First report on bacterial isolation from marbled flounder ( Pseudopleuronectes yokohamae ) associated with skin ulcers

Members of the genus Nocardia are responsible for cutaneous, pulmonary and disseminated human infections. From 2003 to 2008, four nocardioform strains (W8027, W8681, W9071 and W9241(T)) were isolated from patients in the state of Florida, USA. Ribosomal gene sequencing analysis suggested that a novel species of the genus Nocardia had been isolated. These strains were subjected to a taxonomic analysis using a polyphasic approach. Phenotypic analyses included morphological examination, biochemical profiling and antimicrobial susceptibility testing. Molecular studies included 16S rRNA and DNA gyrase B subunit (gyrB) gene sequence analyses and DNA-DNA hybridization. Phylogenetic neighbours were determined through 16S rRNA and gyrB gene sequence analyses. Phenotypic characteristics that differentiated the novel isolates from phylogenetically related species were growth at 45 °C, and three of the four novel strains utilized l-rhamnose. The antimicrobial profiles could not reliably distinguish the novel species from related nocardiae. Analysis showed that the 16S rRNA gene sequences of the four novel isolates were identical. The blast analysis of the near full-length 16S rRNA gene showed 99.2 % sequence similarity to Nocardia araoensis DSM 44729(T), Nocardia arthritidis DSM 44731(T) and Nocardia beijingensis JCM 10666(T), 98.7 % to Nocardia amamiensis DSM 45066(T), 98.2 % to Nocardia pneumoniae JCM 12119(T) and 97.8 % to Nocardia takedensis JCM 13313(T). Analysis of partial gyrB gene sequences showed that the novel isolates had 95.4 % similarity to N. arthritidis DSM 44731(T), 95.3 % to Nocardia gamkensis DSM 44956(T), 94.4 % to N. pneumoniae JCM 12119(T), 93.8 % to Nocardia asiatica DSM 44668(T), 93.5 % to N. amamiensis DSM 45066(T), 93.4 % to N. beijingensis JCM 10666(T) and 93.2 % to N. araoensis DSM 44729(T). The DNA-DNA relatedness values between the four novel strains were 86-89 %; the relatedness value for strain W9241(T) compared with N. beijingensis JCM 10666(T) was 47 % and 46 % with N. araoensis DSM 44729(T), 44 % with N. arthritidis DSM 44731(T), 32 % with N. amamiensis DSM 45066(T) and 20 % with N. asiatica DSM 44668(T). The results of the taxonomic analysis suggested that the new isolates represent a novel species of the genus Nocardia for which the name Nocardia niwae sp. nov. is proposed. The type strain is W9241(T) (=DSM 45340(T)=CCUG 57756(T)).

Genetic relationships among bacterial strains belonging to the genus Aeromonas were inferred from 16S rRNA, gyrB and rpoB gene sequences. Twenty-eight type or collection strains of the recognized species or subspecies and 33 Aeromonas strains isolated from human and animal specimens as well as from environmental samples were included in the study. As reported previously, the 16S rRNA gene sequence is highly conserved within the genus Aeromonas, having only limited resolution for this very tight group of species. Analysis of a 1.1 kb gyrB sequence confirmed that this gene has high resolving power, with maximal interspecies divergence of 15.2 %. Similar results were obtained by sequencing only 517 bp of the rpoB gene, which showed maximal interspecies divergence of 13 %. The topologies of the gyrB- and rpoB-derived trees were similar. The results confirm the close relationship of species within the genus Aeromonas and show that a phylogenetic approach including several genes is suitable for improving the complicated taxonomy of the genus.

Five nocardioform isolates from human clinical sources were evaluated. Analysis of the nearly full-length 16S rRNA gene showed 99.9-100 % similarity among the strains. The results of a comparative phylogenetic analysis of the 16S rRNA gene sequences indicated that the isolates belonged to the genus Nocardia. Phenotypic and molecular analyses were performed on the clinical isolates. Traditional phenotypic analyses included morphological, biochemical/physiological, chemotaxonomic and antimicrobial susceptibility profiling. Molecular studies included 1441-bp 16S rRNA and 1246-bp gyrB gene sequence analyses, as well as DNA-DNA hybridizations. Biochemical analysis failed to differentiate the putative novel species from its phylogenetic neighbours; however, molecular studies were able to distinguish the patient strains and confirm them as members of a single species. Based on 16S rRNA gene sequence analysis, similarity between the isolates and their closest relatives (type strains of Nocardia araoensis, N. arthritidis, N. beijingensis and N. niwae) was ≤99.3 %. Analysis of partial gyrB gene sequences showed 98-99.7 % relatedness among the isolates. Nocardia lijiangensis and N. xishanensis were the closest related species to the isolates based on gyrB gene sequence analysis, and their type strains showed 95.7 and 95.3 % similarity, respectively, to strain W9988(T). Resistance to amikacin and molecular analyses, including DNA-DNA hybridization, distinguished the five patient strains from their phylogenetic neighbours, and the results of this polyphasic study indicated the existence of a novel species of Nocardia, for which we propose the name Nocardia amikacinitolerans sp. nov., with strain W9988(T) ( = DSM 45539(T) = CCUG 59655(T)) as the type strain.

Traditional morphology-based ciliate classification is often time-consuming and inaccurate, necessitating molecular approaches. Although 18S rRNA gene sequencing is widely used for taxonomic analyses of ciliates, its high degree of conservation makes it challenging to achieve species-level resolution. This study explores the potential of internal transcribed spacers (ITS1 and ITS2) and the 28S rRNA gene to improve taxonomic resolution beyond that offered by 18S rRNA gene in free-living and host-associated ciliates. A comparative analysis of ITS, the 18S, and 28S rRNA gene sequences retrieved from public databases indicated that ITS regions exhibit greater inter- and intra-specific sequence dissimilarity compared to 18S rRNA gene, supporting existing literature. We then designed universal primers targeting the ITS and 28S rRNA gene for freshwater and rumen ciliates. These primers were rigorously evaluated for their inclusiveness, specificity, and amplification efficiency using in-silico PCR, experimental PCR, followed by sequencing and metataxonomic analyses of the ciliate communities. In-silico analyses revealed inclusiveness exceeding 80%, while experimental analyses validated their specificity. Metataxonomic analyses of ciliates demonstrated that the ITS and 28S rRNA gene captured significantly greater taxonomic diversity than 18S rRNA gene. Also, ITS1 offered superior taxonomic resolution by detecting the most ciliate species that went unnoticed by the 18S rRNA gene. These findings underscore the superiority of ITS1, and to a lesser extent ITS2, as taxonomic markers for enhancing the resolution of freshwater and rumen ciliate communities. We recommend ITS1 as an alternative marker to overcome the limitations of 18S rRNA gene-based approaches in free-living and host-associated ciliate taxonomy.

In September 2012, water-soaked lesions and soft rot of stipes and pilei were observed in China on the fruiting bodies of Pleurotus eryngii, whose growth had halted. Four bacterial isolates with yellow, smooth and convex colonies, identical morphological characters and 16S rRNA, gyrB, rpoB, infB and atpD gene sequences were isolated from diseased tissues. Molecular phylogeny based on 16S rRNA sequence and MLSA data (combined gyrB, rpoB, infB and atpD) showed that the isolates had the highest similarity with Pantoea dispersa LMG 2603T. However, physiological and biochemical tests performed using API 20 E, API 50 CHB (bioMerieux) and GN2 Microplates (Biolog), and DNA-DNA hybridization (33.9±1.3% relatedness with P. dispersa LMG 2603T), differentiated the isolates from P. dispersa, identifiying them as Pantoea beijingensis (Liu et al., 2013). Based on the 16S rRNA gene sequence, a 98% similarity was found between P. beijingensis and Pantoea sp. PA4 reported as the agent of P. eryngii soft rot in Korea (Kim et al., 2007; Liu et al., 2013), suggesting that our isolates belonged to a species differing from Pantoea sp. PA4. Bacterial suspensions (approximately 1×106 CFU/ml) inoculated on the fruiting bodies induced within 5 to 7 days symptoms similar to those observed in natural infection. Controls remained healthy. Bacterial isolates recovered from typical lesions were identical to the inoculated strains in terms of 16S rRNA gene sequence, physiological and biochemical tests, performed using API 20 E, API 50 CHB (bioMerieux) and GN2 Microplates (Biolog), thus fulfilling Koch’s postulates. P. ananatis was first reported as a pathogen of P. eryngii in Korea (Kim et al., 2007), but to the best of our knowledge, this is the first report of P. beijingensis-induced soft rot disease of P. eryngii in China.

A Gram-negative, rod-shaped and motile bacterial isolate, designated strain NS9(T), isolated from air of the Sainsbury Centre for Visual Arts in Norwich, UK, was subjected to a polyphasic taxonomic study including phylogenetic analyses based on partial 16S rRNA, gyrB and lepA gene sequences and phenotypic characterization. The 16S rRNA gene sequence of NS9(T) identified Massilia haematophila CCUG 38318(T), M. niastensis 5516S-1(T) (both 97.7% similarity), M. aerilata 5516S-11(T) (97.4%) and M. tieshanensis TS3(T) (97.4%) as the next closest relatives. In partial gyrB and lepA sequences, NS9(T) shared the highest similarities with M. haematophila CCUG 38318(T) (94.5%) and M. aerilata 5516-11(T) (94.3%), respectively. These sequence data demonstrate the affiliation of NS9(T) to the genus Massilia. The detection of the predominant ubiquinone Q-8, a polar lipid profile consisting of the major compounds diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a polyamine pattern containing 2-hydroxyputrescine and putrescine were in agreement with the assignment of strain NS9(T) to the genus Massilia. Major fatty acids were summed feature 3 (C16:1ω7c and/or iso-C15 : 0 2-OH), C16:0, C18: 1ω7c and C10:0 3-OH. Dissimilarities in partial lepA and gyrB gene sequences as well as results from DNA-DNA hybridizations demonstrate that strain NS9(T) is a representative of an as-yet undescribed species of the genus Massilia that is also distinguished from its close relatives based on physiological and biochemical traits. Hence, we describe a novel species, for which we propose the name Massilia norwichensis sp. nov., with the type strain NS9(T) ( = CCUG 65457(T) =LMG 28164(T)).

In this study, we attempted species-level identification of frog specimen collected from Faridpur district of Bangladesh beyond it’s location outside Orissa, India. Specimen was identified morphologically at genus level as Fejervarya sp. belonging to the family Dicroglossidae using finger formula F3>F4>F1=F1 where F denote as toe finger. From the study two nucleotide sequences of 16S and 12S rRNA genes were obtained which contained 508bp and 408bp respectively. The Sequences were submitted to Gene Bank database with the accession number OQ231604 and OQ240197 for 16S and 12S rRNA gene sequences. Furthermore, the 16S rRNA gene sequence was used as molecular bar-code for the identified Orissa frog F. orissaensis species from Bangladesh. GC content of partial 12S and 16S rRNA genes have been calculated as 44% and 45% respectively. For 16S rRNA gene sequence there was no intra specific divergence. Whereas the inter specific polymorphic divergence were calculated 4.13% and 6.3% when the collected Orissa frog F. orissaensis was compared with that of F. iskandari and F. kupitzi, respectively. In case of 12S rRNA gene intra specific divergence was found 2.45% where the inter specific divergence were 4.41% and 6.86% when the collected Orissa frog F. orissaensis was compared with that of F. iskandari and F. limnocaris, respectively. Maximum likelihood tree also indicates that our sample Orissa frog formed a monophyletic group with F. orissaensis in both the cases of 16S and 12S rRNA genes and thus can be concluded as closely related. Therefore, the collected specimen was identified to be belonging to Fejervarya orissaensis which would be first report from Bangladesh outside Orissa, India. Bangladesh J. Zool. 51(3): 301-313, 2023

Two novel species belonging to the genus Shewanella are described on the basis of their phenotypic characteristics, phylogenetic analyses of 16S rRNA and gyrB gene sequences and levels of DNA-DNA hybridization. A total of 47 strains belonging to two novel Gram-negative, psychrotolerant, H2S-producing bacterial species were isolated from marine fish (cod and flounder) caught from the Baltic Sea off Denmark. The phenotypic characteristics of strains belonging to group 1 (14 strains) indicated that these represented a non-sucrose-assimilating variant of Shewanella baltica with a DNA G+C content of 47.0 mol%. Strains of group 2 (33 isolates) did not utilize the carbon substrates assimilated by S. baltica except gluconate, N-acetylglucosamine and malate. Their DNA G+C content was 44.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence data placed the two novel species within the genus Shewanella. Group 1 strains showed greatest sequence similarity to Shewanella putrefaciens ATCC 8071T (99.0 %) and with S. baltica NCTC 10375(T) (98.3 %). However, gyrB gene sequence analysis showed these isolates to share only 90.0 % sequence similarity with S. putrefaciens ATCC 8071T and 93.9 % with S. baltica NCTC 10375T. Similarly, DNA-DNA hybridization experiments revealed DNA relatedness levels of 38 % between the group 1 isolates and S. putrefaciens ATCC 8071T and 43 % with S. baltica NCTC 10375T. The group 2 strains shared less than 97 % 16S rRNA gene sequence similarities with recognized Shewanella species. Comparisons between the two novel species indicated 16S rRNA gene sequence similarity of approximately 98 %, gyrB gene sequence similarity of approximately 89 % and DNA-DNA reassociation values of 20-34 %. Based on the evidence presented, two novel species, Shewanella hafniensis sp. nov. (type strain P010T = ATCC BAA-1207T = NBRC 100975T) and Shewanella morhuae sp. nov. (type strain U1417T = ATCC BAA-1205T = NBRC 100978T), are described.

ObjectivesThis study examined feline haemoplasmas (Mycoplasma haemofelis, 'Candidatus Mycoplasma haemominutum' [CMhm] and 'Candidatus Mycoplasma turicensis') infecting Thai domestic cats, using the 16S and 23S rRNA genes as genetic markers.MethodsBlood samples from 20 cats were obtained from a diagnostic laboratory and nucleic acids were extracted from each sample using a commercial kit. PCR targeting the 16S rRNA gene was used to screen haemoplasmas in the samples. Positive PCR samples were further sequenced using the 16S and 23S rRNA genes. The sequences from each genetic marker were analysed using Nucleotide BLAST, phylogeny and genetic network analyses.ResultsAmong the 20 samples, five were infected with haemoplasmas. In the 16S rRNA gene sequencing, four sequences were assigned to CMhm and the remaining sequence was likely to be a closely related species of CMhm. In the 23S rRNA gene sequencing, four sequences from the same samples used for 16S rRNA gene sequencing were identified as CMhm and one sequence could be a putative novel haemoplasma species closely related to CMhm.Conclusions and relevanceOnly CMhm and its closely related species were identified in this study. Although CMhm has been recognised as a low-virulence parasite, cases of severe anaemia in cats infected with CMhm have been found. Thus, such cases could be confirmed via the analysis of 16S and 23S rRNA genes. Furthermore, molecular detection and genetic analyses of feline haemoplasmas in additional cat blood samples should be conducted using PCR assay and DNA sequencing based on universal primers of 16S rRNA and 23S rRNA genes to enable more specific identification.

There are challenges in viridans group streptococci (VGS) identification especially for the mitis group. Few studies have investigated the performance of MALDI-TOF MS system in VGS identification. Using 16S rRNA gene and gyrB gene sequencing as a gold standard, the performance of two MALDI-TOF MS instruments in the identification of 181 VGS clinical isolates was studied. The Bruker Biotyper and Vitek MS IVD systems correctly identified 88.4% and 98.9% of the 181 isolates, respectively. The Vitek MS RUO system was the least reliable, only correctly identifying 38.7% of the isolates to species level with several misidentifications and invalid results. The Bruker Biotyper system was very unreliable in the identification of species within the mitis group. Among 22 non-pneumococci isolates (S. mitis/S. oralis/S. pseudopneumoniae), Biotyper misidentified 21 of them as S. pneumoniae leading to a low sensitivity and low positive predictive value in these species. In contrast, the Vitek MS IVD demonstrated a better resolution for pneumococci and non-pneumococci despite the inability to distinguish between S. mitis/S. oralis. For more accurate species-level identification, further improvements in the VGS spectra databases are needed. Based on MALDI-TOF analysis and selected 16S rRNA gene plus gyrB genes sequencing, we designed a practical VGS identification algorithm.

Partial nucleotide sequences of the gyrB gene were determined for members of the genus Nocardiopsis and subjected to phylogenetic analysis. Interspecies DNA similarity values of partial gyrB gene sequences ranged from 79.9 to 99.7% among the Nocardiopsis species. The average similarity of the gyrB gene (87.7%) was significantly less than that of the 16S rRNA gene (96.65%), indicating a high discriminatory power of the gyrB gene. The topology of neighbor-joining, maximum likelihood and maximum parsimony phylogenetic trees based on nucleic acid sequences and protein sequences of gyrB gene were reconstructed. Compared with the 16S rRNA gene dendrogram, the gyrB gene provided more information for understanding the genetic relationships among Nocardiopsis species. Using the information derived from 16S rRNA and gyrB genes, a more comprehensive understanding of the evolutionary history of Nocardiopsis species was obtained.

Bacteria in the genus Elizabethkingia have emerged as a cause of life-threatening infections in humans. However, accurate species identification of these pathogens relies on molecular techniques. We aimed to evaluate the accuracy of 16S rRNA and complete RNA polymerase β-subunit (rpoB) gene sequences in identifying Elizabethkingia species. A total of 173 Elizabethkingia strains with whole-genome sequences in GenBank were included. The 16S rRNA gene and rpoB gene sequences from the same Elizabethkingia strains were examined. Of the 41 E. meningoseptica strains, all exhibited >99.5% 16S rRNA similarity to its type strain. Only 83% of the 99 E. anophelis strains shared >99.5% 16S rRNA gene similarity with its type strain. All strains of E. meningoseptica and E. anophelis formed a cluster distinct from the other Elizabethkingia species in the 16S rRNA and rpoB gene phylogenetic trees. The polymorphisms of 16S rRNA gene sequences are not sufficient for constructing a phylogenetic tree to discriminate species in the E. miricola cluster (E. miricola, E. bruuniana, E. occulta, and E. ursingii). The complete rpoB gene phylogenetic tree clearly delineates all strains of Elizabethkingia species. The complete rpoB gene sequencing could be a useful complementary phylogenetic marker for the accurate identification of Elizabethkingia species.

PDF HTML阅读 XML下载 导出引用 引用提醒 基于转录组测序挖掘仿刺参“化皮病”相关基因 DOI: 作者: 作者单位: 1. 辽宁省海洋水产科学研究院, 辽宁省海洋水产分子生物学重点实验室, 辽宁 大连 116023;2. 大连出入境检验检疫局, 国家水产品检测重点实验室, 辽宁 大连 116600 作者简介: 杨爱馥(1978-),女,副研究员,博士,研究方向为海洋生物技术.E-mail:yangaifu@sohu.com 通讯作者: 中图分类号: S917 基金项目: 国家自然科学基金项目（31672688）；辽宁省科技计划项目（2015103044）；辽宁省自然科学基金项目（2015020786）；辽宁省海洋与渔业厅科研项目（201503）. Identification of genes associated with skin ulceration syndrome in Apostichopus japonicus based on RNA Sequencing Author: Affiliation: 1. Key Laboratory of Marine Fishery Molecular Biology of Liaoning Province, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China;2. Dalian Entry-Exit Inspection and Quarantine Bureau, National Aquatic Product Safety Testing Key Laboratory, Dalian 116600, China Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:为了寻找仿刺参（）养殖期间的“化皮病”关键调控基因，并分析这些基因所参与的信号通路，对本课题组前期已获得的仿刺参“化皮”I期（早期）、Ⅱ期（中期）和Ⅲ期（后期）3个阶段的病变及其同一个体正常体壁组织之间的差异表达基因（differentially expressed genes，DEGs）进行进一步分析。主成分分析（principal component analysis，PCA）结果显示，“化皮”Ⅱ期病变组织与正常组织之间的差异最小，“化皮”I期与Ⅲ期表达关系比较接近，“化皮”Ⅱ期是一个“转折期”。KEGG富集分析结果显示，补体与凝血级联（Complement and coagulation cascades）通路和细胞外基质受体（ECM-receptor interaction）通路在“化皮”3个阶段都显著改变。通过构建“化皮”过程关键差异表达基因调控网络，发现IgGFc-binding protein （FcGBP）基因和Tenascin （TN）蛋白家族基因在“化皮”不同阶段参与到发生显著变化的信号通路。qRT-PCR验证结果显示，5个DEGs在仿刺参“化皮”不同阶段表达趋势与RNA-Seq结果一致，皮尔逊相关系数值为0.7714。“化皮”过程关键调控基因的筛选将为抗逆品种选育以及“化皮病”的防控提供科学依据。 Abstract:In recent years, diseases caused by bacteria, viruses, and protozoa have severely limited the development of the sea cucumber () aquaculture industry. Among such diseases, skin ulceration syndrome (SUS) has become the most universal and serious, owing to its high mortality rates. Therefore, the identification and analysis of key genes associated with "skin ulceration" and corresponding signal pathways are important for establishing the molecular mechanism of SUS. We previously analyzed the gene expression and transcriptome of three-stage SUS progression (SUS-I, SUS-Ⅱ, SUS-Ⅲ) in . Here, we further investigated the occurrence of differentially expressed genes (DEGs) among ulcerative and normal body wall (BW) samples from the same individuals at three stages of SUS progression. The R-Bioconductor package (R-2.15.3) was used to perform principal component analysis and Venn diagrams of these DEGs. KEGG enrichment analysis was carried out based on an algorithm (refer to materials and methods 1.2), using the entire transcriptome set as the background and a cutoff value of Q ≤ 0.05. The regulatory network for SUS progression in PCA analysis indicated that the number of DEGs among the ulcerative and normal BW samples was smallest at SUS stage Ⅱ and that the gene expression profiles at SUS stages I and Ⅲ were similar. Venn diagram analysis indicated that the 497, 59, and 433 unique DEGs were expressed at stage I, Ⅱ and Ⅲ of SUS progression, respectively. Only 28 DEGs were co-expressed in all three stages. KEGG enrichment analysis indicated that the "Complement and coagulation cascades" and "ECM-receptor interaction" pathways were significantly enriched throughout all three stages of SUS progression. The important SUS-related DEGs, including the FcGBP and TN family genes, were identified by constructing a regulatory network. Using qRT-PCR, five representative DEGs were selected to validate the sequencing results. The Pearson's correlation coefficient () was 0.7714, which confirmed the consistency and accuracy of the two approaches.In sea cucumbers, SUS is characterized by apparent white skin ulcers, as well as by complicated molecular regulation. The significantly affected signal pathways detected among the ulcerative and normal BW in the same individuals at three stages of SUS progression, such as the "Focal adhesion" and "ECM-receptor interaction" pathways, have also been observed in the ulcerative BW of SUS-affected individuals (including SUS stages I, Ⅱ, and Ⅲ), when compared to healthy individuals in our previous studies. The FcGBP gene involved in these two pathways was worthy of further exploration. FcGBP is an Fc fragment of the IgG binding protein in fluids secreted by cells of the stomach and intestinal mucosa layer and might play a role in cell protection and anti-inflammation. FcGBP was up-regulated in crypts of early stage ulcerative colitis in human. In addition, Tenascins are extracellular matrix glycoproteins which can regulate cell adhesion, migration, proliferation and differentiation. The expression of the Aj-TN gene changed significantly during the process of extracellular matrix remodeling during sea cucumber regeneration. In human disease studies, TN proteins are associated with tumor metastasis, skin wound healing, and ulcer healing. The expression of TN-family genes in ulcerative and normal BW was significantly different during SUS progression, which suggests that these genes play important roles in the onset and development of SUS in sea cucumber. These results will be useful in developing strategies for preventing bacterial SUS in sea cucumber. 参考文献 相似文献 引证文献

Proteomic analysis reveals the important roles of alpha-5-collagen and ATP5β during skin ulceration syndrome progression of sea cucumber Apostichopus japonicus

Rhizobial bacteria almost exclusively nodulate members of the families Fabaceae, Mimosaceae and Caesalpiniaceae, but are found on a single non-legume taxon, Parasponia (Ulmaceae). Based on their host-range, their nitrogen-fixing ability and strain competition experiments, bacterial strains isolated from Parasponia were thought to constitute a separate lineage that would account for their exceptional host affinity. This hypothesis was investigated by focusing on four isolates that are representative of the morphological and cultural types of Parasponia-nodulating bradyrhizobia. Their evolutionary relationships with other rhizobia were analysed using 16S rRNA gene sequences and their nodulation properties were explored using the nodA gene as a proxy for host-range specificity. Phylogenetic analyses of the 16S rRNA and nodA gene sequences revealed that bacterial isolates from Parasponia species are embedded among other bradyrhizobia. They did not cluster together in topologies based on the 16S rRNA or nodA gene sequences, but were scattered among other bradyrhizobia belonging to either the Bradyrhizobium japonicum or the Bradyrhizobium elkanii lineages. These data suggest that the ability of some bradyrhizobia to nodulate species of the genus Parasponia does not represent a historical relationship that predates the relationship between rhizobia and legumes, but is probably a more recent host switch for some rhizobia.