cell bacterial protein source derived from multiple species provides a unique insight into the interplay among nutrients in the diet, microbial populations in the diet, and the gut microbiome in D. rerio. Objective Our objective in this study was to evaluate the impact of dietary replacement of fish protein hydrolysate in a standard reference (SR) with a single-cell bacterial protein source on D. rerio gut microbiome. Methods We investigated gut microbial compositions of D. rerio fed an open-formulation standard reference (SR) diet or a bacterial-sourced protein (BP) diet, utilizing microbial taxonomic co-occurrence networks, and predicted functional profiles. Results Microbial communities in the SR diet were primarily composed of Firmicutes. In contrast, the BP diet was mainly composed of Proteobacteria. Alpha diversity revealed significant differences in microbial communities between the 2 diets, and between the guts of D. rerio fed either of the 2 diets. D. rerio fed with the SR diet resulted in abundance of Aeromonas and Vibrio. In contrast, D. rerio fed with a BP diet displayed a large abundance of members from the Rhodobacteraceae family. Taxonomic co-occurrence networks display unique microbial interactions, and key taxons in D. rerio gut samples were dependent on diet and gender. Predicted functional profiling of the microbiome across D. rerio fed SR or BP diets revealed distinct metabolic pathway differences. Female D. rerio fed the BP diet displayed significant upregulation of pathways related to primary and secondary bile acid synthesis. Male D. rerio fed the BP diet revealed similar pathway shifts and, additionally, a significant upregulation of the polyketide sugar unit biosynthesis pathway. Conclusions The use of a BP dramatically affects the composition and activity of the gut microbiome. Future investigations should further address the interplay among biological systems and diet and may offer insights into potential health benefits in preclinical and translational animal models.
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Affiliation(s)
- George BH Green
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Michael B Williams
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeri L. Brandom
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Sophie B Chehade
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Christian X Fay
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Addison L Lawrence
- Texas A&M AgriLife Extension Agriculture and Life Sciences, TAMU College Station, TX, United States
| | - Asim K Bej
- J. Frank Barefield, Jr. Department of Criminal Justice, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Stephen A Watts
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, United States
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2
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Gnat S, Małek W, Oleńska E, Wdowiak-Wróbel S, Kalita M, Rogalski J, Wójcik M. Multilocus sequence analysis supports the taxonomic position of Astragalus glycyphyllos symbionts based on DNA–DNA hybridization. Int J Syst Evol Microbiol 2016; 66:1906-1912. [DOI: 10.1099/ijsem.0.000862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Sebastian Gnat
- Department of Veterinary Microbiology, University of Life Sciences, 13 Akademicka st., 20-950 Lublin, Poland
| | - Wanda Małek
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Ewa Oleńska
- Department of Genetics and Evolution, University of Bialystok, 1J Ciolkowskiego st., 15-245 Bialystok, Poland
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Jerzy Rogalski
- Department of Biochemistry, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Magdalena Wójcik
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
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3
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Ziegler D, Pothier JF, Ardley J, Fossou RK, Pflüger V, de Meyer S, Vogel G, Tonolla M, Howieson J, Reeve W, Perret X. Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS. Appl Microbiol Biotechnol 2015; 99:5547-62. [PMID: 25776061 DOI: 10.1007/s00253-015-6515-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/19/2015] [Accepted: 02/28/2015] [Indexed: 01/25/2023]
Abstract
Accurate identification of soil bacteria that form nitrogen-fixing associations with legume crops is challenging given the phylogenetic diversity of root nodule bacteria (RNB). The labor-intensive and time-consuming 16S ribosomal RNA (rRNA) sequencing and/or multilocus sequence analysis (MLSA) of conserved genes so far remain the favored molecular tools to characterize symbiotic bacteria. With the development of mass spectrometry (MS) as an alternative method to rapidly identify bacterial isolates, we recently showed that matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) can accurately characterize RNB found inside plant nodules or grown in cultures. Here, we report on the development of a MALDI-TOF RNB-specific spectral database built on whole cell MS fingerprints of 116 strains representing the major rhizobial genera. In addition to this RNB-specific module, which was successfully tested on unknown field isolates, a subset of 13 ribosomal proteins extracted from genome data was found to be sufficient for the reliable identification of nodule isolates to rhizobial species as shown in the putatively ascribed ribosomal protein masses (PARPM) database. These results reveal that data gathered from genome sequences can be used to expand spectral libraries to aid the accurate identification of bacterial species by MALDI-TOF MS.
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Affiliation(s)
- Dominik Ziegler
- Department of Botany and Plant Biology, Microbiology Unit, Sciences III, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
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4
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Satoh S, Mimuro M, Tanaka A. Construction of a phylogenetic tree of photosynthetic prokaryotes based on average similarities of whole genome sequences. PLoS One 2013; 8:e70290. [PMID: 23922968 PMCID: PMC3724816 DOI: 10.1371/journal.pone.0070290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 06/18/2013] [Indexed: 12/03/2022] Open
Abstract
Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.
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Affiliation(s)
- Soichirou Satoh
- Graduate School of Life and Environmental Science, Kyoto Prefectural University, Kyoto, Japan
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Mamoru Mimuro
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
- CREST, Japan Science and Technology Agency, Sapporo, Japan
- * E-mail:
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Markmann K, Radutoiu S, Stougaard J. Infection of Lotus japonicus Roots by Mesorhizobium loti. SIGNALING AND COMMUNICATION IN PLANT SYMBIOSIS 2012. [DOI: 10.1007/978-3-642-20966-6_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Vauclare P, Bligny R, Gout E, De Meuron V, Widmer F. Metabolic and structural rearrangement during dark-induced autophagy in soybean (Glycine max L.) nodules: an electron microscopy and 31P and 13C nuclear magnetic resonance study. PLANTA 2010; 231:1495-504. [PMID: 20358222 DOI: 10.1007/s00425-010-1148-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 02/26/2010] [Indexed: 05/13/2023]
Abstract
The effects of dark-induced stress on the evolution of the soluble metabolites present in senescent soybean (Glycine max L.) nodules were analysed in vitro using (13)C- and (31)P-NMR spectroscopy. Sucrose and trehalose were the predominant soluble storage carbons. During dark-induced stress, a decline in sugars and some key glycolytic metabolites was observed. Whereas 84% of the sucrose disappeared, only one-half of the trehalose was utilised. This decline coincides with the depletion of Gln, Asn, Ala and with an accumulation of ureides, which reflect a huge reduction of the N(2) fixation. Concomitantly, phosphodiesters and compounds like P-choline, a good marker of membrane phospholipids hydrolysis and cell autophagy, accumulated in the nodules. An autophagic process was confirmed by the decrease in cell fatty acid content. In addition, a slight increase in unsaturated fatty acids (oleic and linoleic acids) was observed, probably as a response to peroxidation reactions. Electron microscopy analysis revealed that, despite membranes dismantling, most of the bacteroids seem to be structurally intact. Taken together, our results show that the carbohydrate starvation induced in soybean by dark stress triggers a profound metabolic and structural rearrangement in the infected cells of soybean nodule which is representative of symbiotic cessation.
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Affiliation(s)
- Pierre Vauclare
- Laboratory of Plant Biology and Physiology, Biology Building UNIL, Room 5449, 1015 Lausanne, Switzerland.
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7
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Performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of bacterial strains routinely isolated in a clinical microbiology laboratory. J Clin Microbiol 2010; 48:1549-54. [PMID: 20220166 DOI: 10.1128/jcm.01794-09] [Citation(s) in RCA: 385] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been introduced in diagnostic microbiology laboratories for the identification of bacterial and yeast strains isolated from clinical samples. In the present study, we prospectively compared MALDI-TOF MS to the conventional phenotypic method for the identification of routine isolates. Colonies were analyzed by MALDI-TOF MS either by direct deposition on the target plate or after a formic acid-acetonitrile extraction step if no valid result was initially obtained. Among 1,371 isolates identified by conventional methods, 1,278 (93.2%) were putatively identified to the species level by MALDI-TOF MS and 73 (5.3%) were identified to the genus level, but no reliable identification was obtained for 20 (1.5%). Among the 1,278 isolates identified to the species level by MALDI-TOF MS, 63 (4.9%) discordant results were initially identified. Most discordant results (42/63) were due to systematic database-related taxonomical differences, 14 were explained by poor discrimination of the MALDI-TOF MS spectra obtained, and 7 were due to errors in the initial conventional identification. An extraction step was required to obtain a valid MALDI-TOF MS identification for 25.6% of the 1,278 valid isolates. In conclusion, our results show that MALDI-TOF MS is a fast and reliable technique which has the potential to replace conventional phenotypic identification for most bacterial strains routinely isolated in clinical microbiology laboratories.
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8
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Mierzwa B, Wdowiak-Wróbel S, Małek W. Robinia pseudoacacia in Poland and Japan is nodulated by Mesorhizobium amorphae strains. Antonie Van Leeuwenhoek 2010; 97:351-61. [DOI: 10.1007/s10482-010-9414-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 01/08/2010] [Indexed: 11/30/2022]
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Bromfield ESP, Tambong JT, Cloutier S, Prévost D, Laguerre G, van Berkum P, Thi TVT, Assabgui R, Barran LR. Ensifer, Phyllobacterium and Rhizobium species occupy nodules of Medicago sativa (alfalfa) and Melilotus alba (sweet clover) grown at a Canadian site without a history of cultivation. MICROBIOLOGY-SGM 2009; 156:505-520. [PMID: 19875436 DOI: 10.1099/mic.0.034058-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Phage-resistant and -susceptible bacteria from nodules of alfalfa and sweet clover, grown at a site without a known history of cultivation, were identified as diverse genotypes of Ensifer, Rhizobium and Phyllobacterium species based on sequence analysis of ribosomal (16S and 23S rRNA) and protein-encoding (atpD and recA) genes, Southern hybridization/RFLP and a range of phenotypic characteristics. Among phage-resistant bacteria, one genotype of Rhizobium sp. predominated on alfalfa (frequency approximately 68 %) but was recovered infrequently ( approximately 1 %) from sweet clover. A second genotype was isolated infrequently only from alfalfa. These genotypes fixed nitrogen poorly in association with sweet clover and Phaseolus vulgaris, but were moderately effective with alfalfa. They produced a near-neutral reaction on mineral salts agar containing mannitol, which is atypical of the genus Rhizobium. A single isolate of Ensifer sp. and two of Phyllobacterium sp. were recovered only from sweet clover. All were highly resistant to multiple antibiotics. Phylogenetic analysis indicated that Ensifer sp. strain T173 is closely related to, but separate from, the non-symbiotic species 'Sinorhizobium morelense'. Strain T173 is unique in that it possesses a 175 kb symbiotic plasmid and elicits ineffective nodules on alfalfa, sweet clover, Medicago lupulina and Macroptilium atropurpureum. The two Phyllobacterium spp. were non-symbiotic and probably represent bacterial opportunists. Three genotypes of E. meliloti that were symbiotically effective with alfalfa and sweet clover were encountered infrequently. Among phage-susceptible isolates, two genotypes of E. medicae were encountered infrequently and were highly effective with alfalfa, sweet clover and Medicago polymorpha. The ecological and practical implications of the findings are discussed.
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Affiliation(s)
- E S P Bromfield
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A OC6, Canada
| | - J T Tambong
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A OC6, Canada
| | - S Cloutier
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A OC6, Canada
| | - D Prévost
- Agriculture and Agri-Food Canada, 2560 Hochelaga Blvd, Quebec G1V 2J3, Canada
| | - G Laguerre
- INRA, USC 1242 Symbioses Tropicales et Méditerranéennes, F-34398 Montpellier, France
| | - P van Berkum
- USDA ARS, Bldg 006, BARC-West, 10300 Baltimore Ave, Beltsville, MD 20705, USA
| | - T V Tran Thi
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A OC6, Canada
| | - R Assabgui
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A OC6, Canada
| | - L R Barran
- Agriculture and Agri-Food Canada, Ottawa, Ontario K1A OC6, Canada
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11
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Deakin WJ, Broughton WJ. Symbiotic use of pathogenic strategies: rhizobial protein secretion systems. Nat Rev Microbiol 2009. [PMID: 19270720 DOI: 10.1038/nrmicro.2091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Rhizobia - a diverse group of soil bacteria - induce the formation of nitrogen-fixing nodules on the roots of legumes. Nodulation begins when the roots initiate a molecular dialogue with compatible rhizobia in the soil. Most rhizobia reply by secreting lipochitooligosaccharidic nodulation factors that enable entry into the legume. A molecular exchange continues, which, in compatible interactions, permits rhizobia to invade root cortical cells, differentiate into bacteroids and fix nitrogen. Rhizobia also use additional molecular signals, such as secreted proteins or surface polysaccharides. One group of proteins secreted by rhizobia have homologues in bacterial pathogens and may have been co-opted by rhizobia for symbiotic purposes.
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Affiliation(s)
- William J Deakin
- LBMPS, University of Geneva, 30, quai Ernest-Ansermet - Sciences III, CH-1211 Genève 4, Geneva, Switzerland.
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12
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Abstract
Rhizobia - a diverse group of soil bacteria - induce the formation of nitrogen-fixing nodules on the roots of legumes. Nodulation begins when the roots initiate a molecular dialogue with compatible rhizobia in the soil. Most rhizobia reply by secreting lipochitooligosaccharidic nodulation factors that enable entry into the legume. A molecular exchange continues, which, in compatible interactions, permits rhizobia to invade root cortical cells, differentiate into bacteroids and fix nitrogen. Rhizobia also use additional molecular signals, such as secreted proteins or surface polysaccharides. One group of proteins secreted by rhizobia have homologues in bacterial pathogens and may have been co-opted by rhizobia for symbiotic purposes.
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13
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Worliczek HL, Kämpfer P, Rosengarten R, Tindall BJ, Busse HJ. Polar lipid and fatty acid profiles – Re-vitalizing old approaches as a modern tool for the classification of mycoplasmas? Syst Appl Microbiol 2007; 30:355-70. [PMID: 17482408 DOI: 10.1016/j.syapm.2007.03.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A set of 20 Mollicutes strains representing different lines of descent, including the type species of the genus Mycoplasma, Mycoplasma mycoides, Acholeplasma laidlawii and a strain of Mesoplasma, were subjected to polar lipid and fatty acid analyses in order to evaluate their suitability for classification purposes within members of this group. Complex polar lipid and fatty acid profiles were detected for each examined strain. All strains contained the polar lipids phosphocholine-6'-alpha-glucopyranosyl-(1'-3)-1, 2-diacyl-glycerol (MfGL-I), 1-O-alkyl/alkenyl-2-O-acyl-glycero-3-phosphocholine (MfEL), sphingomyelin (SphM), 1-O-alkyl/alkenyl-glycero-3-phosphocholine (lysoMfEL), the unknown aminophospholipid APL1 and the cholesterol Chol2. A total of 19 strains revealed the presence of phosphatidylethanolamine (PE) and/or phosphatidylglycerol (PG), and the presence of diphosphatidylglycerol (DPG) was detected in 13 strains. The unknown aminolipid AL1 was found in the extracts of 17 strains. Unbranched saturated and unsaturated compounds predominated in the fatty acid profiles. Major fatty acids were usually C16:0, C18:0, C18:1 omega9c and 'Summed feature 5' (C18:2 omega6, 9c/C18:0 anteiso). Our results demonstrated that members of the M. mycoides cluster showed rather homogenous polar lipid and fatty acid profiles. In contrast, each of the other strains was characterized by a unique polar lipid profile and significant quantitative differences in the presence of certain fatty acids. These results indicate that analyses of both polar lipid and fatty acid profiles could be a useful tool for classification of mycoplasmas.
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Affiliation(s)
- Hanna Lucia Worliczek
- Institute for Bacteriology, Mycology and Hygiene, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria
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14
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Martens M, Delaere M, Coopman R, De Vos P, Gillis M, Willems A. Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol 2007; 57:489-503. [PMID: 17329774 DOI: 10.1099/ijs.0.64344-0] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multilocus sequence analysis (MLSA) was performed on representatives of Ensifer (including species previously assigned to the genus Sinorhizobium) and related taxa. Neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) phylogenies of dnaK, gltA, glnA, recA, thrC and 16S rRNA genes were compared. The data confirm that the potential for discrimination of Ensifer species is greater using MLSA of housekeeping genes than 16S rRNA genes. In incongruence-length difference tests, the 16S rRNA gene was found to be significantly incongruent with the other genes, indicating that this gene should not be used as a single indicator of relatedness in this group. Significant congruence was detected for dnaK, glnA and thrC. Analyses of concatenated sequences of dnaK, glnA and thrC genes yielded very similar NJ, MP and ML trees, with high bootstrap support. In addition, analysis of a concatenation of all six genes essentially produced the same result, levelling out potentially conflicting phylogenetic signals. This new evidence supports the proposal to unite Ensifer and Sinorhizobium in a single genus. Support for an alternative solution preserving the two genera is less strong. In view of the opinions expressed by the Judicial Commission, the name of the genus should be Ensifer, as proposed by Young [Young, J. M. (2003). Int J Syst Evol Microbiol
53, 2107–2110]. Data obtained previously and these new data indicate that Ensifer adhaerens and ‘Sinorhizobium morelense’ are not heterotypic synonyms, but represent separate species. However, transfer to the genus Ensifer is not possible at present because the species name is the subject of a pending Request for an Opinion, which would affect whether a novel species in the genus Ensifer or a new combination based on a basonym would be created.
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Affiliation(s)
- Miet Martens
- Laboratorium voor Microbiologie (WE10), Universiteit Gent, KL Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Manuel Delaere
- Laboratorium voor Microbiologie (WE10), Universiteit Gent, KL Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Renata Coopman
- Laboratorium voor Microbiologie (WE10), Universiteit Gent, KL Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Paul De Vos
- Laboratorium voor Microbiologie (WE10), Universiteit Gent, KL Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Monique Gillis
- Laboratorium voor Microbiologie (WE10), Universiteit Gent, KL Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Anne Willems
- Laboratorium voor Microbiologie (WE10), Universiteit Gent, KL Ledeganckstraat 35, B-9000 Gent, Belgium
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Wang FQ, Wang ET, Zhang YF, Chen WX. Characterization of rhizobia isolated from Albizia spp. in comparison with microsymbionts of Acacia spp. and Leucaena leucocephala grown in China. Syst Appl Microbiol 2006; 29:502-17. [PMID: 16406708 DOI: 10.1016/j.syapm.2005.12.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Indexed: 10/25/2022]
Abstract
This is the first systematic study of rhizobia associated with Albizia trees. The analyses of PCR-RFLP and sequencing of 16S rRNA genes, SDS-PAGE of whole-cell proteins and clustering of phenotypic characters grouped the 31 rhizobial strains isolated from Albizia into eight putative species within the genera Bradyrhizobium, Mesorhizobium and Rhizobium. Among these eight rhizobial species, five were unique to Albizia and the remaining three were shared with Acacia and Leucaena, two legume trees coexisting with Albizia in China. These results indicated that Albizia species nodulate with a wide range of rhizobial species and had preference of microsymbionts different from Acacia and Leucaena. The definition of four novel groups, Mesorhizobium sp., Rhizobium sp. I, Rhizobium sp. II and "R. giardinii", indicates that further studies with enlarged rhizobial population are necessary to better understand the diversity and to clarify the taxonomic relationships of Albizia-associated rhizobia.
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MESH Headings
- Acacia/microbiology
- Albizzia/microbiology
- Bacterial Proteins/analysis
- Bacterial Proteins/isolation & purification
- Biodiversity
- China
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Polyacrylamide Gel
- Genes, rRNA
- Molecular Sequence Data
- Phylogeny
- Polymorphism, Restriction Fragment Length
- Proteome/analysis
- Proteome/isolation & purification
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Rhizobiaceae/chemistry
- Rhizobiaceae/classification
- Rhizobiaceae/genetics
- Rhizobiaceae/isolation & purification
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Feng Qin Wang
- Key Laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture/College of Biological Sciences, China Agricultural University, Beijing 100094, China
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Dewhirst FE, Shen Z, Scimeca MS, Stokes LN, Boumenna T, Chen T, Paster BJ, Fox JG. Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics. J Bacteriol 2005; 187:6106-18. [PMID: 16109952 PMCID: PMC1196133 DOI: 10.1128/jb.187.17.6106-6118.2005] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31' and 27'. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.
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Affiliation(s)
- Floyd E Dewhirst
- Department of Molecular Genetics, The Forsyth Institute, Boston, Massachusetts 02115, USA
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17
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Gupta RS. Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for alpha-proteobacterial evolution. Crit Rev Microbiol 2005; 31:101-35. [PMID: 15986834 DOI: 10.1080/10408410590922393] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Alpha (alpha) proteobacteria comprise a large and metabolically diverse group. No biochemical or molecular feature is presently known that can distinguish these bacteria from other groups. The evolutionary relationships among this group, which includes numerous pathogens and agriculturally important microbes, are also not understood. Shared conserved inserts and deletions (i.e., indels or signatures) in molecular sequences provide a powerful means for identification of different groups in clear terms, and for evolutionary studies (see www.bacterialphylogeny.com). This review describes, for the first time, a large number of conserved indels in broadly distributed proteins that are distinctive and unifying characteristics of either all alpha-proteobacteria, or many of its constituent subgroups (i.e., orders, families, etc.). These signatures were identified by systematic analyses of proteins found in the Rickettsia prowazekii (RP) genome. Conserved indels that are unique to alpha-proteobacteria are present in the following proteins: Cytochrome c oxidase assembly protein Ctag, PurC, DnaB, ATP synthase alpha-subunit, exonuclease VII, prolipoprotein phosphatidylglycerol transferase, RP-400, FtsK, puruvate phosphate dikinase, cytochrome b, MutY, and homoserine dehydrogenase. The signatures in succinyl-CoA synthetase, cytochrome oxidase I, alanyl-tRNA synthetase, and MutS proteins are found in all alpha-proteobacteria, except the Rickettsiales, indicating that this group has diverged prior to the introduction of these signatures. A number of proteins contain conserved indels that are specific for Rickettsiales (XerD integrase and leucine aminopeptidase), Rickettsiaceae (Mfd, ribosomal protein L19, FtsZ, Sigma 70 and exonuclease VII), or Anaplasmataceae (Tgt and RP-314), and they distinguish these groups from all others. Signatures in DnaA, RP-057, and DNA ligase A are commonly shared by various Rhizobiales, Rhodobacterales, and Caulobacter, suggesting that these groups shared a common ancestor exclusive of other alpha-proteobacteria. A specific relationship between Rhodobacterales and Caulobacter is indicated by a large insert in the Asn-Gln amidotransferase. The Rhizobiales group of species are distinguished from others by a large insert in the Trp-tRNA synthetase. Signature sequences in a number of other proteins (viz. oxoglutarate dehydogenase, succinyl-CoA synthase, LytB, DNA gyrase A, LepA, and Ser-tRNA synthetase) serve to distinguish the Rhizobiaceae, Brucellaceae, and Phyllobacteriaceae families from Bradyrhizobiaceae and Methylobacteriaceae. Based on the distribution patterns of these signatures, it is now possible to logically deduce a model for the branching order among alpha-proteobacteria, which is as follows: Rickettsiales --> Rhodospirillales-Sphingomonadales --> Rhodobacterales-Caulobacterales --> Rhizobiales (Rhizobiaceaea-Brucellaceae-Phyllobacteriaceae, and Bradyrhizobiaceae). The deduced branching order is also consistent with the topologies in the 16 rRNA and other phylogenetic trees. Signature sequences in a number of other proteins provide evidence that alpha-proteobacteria is a late branching taxa within Bacteria, which branched after the delta,epsilon-subdivisions but prior to the beta,gamma-proteobacteria. The shared presence of many of these signatures in the mitochondrial (eukaryotic) homologs also provides evidence of the alpha-proteobacterial ancestry of mitochondria.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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18
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Liu J, Wang ET, Chen WX. Diverse rhizobia associated with woody legumes Wisteria sinensis, Cercis racemosa and Amorpha fruticosa grown in the temperate zone of China. Syst Appl Microbiol 2005; 28:465-77. [PMID: 16094873 DOI: 10.1016/j.syapm.2005.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Fifty-nine bacterial isolates from root nodules of the woody legumes Wisteria sinensis, Cercis racemosa and Amorpha fruticosa grown in the central and eastern regions of China were characterized with phenotypic analysis, PCR-based 16S and 23S rRNA gene RFLP, Box PCR and 16S rRNA gene sequencing. Seven main phena were defined in numerical taxonomy, which corresponded to distinct groups within the genera Agrobacterium, Bradyrhizobium, Mesorhizobium and Rhizobium in 16S and 23S rRNA gene PCR-RFLP. The phylogenetic relationships of the 16S rRNA genes supported the grouping results of PCR-RFLP. Most of the isolates from Amorpha fruticosa were classified into two groups closely related to Mesorhizobium amorphae. Seventeen of the 21 isolates from Wisteria sinensis were identified as two groups related to Rhizobium and Agrobacterium. Six out of 10 isolates from Cercis racemosa were identified as a group related to Bradyrhizobium. Our results indicated that each of the investigated legumes nodulated mainly with one or two rhizobial groups, although isolates from different plants intermingled in some small bacterial groups. In addition, correlation between geographic origin and grouping results was found in the isolates from Amorpha fruticosa. These results revealed that the symbiotic bacteria might have been selected by both the legume hosts and the geographic factors.
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MESH Headings
- Alphaproteobacteria/classification
- Alphaproteobacteria/genetics
- Alphaproteobacteria/isolation & purification
- Bradyrhizobium/classification
- Bradyrhizobium/genetics
- Bradyrhizobium/isolation & purification
- China
- Climate
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Ribosomal/analysis
- DNA, Ribosomal/genetics
- Fabaceae/growth & development
- Fabaceae/microbiology
- Genes, rRNA
- Molecular Sequence Data
- Phenotype
- Phylogeny
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Rhizobium/classification
- Rhizobium/genetics
- Rhizobium/isolation & purification
- Sequence Analysis, DNA
- Species Specificity
- Symbiosis
- Wisteria/growth & development
- Wisteria/microbiology
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Affiliation(s)
- Jie Liu
- Key laboratory of Agro-Microbial Resource and Application, Ministry of Agriculture/Department of Microbiology, College of Biological Sciences, China Agricultural University, 100094 Beijing, PR China
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Teyssier C, Marchandin H, Jumas-Bilak E. [The genome of alpha-proteobacteria : complexity, reduction, diversity and fluidity]. Can J Microbiol 2004; 50:383-96. [PMID: 15284884 DOI: 10.1139/w04-033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The alpha-proteobacteria displayed diverse and often unconventional life-styles. In particular, they keep close relationships with the eucaryotic cell. Their genomic organization is often atypical. Indeed, complex genomes, with two or more chromosomes that could be linear and sometimes associated with plasmids larger than one megabase, have been described. Moreover, polymorphism in genome size and topology as well as in replicon number was observed among very related bacteria, even in a same species. Alpha-proteobacteria provide a good model to study the reductive evolution, the role and origin of multiple chromosomes, and the genomic fluidity. The amount of new data harvested in the last decade should lead us to better understand emergence of bacterial life-styles and to build the conceptual basis to improve the definition of the bacterial species.
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Affiliation(s)
- Corinne Teyssier
- Laboratoire de bactériologie, Faculté de pharmacie, Montpellier CEDEX 5, France
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20
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Brewin NJ. Plant Cell Wall Remodelling in the Rhizobium–Legume Symbiosis. CRITICAL REVIEWS IN PLANT SCIENCES 2004; 23:293-316. [PMID: 0 DOI: 10.1080/07352680490480734] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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21
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Streit WR, Schmitz RA, Perret X, Staehelin C, Deakin WJ, Raasch C, Liesegang H, Broughton WJ. An evolutionary hot spot: the pNGR234b replicon of Rhizobium sp. strain NGR234. J Bacteriol 2004; 186:535-42. [PMID: 14702322 PMCID: PMC305759 DOI: 10.1128/jb.186.2.535-542.2004] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobium sp. strain NGR234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. Since the overall organization of the NGR234 genome is strikingly similar to that of the narrow-host-range symbiont Rhizobium meliloti strain 1021 (also known as Sinorhizobium meliloti), the obvious question is why are the spectra of hosts so different? Study of the early symbiotic genes of both bacteria (carried by the SymA plasmids) did not provide obvious answers. Yet, both rhizobia also possess second megaplasmids that bear, among many other genes, those that are involved in the synthesis of extracellular polysaccharides (EPSs). EPSs are involved in fine-tuning symbiotic interactions and thus may help answer the broad- versus narrow-host-range question. Accordingly, we sequenced two fragments (total, 594 kb) that encode 575 open reading frames (ORFs). Comparisons revealed 19 conserved gene clusters with high similarity to R. meliloti, suggesting that a minimum of 28% (158 ORFs) of the genetic information may have been acquired from a common ancestor. The largest conserved cluster carried the exo and exs genes and contained 31 ORFs. In addition, nine highly conserved regions with high similarity to Agrobacterium tumefaciens C58, Bradyrhizobium japonicum USDA110, and Mesorhizobium loti strain MAFF303099, as well as two conserved clusters that are highly homologous to similar regions in the plant pathogen Erwinia carotovora, were identified. Altogether, these findings suggest that >/==" BORDER="0">40% of the pNGR234b genes are not strain specific and were probably acquired from a wide variety of other microbes. The presence of 26 ORFs coding for transposases and site-specific integrases supports this contention. Surprisingly, several genes involved in the degradation of aromatic carbon sources and genes coding for a type IV pilus were also found.
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Affiliation(s)
- W R Streit
- Institut für Mikrobiologie und Genetik, Universität Göttingen, Göttingen, Germany.
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22
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Young JM, Kuykendall LD, Martínez-Romero E, Kerr A, Sawada H. Classification and nomenclature of Agrobacterium and Rhizobium. Int J Syst Evol Microbiol 2003; 53:1689-1695. [PMID: 13130069 DOI: 10.1099/ijs.0.02762-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Farrand et al. [Int J Syst Evol Microbiol 53 (2003), 1681-1687] have presented a critique of the proposal of Young et al. [Int J Syst Evol Microbiol 51 (2001), 89-103] to revise the nomenclature and classification of RHIZOBIUM: They argued that Young et al. (2001) are mistaken in their reclassification of all Agrobacterium species within Rhizobium, and that the resulting nomenclatural revision is 'unnecessary and unwarranted'. These objections arise because the authors appear not to understand the role of formal nomenclature, and fail to distinguish between formal and special-purpose nomenclatures (Bacteriological Code, 1990 Revision). The arguments set out by Farrand et al. (2003) can be addressed in terms of (1) the taxonomic status of the genera Agrobacterium and Rhizobium; (2) the status of species and biovars and their nomenclature; and (3) the role of transmissible genomic elements in classification and nomenclature. Finally, an attempt is made to unravel the confusion underpinning their discussion with a consideration of the relationship between formal and special-purpose nomenclatures.
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Affiliation(s)
- J M Young
- Landcare Research, Private Bag 92170, Auckland 1003, New Zealand
| | - L D Kuykendall
- Plant Sciences Institute, Beltsville Agricultural Research Center, USDA-ARS, 10300 Baltimore Ave., Beltsville, MD 20705, USA
| | - E Martínez-Romero
- Centro de Investigación sobre Fijación de Nitrógeno, UNAM. AP 565 - A, Cuernavaca, Morelos, Mexico
| | - A Kerr
- 419 Carrington Street, Adelaide, South Australia 5000, Australia
| | - H Sawada
- National Institute of Agro-Environmental Sciences, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
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